def get_interstitials(structure, ttol=0.5):
""" Function to return unique interstitial sites in the given structure
Parameters
structure = poscar file (using read.poscar)
ttol = tolerance
Returns
unique_int_list = list of unique intestital sites (cartesian (x,y,z) as list) in the given structure
"""
s = deepcopy(structure)
prim = primitive(s)
spg = spglib.get_spacegroup(prim, 0.1)
### Step 1: get unique sites in the primitive of the given structure
uniq_sites = get_unique_wyckoff(prim)
### Step 2: get all interstitial sites from Voronoi method
ints2 = get_all_interstitials(prim, uniq_sites)
### get interstital sites within primitive cell
ints_prim = get_ints_in_prim_cell(prim, ints2)
### Step 3: get unique interstitials after symmetry analysis
ints3 = get_unique_ints(prim, ints_prim, ttol=ttol)
return ints3
def prepareet(self):
atoms = io.read('POSCAR')
from pyspglib import spglib
s = spglib.get_spacegroup(atoms)
from aces.scanf import sscanf
sgN = sscanf(s, '%s (%d)')[1]
sg = Spacegroup(sgN)
atoms.info = {'spacegroup': sg}
nelect = self.getNelect(outcar='band/OUTCAR')
# The remaining part takes care of writing the files required by
# BoltzTraP.
bandstructure = vasp2boltz.get_vasp_bandstructure(pathname='band/')
tl.mkcd('et')
vasp2boltz.write_bandstructure_boltztrap(
bandstructure, filename='et.energy')
vasp2boltz.write_structure_boltztrap(atoms, filename='et.struct')
vasp2boltz.write_intrans_boltztrap(
n_electrons=nelect, filename='et.intrans')
s = tl.read('et.energy')
s = s.replace('HTE', 'et')
tl.write(s, 'et.energy')
s = tl.read('et.struct')
s = s.replace('HTE', 'et')
tl.write(s, 'et.struct')
tl.cd('..')
def prepareet(self):
atoms = io.read('POSCAR')
from pyspglib import spglib
s = spglib.get_spacegroup(atoms)
from aces.scanf import sscanf
sgN = sscanf(s, '%s (%d)')[1]
sg = Spacegroup(sgN)
atoms.info = {'spacegroup': sg}
nelect = self.getNelect(outcar='band/OUTCAR')
# The remaining part takes care of writing the files required by
# BoltzTraP.
bandstructure = vasp2boltz.get_vasp_bandstructure(pathname='band/')
tl.mkcd('et')
vasp2boltz.write_bandstructure_boltztrap(bandstructure,
filename='et.energy')
vasp2boltz.write_structure_boltztrap(atoms, filename='et.struct')
vasp2boltz.write_intrans_boltztrap(n_electrons=nelect,
filename='et.intrans')
s = tl.read('et.energy')
s = s.replace('HTE', 'et')
tl.write(s, 'et.energy')
s = tl.read('et.struct')
s = s.replace('HTE', 'et')
tl.write(s, 'et.struct')
tl.cd('..')
def spglib_get_spacegroup(struct, **kwds):
"""Find spacegroup for given Structure.
Uses pyspglib.
Parameters
----------
struct : Structure
**kwds : keywords
passed to ``spglib.get_spacegroup()``, e.g. `symprec` and
`angle_tolerance` last time I checked
Returns
-------
spg_num, spg_sym
spg_num : int
space group number
spg_sym : str
space group symbol
Notes
-----
The used function ``spglib.get_spacegroup()`` returns a string, which we
split into `spg_num` and `spg_sym`.
