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 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 rdf_average(infiles,nspcs,nr,ffmt=None,dr=0.1,rmax=3.0,average=True,
normalize=True):
agr= np.zeros((nspcs+1,nspcs+1,nr),dtype=float)
nsum= 0
for infname in infiles:
if not os.path.exists(infname):
print("[Error] File, {0}, does not exist !!!".format(infname))
sys.exit()
asys= NAPSystem(fname=infname,ffmt=ffmt)
print(' File =',infname)
rd,gr,n= rdf(asys,nspcs,dr,rmax,normalize=normalize)
nsum += n
agr += gr
# agr /= len(infiles)
if average:
agr /= nsum
return rd,agr
def adf_average(infiles, ffmt='akr', dang=1.0, rcut=3.0, id0=0, id1=0, id2=0):
na = int(180.0 / dang) + 1
df = np.zeros(na, dtype=float)
aadf = np.zeros(na, dtype=float)
nsum = 0
for infname in infiles:
if not os.path.exists(infname):
print "[Error] File, {0}, does not exist !!!".format(infname)
sys.exit()
asys = NAPSystem(fname=infname, ffmt=ffmt)
print ' infname=', infname
angd, df, n = adf(asys, dang, rcut, id0, id1, id2)
aadf += df
nsum += n
#aadf /= len(infiles)
aadf /= nsum
return angd, aadf
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
#!/bin/env python
import sys,os
from napsys import NAPSystem
infname= sys.argv[1]
print 'input file: ',infname
aSys= NAPSystem()
aSys.read_akr(infname)
natm= len(aSys.atoms)
outfname= infname+".voro"
f= open(outfname,'w')
alc= aSys.alc
ax= aSys.a1[0]
ay= aSys.a2[1]
az= aSys.a3[2]
for ia in range(natm):
pos= aSys.atoms[ia].pos
f.write(' {0:4d}'.format(ia+1))
f.write(' {0:10.3f}'.format(alc*ax*pos[0]))
f.write(' {0:10.3f}'.format(alc*ay*pos[1]))
f.write(' {0:10.3f}'.format(alc*az*pos[2]))
f.write('\n')
f.close()
print 'Use voro++ as follows:'
cmd= 'voro++ -p -c " %i %q %v %s %A"' \
+' 0.0 {0:5.1f}'.format(alc*ax) \
+' 0.0 {0:5.1f}'.format(alc*ay) \
+' 0.0 {0:5.1f}'.format(alc*az) \
write_banner() nsmpl = options.nsmpl print ' num of points = ', nsmpl rcut = options.rcut 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)
print(' [Error] ntwindow <= 0 !!!')
print(' Chech the parameters nmeasure and nshift, and input files.')
sys.exit()
#...make output data files
outfname = 'dat.msd-{0}'.format(id)
outfile = open(outfname, 'w')
p0 = np.zeros((nmeasure, 3))
pp = np.zeros(3)
msd = np.zeros((len(infiles), nmeasure, 3))
npbc = np.zeros((3, ), dtype=int)
hmat = np.zeros((3, 3))
for ifile in range(len(infiles)):
file = infiles[ifile]
system = NAPSystem()
system.read_akr(file)
hmat[0] = system.a1 * system.alc
hmat[1] = system.a2 * system.alc
hmat[2] = system.a3 * system.alc
#...human-readable ID to computer-oriented ID
i = id - 1
ai = system.atoms[i]
pi = ai.pos
if ifile == 0:
pp = pi
else:
#...correct periodic motion
dev = pi - pp
if dev[0] > 0.5:
npbc[0] += -1
for file in args:
infiles.append(file)
infiles.sort()
#...compute sampling time-window from nmeasure and nshift
ntwindow= len(infiles) -(nmeasure-1)*nshift
print ' ntwindow=',ntwindow
if ntwindow <= 0:
print ' [Error] ntwindow <= 0 !!!'
print ' Chech the parameters nmeasure and nshift, and input files.'
sys.exit()
#...set global values
infile= infiles[0]
system=NAPSystem()
system.read_akr(infile)
natm= len(system.atoms)
psid= np.zeros((natm,),dtype=np.int8)
nas= 0
for ia in range(natm):
if sid == 0:
psid[ia] = 1
nas += 1
elif system.atoms[ia].sid == sid:
psid[ia] = 1
nas += 1
print ' num of all atoms = ',natm
print ' num of atoms to be considered = ',nas
print ' accumurating data',
help="cutoff radius of the potential.")
parser.add_option("--pmdexec",
dest="pmdexec",
type="string",
default='../pmd/pmd',
help="path to the pmd executable.")
(options, args) = parser.parse_args()
displace = options.displace
print ' displacement = ', displace, ' Ang.'
rcut = options.rcut
print ' rcut = ', rcut, ' Ang.'
pmdexec = options.pmdexec
infname = args[0]
sys0 = NAPSystem()
sys0.read_pmd(infname)
sys0.write_POSCAR()
print ' POSCAR was written.'
