def test_gruber():
from numpy import dot
from numpy.linalg import inv
from pylada.math import gruber, is_integer
from pylada.error import internal, input
cell = [[0, 0.5, 0.5], [0.5, 0, 0.5], [0.5, 0.5, 0]]
lim = 5
for a00 in [-1, 1]:
for a10 in xrange(-lim, lim+1):
for a11 in [-1, 1]:
for a20 in xrange(-lim, lim+1):
for a21 in xrange(-lim, lim+1):
for a22 in [-1, 1]:
a = [[a00, 0, 0], [a10, a11, 0], [a20, a21, a22]]
g = gruber(dot(cell, a))
assert is_integer(dot(inv(cell), g))
assert is_integer(dot(inv(g), cell))
try: gruber([[0, 0, 0], [1, 2, 0], [4, 5, 6]])
except input: pass
else: raise Exception()
try: gruber([[1, 0, 0], [1, 1, 0], [4, 5, 1]], itermax=2)
except internal: pass
else: raise Exception()
def test_gruber():
from numpy import dot
from numpy.linalg import inv
from pylada.math import gruber, is_integer
from pylada.error import internal, input
cell = [[0, 0.5, 0.5], [0.5, 0, 0.5], [0.5, 0.5, 0]]
lim = 5
for a00 in [-1, 1]:
for a10 in xrange(-lim, lim+1):
for a11 in [-1, 1]:
for a20 in xrange(-lim, lim+1):
for a21 in xrange(-lim, lim+1):
for a22 in [-1, 1]:
a = [[a00, 0, 0], [a10, a11, 0], [a20, a21, a22]]
testcell = dot(cell, a)
g = gruber(testcell)
print testcell
print g
assert is_integer(dot(inv(cell), g))
assert is_integer(dot(inv(g), cell))
try: gruber([[0, 0, 0], [1, 2, 0], [4, 5, 6]])
except input: pass
else: raise Exception()
try: gruber([[1, 0, 0], [1, 1, 0], [4, 5, 1]], itermax=2)
except internal: pass
else: raise Exception()
def main3():
from pylada.math import gruber
fname1 = "geometry/test_poscars/hackit.pos"
A0 = pcread.poscar(fname1)
m = np.array([[1,0,0],[0,1,1],[0,0,2]])
A = supercell(A0,np.dot(A0.cell, m))
Ag = gruber(A.cell)
m = np.array([[2,0,0],[0,1,0],[0,0,1]])
B = supercell(A0,np.dot(A0.cell, m))
Bg = gruber(B.cell)
sa = cell_stats(Ag)
print sa
A2 = ang2vec(sa[3][0],sa[3][1],sa[3][2],sa[4][0],sa[4][1],sa[4][2])
print Ag
print A2
sb = cell_stats(Bg)
B2 = ang2vec(sb[3][0],sb[3][1],sb[3][2],sb[4][0],sb[4][1],sb[4][2])
print Bg
print B2
def check(structure):
from numpy import multiply, cast, any
from numpy.linalg import inv
from pylada.crystal.cppwrappers import periodic_dnc
from pylada.math import gruber
mesh, boxes = periodic_dnc(structure, nperbox=30, overlap=0.125, return_mesh = True)
invcell = gruber(structure.cell)
invcell[:, 0] /= float(mesh[0])
invcell[:, 1] /= float(mesh[1])
invcell[:, 2] /= float(mesh[2])
invcell = inv(invcell)
for box in boxes:
assert any(u[2] for u in box)
for atom, trans, inbox in box:
if inbox: break
index = indices(invcell, trans+atom.pos, mesh)
for atom, trans, inbox in box:
pi = indices(invcell, trans+atom.pos, mesh)
if inbox: assert all(abs(pi - index) < 1e-8), (pi, index)
else:
assert any( abs(u-v) == 1 \
or (w>1 and abs(u-v) == w-1) \
or w == 1 for u, v, w in zip(pi, index, mesh) )
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
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