"""
ret = spglib.get_spacegroup(struct.get_fake_ase_atoms(), **kwds)
spl = ret.split()
spg_sym = spl[0]
spg_num = spl[1]
spg_num = spg_num.replace('(','').replace(')','')
spg_num = int(spg_num)
return spg_num,spg_sym
def get_duplicates(massextr, te_diff=0.01):
""" function to identify unique intersitials
Parameters
massextr = Pylada mass extraction object (directory with all intersitials directories)
te_diff = difference in total energy among interstitials, default = 0.01 eV
Returns
dict = {key='foldername', total_energy, index}
Note"
index = all the foldername (intersitials) with same index are effectively considered equivalent
Criteria for duplicates
1. Total_energy_difference <= 0.01 eV
2. Space_group
3. comparing first neighbor list for all the sites in the structure
"""
dict_E = massextr.total_energies
dict_Str = massextr.structure
dict2 = {}
g = 0
for k in dict_E.keys():
g = g + 1
dict2[k] = [dict_E[k]]
dict2[k].append(g)
folder_list = [l for l in massextr]
folder_combs = combinations(folder_list, 2)
for i in folder_combs:
diff_E = abs(dict2[i[0]][0] - dict2[i[1]][0])
str1 = dict_Str[i[0]]
str2 = dict_Str[i[1]]
spg1 = spglib.get_spacegroup(str1)
spg2 = spglib.get_spacegroup(str2)
ngh_list_1 = sorted(
[len(neighbors(str1, 1, atom.pos, 0.2)) for atom in str1])
ngh_list_2 = sorted(
[len(neighbors(str2, 1, atom.pos, 0.2)) for atom in str2])
if diff_E <= te_diff:
if spg1 == spg2:
if ngh_list_1 == ngh_list_2:
dict2[i[1]][1] = dict2[i[0]][1]
return (dict2)
def analysis(struct, symprec=1e-5):
ensure_pyspg_is_imported()
atoms = structure_to_spglib_atoms(struct)
val = spglib.get_spacegroup(atoms)
print("Spacegroup is:", val)
val = spglib.refine_cell(atoms, symprec=symprec)
print("Primitive", val)
def primitive(struct, symprec=1e-5):
ensure_pyspg_is_imported()
atoms = structure_to_spglib_atoms(struct)
prim = spglib.refine_cell(atoms, symprec=symprec)
sg = spglib.get_spacegroup(atoms)
struct = httk.iface.spglib_if.spglib_out_to_struct(prim)
struct.comment = "Spacegroup: " + sg
return struct
def get_sg(lattice):
"""
Get the space-group of the system.
Args:
lattice: the ASE crystal class
Returns:
sg (int): integer number of the spacegroup
"""
spacegroup = spglib.get_spacegroup(lattice, symprec=1e-5)
space_split=spacegroup.split()
spg_num = space_split[1].replace('(','').replace(')','')
sg = Spacegroup(int(spg_num))
return sg
def get_sg(lattice):
"""
Get the space-group of the system.
Args:
lattice: the ASE crystal class
Returns:
sg (int): integer number of the spacegroup
"""
spacegroup = spglib.get_spacegroup(lattice, symprec=1e-5)
space_split=spacegroup.split()
spg_num = space_split[1].replace('(','').replace(')','')
sg = Spacegroup(int(spg_num))
return sg
def writeCIF (cell, prec, basename):
# Find spacegroup name and number
sg = spglib.get_spacegroup(cell, symprec=prec)
sg, sgid = sg.split(" (")
sgid = sgid.replace(")", "")
# Find detailed info about the refined cell
lattice, scaled_positions, numbers = spglib.refine_cell (cell, prec)
a, b, c, alpha, beta, gamma = cellParameters (lattice)
f = open((basename + " " + sg + ".cif").replace("/","|"), "w")
f.write ("# Symmetrized structure with precision = %g\n" % prec)
f.write (("data_" + basename + sg + "\n").replace(" ", "_"))
f.write ("_cell_length_a %.7g\n" % a)
f.write ("_cell_length_b %.7g\n" % b)
f.write ("_cell_length_c %.7g\n" % c)
f.write ("_cell_angle_alpha %.7g\n" % alpha)
f.write ("_cell_angle_beta %.7g\n" % beta)
f.write ("_cell_angle_gamma %.7g\n" % gamma)
f.write ("_symmetry_space_group_name_H-M '" + sg + "'\n")
f.write ("_symmetry_Int_Tables_number " + str(sgid) + "\n")
# Write out atomic positions
f.write ("""
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_occupancy
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
""")
for pos, at in zip(scaled_positions, numbers):
sym = element_symbols[at]
f.write ("%s %s 1.0 %.7f %.7f %.7f\n" % (sym, sym, pos[0], pos[1], pos[2]))
f.close()
def get_lattice_type(self):
'''
Find the symmetry of the crystal using spglib symmetry finder.
Assign to sg_name i sg_nr members name of the space group and
its number extracted from the result. Based on the group number
identify also the lattice type (assigned to sg_type member) and
the Bravais lattice of the crystal (assigned to bravais member).
The returned value is the lattice type number.
The lattice type numbers are
(see also Crystal.ls, the numbering starts from 1):
Triclinic (1), Monoclinic (2), Orthorombic (3), Tetragonal (4)
Trigonal (5), Hexagonal (6), Cubic (7)
'''