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
if __name__ == "__main__":
args = docopt(__doc__)
infmt = args['--in-format']
outfmt = args['--out-format']
infname = args['INFILE']
outfname = args['OUTFILE']
specorder = args['--specorder'].split(',')
strain = float(args['--strain'])
print('args:')
print(args)
psys0 = NAPSystem(fname=infname, ffmt=infmt, specorder=specorder)
if not outfmt == None:
outfmt = parse_filename(outfname)
if args['isotropic']:
psys = isotropic(psys0, strain)
elif args['uniaxial']:
psys = uniaxial(psys0, strain)[0]
elif args['shear']:
psys = shear(psys0, strain)[0]
if outfmt == 'pmd':
psys.write_pmd(outfname)
elif outfmt == 'smd':
psys.write_pmd(outfname)
import numpy as np
sys.path.append(__file__)
from atom import Atom
from napsys import NAPSystem
__author__ = 'Ryo KOBAYASHI'
__version__ = '160510'
if __name__ == '__main__':
args = docopt(__doc__,version=__version__)
infile = args['INFILE']
specorder = args['--specorder'].split(',')
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),100)):
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],
n3= int(2.0*rcut/vol*area12)+1
return n1,n2,n3
################################################ Main routine ##########
if __name__ == "__main__":
args= docopt(__doc__)
rcut= float(args['--cutoff'])
pmddir= args['--pmddir']
execname= args['--exec']
infname= args['PMDFILE']
plot= args['--plot']
#print(args)
sys0= NAPSystem()
sys0.read_pmd(infname)
sys0.write_POSCAR()
print(' POSCAR was written.')
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)
print("n1,n2,n3 = {0:d} {1:d} {2:d}".format(n1,n2,n3))
# Make displaced POSCARS via phonopy
os.system("phonopy -d --dim=\"{0:d} {1:d} {2:d}\"".format(n1,n2,n3))
write_banner() nsmpl = options.nsmpl print " num of points = ", nsmpl rcut = options.rcut 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)
parser.add_option("-r",dest="rcut",type="float",
default=3.772,
help="cutoff radius of the potential.")
parser.add_option("--pmdexec",dest="pmdexec",type="string",
default='../pmd/pmd',
help="path to the pmd executable.")
(options,args)= parser.parse_args()
displace= options.displace
print ' displacement = ',displace,' Ang.'
rcut= options.rcut
print ' rcut = ',rcut,' Ang.'
pmdexec= options.pmdexec
infname= args[0]
sys0= NAPSystem()
sys0.read_pmd(infname)
sys0.write_POSCAR()
print ' POSCAR was written.'
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 ' Chech the parameters nmeasure and nshift, and input files.'
sys.exit()
#...make output data files
outfname='dat.msd-{0}'.format(id)
outfile= open(outfname,'w')
p0= np.zeros((nmeasure,3))
pp= np.zeros(3)
msd= np.zeros((len(infiles),nmeasure,3))
npbc= np.zeros((3,),dtype=int)
hmat= np.zeros((3,3))
for ifile in range(len(infiles)):
file= infiles[ifile]
system= NAPSystem()
system.read_akr(file)
hmat[0]= system.a1 *system.alc
hmat[1]= system.a2 *system.alc
hmat[2]= system.a3 *system.alc
#...human-readable ID to computer-oriented ID
i= id-1
ai= system.atoms[i]
pi= ai.pos
if ifile == 0:
pp= pi
else:
#...correct periodic motion
dev= pi -pp
if dev[0] > 0.5:
npbc[0] += -1
write_banner()
nsmpl= options.nsmpl
print(' num of points = ',nsmpl)
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)
#!/bin/env python
from __future__ import print_function
import sys, os
from napsys import NAPSystem
infname = sys.argv[1]
print('input file: ', infname)
aSys = NAPSystem()
aSys.read_akr(infname)
natm = len(aSys.atoms)
outfname = infname + ".voro"
f = open(outfname, 'w')
alc = aSys.alc
ax = aSys.a1[0]
ay = aSys.a2[1]
az = aSys.a3[2]
for ia in range(natm):
pos = aSys.atoms[ia].pos
f.write(' {0:4d}'.format(ia + 1))
f.write(' {0:10.3f}'.format(alc * ax * pos[0]))
f.write(' {0:10.3f}'.format(alc * ay * pos[1]))
f.write(' {0:10.3f}'.format(alc * az * pos[2]))
f.write('\n')
f.close()
print('Use voro++ as follows:')
cmd= 'voro++ -p -c " %i %q %v %s %A"' \
+' 0.0 {0:5.1f}'.format(alc*ax) \