# Table of lattice types and correcponding group numbers dividing
# the ranges. See get_lattice_type method for precise definition.
lattice_types=[
[3, "Triclinic"],
[16, "Monoclinic"],
[75, "Orthorombic"],
[143, "Tetragonal"],
[168, "Trigonal"],
[195, "Hexagonal"],
[231, "Cubic"]
]
sg=spg.get_spacegroup(self)
m=re.match('([A-Z].*\\b)\s*\(([0-9]*)\)',sg)
self.sg_name=m.group(1)
self.sg_nr=string.atoi(m.group(2))
for n,l in enumerate(lattice_types) :
if self.sg_nr < l[0] :
lattice=l[1]
lattype=n+1
break
self.sg_type=lattype
self.bravais=lattice
return lattype
def test_shift(src):
from pylada.crystal.iterator import equivalence as equivalence_iterator
from pmpaths import my_space_group, my_equivalence_iterator
from copy import deepcopy
src0 = deepcopy(src)
src_sg = my_space_group(src)
dofmin = 1000
dmin = 1e10
groups = [u for u in my_equivalence_iterator(src, src_sg)]
print "groups of equiv atom indices in src:", groups
nshift = len(groups)
for igroup in range(nshift):
src1 = deepcopy(src0)
iorg = groups[igroup][0]
shift = deepcopy(src[iorg].pos) # note, uncentered sourc here
for ia in range(len(src)):
src1[ia].pos = src0[ia].pos - shift
sg = spglib.get_spacegroup(src1, symprec=1e-5, angle_tolerance=-1.0)
print "shift, sg", shift, sg
[(0, 0, 0), (0.25, 0.25, 0.25)], # Atomic positions (fractional coordinates)
spacegroup=216, # International number of the spacegroup of the crystal
cellpar=[a, a, a, 90, 90, 90]) # Unit cell (a, b, c, alpha, beta, gamma) in Angstrom, Degrees
# Write the image to disk file
ase.io.write('crystal.png', # The file where the picture get stored
cryst, # The object holding the crystal definition
format='png', # Format of the file
show_unit_cell=2, # Draw the unit cell boundaries
rotation='115y,15x', # Rotate the scene by 115deg around Y axis and 15deg around X axis
scale=30) # Scale of the picture
# Display the image
Image(filename='crystal.png')
print 'Space group:', spglib.get_spacegroup(cryst)
# Create a Quantum Espresso calculator for our work.
# This object encapsulates all parameters of the calculation,
# not the system we are investigating.
qe=QuantumEspresso(label='SiC', # Label for calculations
wdir='.', # Working directory
pseudo_dir='/usr/share/espresso/pseudo', # Directory with pseudopotentials
kpts=[2,2,2], # K-space sampling for the SCF calculation
xc='pz', # Exchange functional type in the name of the pseudopotentials
pp_type='vbc', # Variant of the pseudopotential
pp_format='UPF', # Format of the pseudopotential files
ecutwfc=20, # Energy cut-off (in Rydberg)
use_symmetry=False, procs=8) # Use symmetry in the calculation ?
print qe.directory
import os, sys
def wait_for_results(systems):
for n,r in enumerate(systems):
print(n+1,end='')
while not r.get_calculator().calc_finished() :
print('.',end='')
sys.stdout.flush()
sleep(10)
print(end=' ')
sys.stdout.flush()
print()
a=4 ; c=crystal('Si',[(0,0,0)],spacegroup=221,cellpar=[a,a,a,90,90,90])
spglib.get_spacegroup(c)
block=False
calc = ClusterVasp(block=block)
calc.set(prec = 'Accurate', xc = 'PBE', lreal = False,
nsw=30, ediff=1e-8, ibrion=2, kpts=[3,3,3])
calc.set(isif=3)
c.set_calculator(calc)
l=ParCalculate(c,calc,cleanup=False,block=block)
s = l[0]
from jasp import *
with jasp('bulk/tio2/step2-1.05') as calc:
calc.clone('bulk/tio2/step3')
with jasp('bulk/tio2/step3',
isif=3) as calc:
calc.calculate()
atoms = calc.get_atoms()
print calc
from pyspglib import spglib
print '\nThe spacegroup is {0}'.format(spglib.get_spacegroup(atoms))
import os, sys
def wait_for_results(systems):
for n,r in enumerate(systems):
print(n+1,end='')
while not r.get_calculator().calc_finished() :
print('.',end='')
sys.stdout.flush()
sleep(10)
print(end=' ')
sys.stdout.flush()
print()
a=4 ; c=crystal('Si',[(0,0,0)],spacegroup=221,cellpar=[a,a,a,90,90,90])
spglib.get_spacegroup(c)
block=False
calc = ClusterVasp(block=block)
calc.set(prec = 'Accurate', xc = 'PBE', lreal = False,
nsw=30, ediff=1e-8, ibrion=2, kpts=[3,3,3])
calc.set(isif=3)
c.set_calculator(calc)
l=ParCalculate(c,calc,cleanup=False,block=block)
s = l[0]
print('created new file.')
with open('fit.out') as fh:
for line in fh:
fields = line.split()
X = float(fields[0])
formation_energy = float(fields[1])
id1 = fields[-1]
# get number of rows. since we use 0-indexing, the next row is NROWS
NROWS0 = len(sh0.get_rows())
NROWS1 = len(sh1.get_rows())
with jasp(id1) as calc:
atoms = calc.get_atoms()
composition = atoms.get_chemical_symbols(reduce=True)
spacegroup = spglib.get_spacegroup(atoms, symprec=1e-5)
natoms = len(atoms)
try:
x, V0, e0, B = analyze_eos()
except TypeError:
x, V0, e0, B = None, None, None, None
magmom = atoms.get_magnetic_moment()
# now we want to write out a row of
data = [
id1, composition, spacegroup, natoms, formation_energy, B,
magmom
]
for i, d in enumerate(data):
sh0.write(NROWS0, i, d)
try:
cell = ase.io.read(sys.argv[1])
except Exception as e:
print("Could not read CIF structure from file '" + sys.argv[1] + "'")
print("Error message is: " + str(e))
sys.exit(1)
if sys.argv[1][-4:] == ".cif":
basename = sys.argv[1][:-4]
else:
basename = sys.argv[1]
l = [ 1, 2, 3, 4, 5, 6, 7, 8, 9 ]
l = ( [ 1e-10, 1e-9, 1e-8, 1e-7, 1e-6 ]
+ [ i*j for i in [ 1e-5, 1e-4, 1e-3, 1e-2, 1e-1 ] for j in l ] )
old = ""
print("# Tolerance\tSpace group")
for prec in l:
s = spglib.get_spacegroup(cell, symprec=prec)
if s != old:
print("%g\t\t%s" % (prec, s))
writeCIF (cell, prec, basename)
old = s
sys.exit(0)
def anim_main(options):
sgnum = []
sgfull = []
dat = []
c2dat = []
c2 = False
for iter in range(options.frames):
fname = "traj.%d.POSCAR" % iter
fname = os.path.join(options.trajdir, fname)
structure = pcread.poscar(fname)
row = []
if (c2):
c2row = []
for i in range(len(structure)):
## should just be doing this and be done:
# nb = neighbors(structure, 1, structure[i].pos, options.tol)
## but not quite working, so do this:
nnb = get_nnb(structure, i, options.tol)
if (c2):
#vladan cs = coordination_shells(structure, 2, structure[i].pos, options.tol)
cs = get_2shells(structure, i, options.tol)
# print "cs = ", cs
# print "nb = ", nb
# row.append(len(nb))
row.append(nnb)
#row.append(len(cs[0])) # size of of 1st shell
if (c2):
#vladan c2row.append([len(cs[0]),len(cs[0])]) # size of of 2nd shell
c2row.append([len(cs[0]), len(cs[1])]) # size of of 2nd shell
sg = spglib.get_spacegroup(structure,
symprec=1e-4,
angle_tolerance=2.0)
sgfull.append(sg)
sg = sg.split("(")[1].split(")")[0]
sgnum.append(int(sg))
dat.append(row)
if (c2):
c2dat.append(c2row)
tot_coord_lost = 0
tot_coord_gained = 0
natoms = len(structure)
if options.verbose > 0:
print "#coordination for %s to %s transition:" % (options.B, options.A)
if (options.verbose > 1):
s = "#frame spacegroup : "
for i in range(len(structure)):
s += "atom%d " % i
print s
for i in range(len(dat)):
s = "%d %s %d : " % (i, sgfull[i], sgnum[i])
row = dat[i]
if (c2):
c2row = c2dat[i]
for j in range(len(row)):
if (i > 0):
tot_coord_lost += max(
0, last_row[j] - row[j]
) ## counting how many total bonds have broken, not how many restored
tot_coord_gained += max(
0, row[j] - last_row[j]
) ## counting how many total bonds gained, not how many broken
if (c2):
s += "%d/%d,%d " % (row[j], c2row[j][0], c2row[j][1])
else:
s += "%d " % (row[j])
if (options.verbose > 1):
print s
last_row = row
speed = "FAST" if (tot_coord_lost == 0
or tot_coord_gained == 0) else "SLOW"
if (options.verbose > 0):
print "#Total of %.2f (%.2f) bonds per atom broken (resp.,made) in %s to %s transition." % (
tot_coord_lost / float(natoms), tot_coord_gained / float(natoms),
options.B, options.A)
print "This transition is likely to be ", speed
if (options.A != None and options.verbose > 1):
structure = pcread.poscar(options.A)
sg = spglib.get_spacegroup(structure,
symprec=1e-5,
angle_tolerance=-1.0)
# sg = sg.split("(")[1].split(")")[0]
s = "#A %s " % (sg)
for i in range(len(structure)):
nnb = get_nnb(structure, i, options.tol)
s += "%d " % nnb
print s
# test_shift(structure)
if (options.B != None and options.verbose > 1):
structure = pcread.poscar(options.B)
sg = spglib.get_spacegroup(structure,
symprec=1e-5,
angle_tolerance=-1.0)
# sg = sg.split("(")[1].split(")")[0]
s = "#B %s " % (sg)
for i in range(len(structure)):
nnb = get_nnb(structure, i, options.tol)
s += "%d " % nnb
print s
return speed == "FAST"
#!/usr/bin/env python
import ase.io.vasp as io
from pyspglib import spglib
from optparse import OptionParser
parser = OptionParser()
parser.add_option("-f", "--file",
action="store", type="string", dest="file", default="POSCAR",
help="Path to input file [default: ./POSCAR]")
parser.add_option("-p", "--prec",
action="store", type="float", dest="prec", default=0.001,
help="Precision for symmetry test [default: 0.001]")
(options, args) = parser.parse_args()
bulk = io.read_vasp(options.file)
spacegroup = spglib.get_spacegroup(bulk, symprec=options.prec)
print "Spacegroup information."
print "-----------------------"
print spacegroup
print "-----------------------"
def write_cell_params(fh, a, p):
'''
Write the specification of the cell using a traditional A,B,C,
alpha, beta, gamma scheme. The symmetry and parameters are determined
from the atoms (a) object. The atoms object is translated into a
primitive unit cell but *not* converted. This is just an internal procedure.
If you wish to work with primitive unit cells in ASE, you need to make
a conversion yourself. The cell params are in angstrom.
Input
-----
fh file handle of the opened pw.in file
a atoms object
p parameters dictionary
Output
------
Primitive cell tuple of arrays: (lattice, atoms, atomic numbers)
'''
assert(p['use_symmetry'])
# Get a spacegroup name and number for the a
sg,sgn=spglib.get_spacegroup(a).split()
# Extract the number
sgn=int(sgn[1:-1])
# Extract the lattice type
ltyp=sg[0]
# Find a primitive unit cell for the system
# puc is a tuple of (lattice, atoms, atomic numbers)
puc=spglib.find_primitive(a)
cell=puc[0]
apos=puc[1]
anum=puc[2]
icell=a.get_cell()
A=norm(icell[0])
B=norm(icell[1])
C=norm(icell[2])
# Select appropriate ibrav
if sgn >= 195 :
# Cubic lattice
if ltyp=='P':
p['ibrav']=1 # Primitive
qepc=array([[1,0,0],[0,1,0],[0,0,1]])
elif ltyp=='F':
p['ibrav']=2 # FCC
qepc=array([[-1,0,1],[0,1,1],[-1,1,0]])/2.0
elif ltyp=='I':
p['ibrav']=3 # BCC
qepc=array([[1,1,1],[-1,1,1],[-1,-1,1]])/2.0
else :
print 'Impossible lattice symmetry! Contact the author!'
raise NotImplementedError
#a=sqrt(2)*norm(cell[0])
qepc=A*qepc
fh.write(' A = %f,\n' % (A,))
elif sgn >= 143 :
# Hexagonal and trigonal
if ltyp=='P' :
p['ibrav']=4 # Primitive
qepc=array([[1,0,0],[-1/2,sqrt(3)/2,0],[0,0,C/A]])
elif ltyp=='R' :
p['ibrav']=5 # Trigonal rhombohedral
raise NotImplementedError
else :
print 'Impossible lattice symmetry! Contact the author!'
raise NotImplementedError
qepc=A*qepc
fh.write(' A = %f,\n' % (A,))
fh.write(' C = %f,\n' % (C,))
elif sgn >= 75 :
raise NotImplementedError
elif sgn ==1 :
# P1 symmetry - no special primitive cell signal to the caller
p['ibrav']=0
return None
else :
raise NotImplementedError
cp=Atoms(cell=puc[0], scaled_positions=puc[1], numbers=puc[2], pbc=True)
qepc=Atoms(cell=qepc,
positions=cp.get_positions(),
numbers=cp.get_atomic_numbers(), pbc=True)
return qepc.get_cell(), qepc.get_scaled_positions(), qepc.get_atomic_numbers()
from vasp import Vasp
calc = Vasp('bulk/tio2/step2-1.05')
calc.clone('bulk/tio2/step3')
calc = Vasp('bulk/tio2/step3',
isif=3)
calc.wait()
print calc
from pyspglib import spglib
print '\nThe spacegroup is {0}'.format(spglib.get_spacegroup(calc.atoms))
def make_anim(A, B, Tm, shift, pairs, options):
# combined view of the unit call and atom transforms
# A is target, B is src, after src has been rotated and its unit cell axes permuted so that they
# "most align" with those of A. Then transform is just two parts: first is unit cell Tform "Tm"
# next is mapping in pairs
### no longer true: which is expressed in 3N-dim space as bigA.
from copy import deepcopy
from util import write_struct, write_xyz, transform_cell, write_tcl
if options.verbose > 1:
print "Exploring minimal path we have discovered..."
# the results come out a little convoluated b/c of all the steps, so here we gather the
# actual start and finish positions.
details = False
print B.cell
print "maps to"
print A.cell
print "with internal atom shift"
print shift
print "and atom idx pairing"
ppidx = pairs[0]
ppos = pairs[1]
ainv = npl.inv(A.cell)
apos = []
bpos = []
for i in range(len(ppidx)):
p = ppidx[i]
q = ppos[i]
print p, q ##, into_cell(np.dot(B.cell, np.dot(ainv, q[4])), B.cell)
apos.append(q[3]) # target atom position
bpos.append(q[4]) # src atom position
if (options.verbose > 2):
print "and A is just"
print A.cell
for a in A:
print a.pos, into_cell(a.pos, A.cell)
print "and B is just"
print B.cell
for b in B:
print b.pos, into_cell(b.pos, B.cell)
if (not os.path.exists(options.trajdir)):
os.mkdir(options.trajdir)
savedir = os.getcwd()
os.chdir(options.trajdir)
if (options.verbose > 1):
print "saving starting anim"
Bpath = deepcopy(B)
tag = "Bpath0"
write_xyz(options, Bpath, tag, options.output_tiles)
fout = file("%s.tcl" % tag, "w")
write_struct(fout,
Bpath,
"%s.xyz" % tag,
0,
center=False,
bonds=True,
bond_len=options.bond_len)
fout.close()
# now write frames
eye2 = 2.0 * np.identity(3) # for writing a big cell if we want
dt = 1.0 / (options.frames - 1)
t = 0
iter = 0
eps = 1e-6
curpos = []
while t <= 1 + eps:
Bpath = deepcopy(B)
Bpath.cell = t * A.cell + (1.0 - t) * B.cell
for i in range(len(apos)):
p = t * apos[i] + (1.0 - t) * bpos[
i] # this is an abs position, but in A's frame of reference (both apos and bpos are created with
# B.cell transformed to A.cell. Here we are mapping to cells in between original B.cell and A.cell)
# Note apos and bpos are not taken directly from A, B input cells but are part of the "pairing" data
c = np.dot(ainv, p) # so get the coords
pos = np.dot(Bpath.cell,
c) # and express it w.r.t. evolving Bpath frame
if (iter == 0):
Bpath[i].pos = into_cell(
pos, Bpath.cell) # then make sure it's _in_ the unit cell
curpos.append(Bpath[i].pos)
else:
Bpath[i].pos = closest_to(pos, Bpath.cell, curpos[i])
curpos[i] = Bpath[i].pos
if (iter == 0): ## testing/bug fixing
Bstart = deepcopy(Bpath)
if (options.verbose > 2):
from pylada.crystal import space_group, primitive
from pylada.math import gruber
Btest = primitive(Bpath)
g = gruber(Btest.cell)
print "src has primitive cell:"
print Btest.cell
# print g
Btest = supercell(Btest, g)
spacegroup = space_group(Btest)
sg = spglib.get_spacegroup(Btest,
symprec=1e-4,
angle_tolerance=2.0)
print "src has %d syms and sg %s" % (len(spacegroup), str(sg))
sg = spglib.get_spacegroup(Bpath, symprec=1e-4, angle_tolerance=2.0)
# sg = spglib.get_spacegroup(Bpath, symprec=1e-1, angle_tolerance=10.0) ### debugging
if (options.verbose > 1):
print t, sg, tag
if (iter == options.frames - 1): ## testing/bug fixing
Bend = deepcopy(Bpath)
if (options.verbose > 2):
from pylada.crystal import space_group, primitive
from pylada.math import gruber
Btest = primitive(Bpath)
g = gruber(Btest.cell)
print "target has primitive cell:"
print Btest.cell
# print g
Btest = supercell(Btest, g)
spacegroup = space_group(Btest)
sg = spglib.get_spacegroup(Btest,
symprec=1e-4,
angle_tolerance=2.0)
print "target has %d syms and sg %s" % (len(spacegroup),
str(sg))
tag = "traj.%d" % iter
write_xyz(options, Bpath, tag, options.output_tiles)
fout = file("%s.tcl" % tag, "w")
write_struct(fout,
Bpath,
"%s.xyz" % tag,
0,
center=False,
bonds=True,
bond_len=options.bond_len)
fout.close()
# write poscar we can analyze later
# bigB = supercell(Bpath, np.dot(eye2,Bpath.cell)) # for writing a big poscar
with open("%s.POSCAR" % tag, "w") as f:
pcwrite.poscar(Bpath, f, vasp5=True)
t += dt
iter += 1
os.chdir(savedir)
if (options.verbose > 2):
write_tcl(options, Bend, Bstart, pairs[1], "pairs")
# some special work to verify we really arrived at B:
# Borig = pcread.poscar(options.A)
# M = np.dot(Borig.cell, npl.inv(Bpath.cell))
# Bfinal = transform_cell(M,Bpath)
# bigB = supercell(Bfinal, np.dot(eye2,Bfinal.cell)) ## this is a special "doubling" test
# with open("final.POSCAR", "w") as f: pcwrite.poscar(bigB, f, vasp5=True)
# with open("final.POSCAR", "w") as f: pcwrite.poscar(Bfinal, f, vasp5=True)
# sg = spglib.get_spacegroup(Bfinal, symprec=1e-4, angle_tolerance=2.0) ## this is "B in A coords"
# print "spacegroup of final structure: ", sg
sg = spglib.get_spacegroup(B, symprec=1e-4, angle_tolerance=2.0)
if (options.verbose > 0):
print "spacegroup of initial structure (B, [Bflip in code]) ", sg
sg = spglib.get_spacegroup(A, symprec=1e-4, angle_tolerance=2.0)
if (options.verbose > 1):
print "spacegroup of target structure (A) ", sg
c = 3.52
MgB2 = Atoms( symbols=['Mg']+['B']*2,
cell=[ ( a, 0, 0 ),
( -a/2, a/2*np.sqrt(3), 0 ),
( 0, 0, c ) ],
scaled_positions=[ ( 0, 0, 0 ),
( 1.0/3, 2.0/3, 0.5 ),
( 2.0/3, 1.0/3, 0.5 ) ],
pbc=True )
# For VASP case
# import vasp
# bulk = vasp.read_vasp(sys.argv[1])
print "[get_spacegroup]"
print " Spacegroup of Silicon is ", spglib.get_spacegroup(silicon)
print ""
print "[get_spacegroup]"
print " Spacegroup of Rutile is ", spglib.get_spacegroup(rutile)
print ""
print "[get_spacegroup]"
print " Spacegroup of MgB2 is ", spglib.get_spacegroup(MgB2)
print ""
print "[get_symmetry]"
print " Symmetry operations of Rutile unitcell are:"
print ""
symmetry = spglib.get_symmetry( rutile )
for i in range(symmetry['rotations'].shape[0]):
print " --------------- %4d ---------------" % (i+1)
rot = symmetry['rotations'][i]
trans = symmetry['translations'][i]
print("created new file.")
with open("fit.out") as fh:
for line in fh:
fields = line.split()
X = float(fields[0])
formation_energy = float(fields[1])
id1 = fields[-1]
# get number of rows. since we use 0-indexing, the next row is NROWS
NROWS0 = len(sh0.get_rows())
NROWS1 = len(sh1.get_rows())
with jasp(id1) as calc:
atoms = calc.get_atoms()
composition = atoms.get_chemical_symbols(reduce=True)
spacegroup = spglib.get_spacegroup(atoms, symprec=1e-5)
natoms = len(atoms)
try:
x, V0, e0, B = analyze_eos()
except TypeError:
x, V0, e0, B = None, None, None, None
magmom = atoms.get_magnetic_moment()
# now we want to write out a row of
data = [id1, composition, spacegroup, natoms, formation_energy, B, magmom]
for i, d in enumerate(data):
sh0.write(NROWS0, i, d)
# now for sheet 1 - unit cell parameters
uc = atoms.get_cell()
def raw_anim(A, B, options):
# just animate between A and B, straight up!
### this option is under development
savedir = os.getcwd()
os.chdir(options.trajdir)
structure = pcread.poscar(options.A)
structure = pcread.poscar(options.B)
print "saving starting anim"
Bpath = deepcopy(B)
tag = "Bpath0"
write_xyz(options, Bpath, tag, options.output_tiles)
fout = file("%s.tcl" % tag, "w")
write_struct(fout,
Bpath,
"%s.xyz" % tag,
0,
center=False,
bonds=True,
bond_len=options.bond_len)
fout.close()
# now write frames
dt = 1.0 / (options.frames - 1)
t = 0
iter = 0
eps = 1e-6
curpos = []
while t <= 1 + eps:
Bpath = deepcopy(B)
Bpath.cell = t * A.cell + (1.0 - t) * B.cell
for i in range(len(apos)):
pos = t * A[i].pos[i] + (1.0 - t) * B[i].pos[i]
if (iter == 0):
Bpath[i].pos = into_cell(
pos, Bpath.cell) # then make sure it's _in_ the unit cell
curpos.append(Bpath[i].pos)
else:
Bpath[i].pos = closest_to(pos, Bpath.cell, curpos[i])
curpos[i] = Bpath[i].pos
if (iter == 0): ## testing/bug fixing
from pylada.crystal import space_group, primitive
from pylada.math import gruber
Btest = primitive(Bpath)
g = gruber(Btest.cell)
print "src has cell:"
print Btest.cell
# print g
Btest = supercell(Btest, g)
spacegroup = space_group(Btest)
sg = spglib.get_spacegroup(Btest,
symprec=1e-4,
angle_tolerance=2.0)
print "src has %d syms and sg %s" % (len(spacegroup), str(sg))
Bstart = deepcopy(Bpath)
sg = spglib.get_spacegroup(Bpath, symprec=1e-4, angle_tolerance=2.0)
# sg = spglib.get_spacegroup(Bpath, symprec=1e-1, angle_tolerance=10.0) ### debugging
print t, sg, tag
if (iter == options.frames - 1): ## testing/bug fixing
from pylada.crystal import space_group, primitive
from pylada.math import gruber
Btest = primitive(Bpath)
g = gruber(Btest.cell)
print "target has cell:"
print Btest.cell
# print g
Btest = supercell(Btest, g)
spacegroup = space_group(Btest)
sg = spglib.get_spacegroup(Btest,
symprec=1e-4,
angle_tolerance=2.0)
print "target has %d syms and sg %s" % (len(spacegroup), str(sg))
Bend = deepcopy(Bpath)
tag = "traj.%d" % iter
write_xyz(options, Bpath, tag, options.output_tiles)
fout = file("%s.tcl" % tag, "w")
write_struct(fout,
Bpath,
"%s.xyz" % tag,
0,
center=False,
bonds=True,
bond_len=options.bond_len)
fout.close()
# write poscar we can analyze later
# bigB = supercell(Bpath, np.dot(eye2,Bpath.cell)) # for writing a big poscar
with open("%s.POSCAR" % tag, "w") as f:
pcwrite.poscar(Bpath, f, vasp5=True)
t += dt
iter += 1
os.chdir(savedir)
if (options.verbose > 2):
write_tcl(options, Bend, Bstart, pairs[1], "pairs")
# some special work to verify we really arrived at B:
# Borig = pcread.poscar(options.A)
# M = np.dot(Borig.cell, npl.inv(Bpath.cell))
# Bfinal = transform_cell(M,Bpath)
# bigB = supercell(Bfinal, np.dot(eye2,Bfinal.cell)) ## this is a special "doubling" test
# with open("final.POSCAR", "w") as f: pcwrite.poscar(bigB, f, vasp5=True)
# with open("final.POSCAR", "w") as f: pcwrite.poscar(Bfinal, f, vasp5=True)
# sg = spglib.get_spacegroup(Bfinal, symprec=1e-4, angle_tolerance=2.0) ## this is "B in A coords"
# print "spacegroup of final structure: ", sg
sg = spglib.get_spacegroup(B, symprec=1e-4, angle_tolerance=2.0)
print "spacegroup of initial structure (B, [Bflip in code]) ", sg
sg = spglib.get_spacegroup(A, symprec=1e-4, angle_tolerance=2.0)
print "spacegroup of target structure (A) ", sg
#!/usr/bin/env python
import ase.io.vasp as io
from pyspglib import spglib
from optparse import OptionParser
parser = OptionParser()
parser.add_option("-f",
"--file",
action="store",
type="string",
dest="file",
default="POSCAR",
help="Path to input file [default: ./POSCAR]")
parser.add_option("-p",
"--prec",
action="store",
type="float",
dest="prec",
default=0.001,
help="Precision for symmetry test [default: 0.001]")
(options, args) = parser.parse_args()
bulk = io.read_vasp(options.file)
spacegroup = spglib.get_spacegroup(bulk, symprec=options.prec)
print "Spacegroup information."
print "-----------------------"
print spacegroup
print "-----------------------"
pbc=True)
a = 3.07
c = 3.52
MgB2 = Atoms(symbols=['Mg'] + ['B'] * 2,
cell=[(a, 0, 0), (-a / 2, a / 2 * np.sqrt(3), 0), (0, 0, c)],
scaled_positions=[(0, 0, 0), (1.0 / 3, 2.0 / 3, 0.5),
(2.0 / 3, 1.0 / 3, 0.5)],
pbc=True)
# For VASP case
# import vasp
# bulk = vasp.read_vasp(sys.argv[1])
print "[get_spacegroup]"
print " Spacegroup of Silicon is ", spglib.get_spacegroup(silicon)
print ""
print "[get_spacegroup]"
print " Spacegroup of Rutile is ", spglib.get_spacegroup(rutile)
print ""
print "[get_spacegroup]"
print " Spacegroup of MgB2 is ", spglib.get_spacegroup(MgB2)
print ""
print "[get_symmetry]"
print " Symmetry operations of Rutile unitcell are:"
print ""
symmetry = spglib.get_symmetry(rutile)
for i in range(symmetry['rotations'].shape[0]):
print " --------------- %4d ---------------" % (i + 1)
rot = symmetry['rotations'][i]
trans = symmetry['translations'][i]
def view_spacegroup(filename='POSCAR',symprec=1e-3):
atoms=read_vasp(filename)
print("SPACEGROUP: %s"%spglib.get_spacegroup(atoms,symprec=symprec))