def minimize(*xxx):
global args, u
## test mimimization for correction
if args.testmin:
vo = Voron(*u.rep) ## original Voronoi cell
u = u.to_min()
u_exp = u * 1
u_exp.to_decart()
drawgl.clear()
drawgl(vo)
## draw all atoms which are in "vo"
for n, ats in u_exp:
r, col = UCell.data[n]
col = [x / 255.0 for x in col]
for v in vo.has(ats):
drawgl(v, r=r, color=col, invis=False)
## now draw all cloned Voronoi cells
#import reper2dots
#for v in vo.cut( u.rep.to_dots( 1, 1, 1 ) ):
# drawgl( Voron( *u.rep, pos = v ) )
drawgl(Voron(*u.rep))
## usual minimization process
else:
u = u.to_min()
print '------------'
print 'sort of minimized cell: ', u.rep.to_zell().to_sort().name
print 'zell of minimized cell: ', u.rep.to_zell().norm()
draw_with(drawgl)
def redraw():
global p1,p2,p3
print "p1 = %s, p2 = %s, p3 = %s" % (p1,p2,p3)
z = Zell( p1, 0, p2, p2, p3, p1 )
vo = Voron( *z.to_reper() )
drawgl.clear()
drawgl( vo )
def redraw():
global p1, p2, p3
print "p1 = %s, p2 = %s, p3 = %s" % (p1, p2, p3)
z = Zell(p1, 0, p2, p2, p3, p1)
vo = Voron(*z.to_reper())
drawgl.clear()
drawgl(vo)
def w_si(*args):
drawgl.clear()
drawgl(vo)
for v in si:
drawgl(v)
for vv in o:
if abs((v - vv).vlen() - d2) < 0.1:
drawgl(Vec(*vv), style='line', start=v)
drawgl(Vec(*vv), r=0.1, color=(0, 0, 1))
def w_si( *args ):
drawgl.clear()
drawgl( vo )
for v in si:
drawgl( v )
for vv in o:
if abs( (v - vv).vlen() - d2 ) < 0.1:
drawgl( Vec( *vv ), style='line', start=v )
drawgl( Vec( *vv ), r=0.1, color=(0,0,1) )
def draw(nc, n):
drawgl.clear()
vo3.draw()
vo1.draw()
for p in plns[n].touch(fd1):
p.draw(r=0.02, color=(0, 1, 0))
for p in plns[n].touch(fd2):
p.draw(r=0.04, color=(1, 0, 0))
def draw(nc, n):
drawgl.clear()
vo3.draw()
vo1.draw()
for p in plns[n].touch(fd1):
p.draw(r=0.02, color=(0, 1, 0))
for p in plns[n].touch(fd2):
p.draw(r=0.04, color=(1, 0, 0))
def redraw():
global vc, pos, delta
v = vc.norm() * delta * pos
p = vc.to_plane(v)
drawgl.clear()
drawgl(vo_h)
drawgl(p)
for x in p.touch(ds1_h):
drawgl(x, r=0.10, color=(0, 1, 0))
for x in p.touch(ds2_h):
drawgl(x, r=0.11, color=(1, 0, 0))
def redraw():
global vc, pos, delta
v = vc.norm() * delta * pos
p = vc.to_plane( v )
drawgl.clear()
drawgl( vo_h )
drawgl( p )
for x in p.touch( ds1_h ):
drawgl( x, r = 0.10, color=(0,1,0) )
for x in p.touch( ds2_h ):
drawgl( x, r = 0.11, color=(1,0,0) )
def draw( n ):
drawgl.clear()
drawgl( vo3 )
vn = edg.norm()
pln = vn.to_plane( vn * dr * n )
drawgl( pln )
for p in pln.touch( vo3.has( ds1 ) ):
drawgl( p, color=(0,1,0) )
for p in pln.touch( vo3.has( ds2 ) ):
drawgl( p, r=0.04, color=(1,0,0) )
def draw(n):
drawgl.clear()
drawgl(vo3)
vn = edg.norm()
pln = vn.to_plane(vn * dr * n)
drawgl(pln)
for p in pln.touch(vo3.has(ds1)):
drawgl(p, color=(0, 1, 0))
for p in pln.touch(vo3.has(ds2)):
drawgl(p, r=0.04, color=(1, 0, 0))
def redraw():
global pos, reps
#### constructing sublattice reper
#r1 = Zell( -1, 0, -1, -1, 0, -1 ).to_reper()
r1, r2 = reps[ pos ]
vo1 = Voron( *r1 )
vo2 = Voron( *r2 )
drawgl.clear()
drawgl( vo1 )
drawgl( vo2 )
print r1, r2
def fill_hex(*args):
print args
drawgl.clear()
drawgl(vo1)
drawgl(vo21)
drawgl(vo22)
drawgl(vhex)
for p in vhex.has(ds1):
drawgl(p, r=0.02, color=(0, 1, 0))
for p in vhex.has(ds2):
drawgl(p, r=0.04, color=(1, 0, 0))
def draw():
print num
drawgl.clear()
#drawgl( vo1 )
#drawgl( vo2 )
drawgl( vhex )
pln = n.to_plane( r0 + num * dr )
for p in pln.touch( vhex.has( ds1 ) ):
drawgl( p, r=0.02, color = (0,1,0) )
for p in pln.touch( vhex.has( ds2 ) ):
drawgl( p, r=0.04, color = (1,0,0) )
def draw():
print num
drawgl.clear()
#drawgl( vo1 )
#drawgl( vo2 )
drawgl(vhex)
pln = n.to_plane(r0 + num * dr)
for p in pln.touch(vhex.has(ds1)):
drawgl(p, r=0.02, color=(0, 1, 0))
for p in pln.touch(vhex.has(ds2)):
drawgl(p, r=0.04, color=(1, 0, 0))
def fill_hex( *args ):
print args
drawgl.clear()
drawgl( vo1 )
drawgl( vo21 )
drawgl( vo22 )
drawgl( vhex )
for p in vhex.has( ds1 ):
drawgl( p, r=0.02, color = (0,1,0) )
for p in vhex.has( ds2 ):
drawgl( p, r=0.04, color = (1,0,0) )
def minimize( *xxx ):
global args, u
## test mimimization for correction
if args.testmin:
vo = Voron( *u.rep ) ## original Voronoi cell
u = u.to_min()
u_exp = u * 1
u_exp.to_decart()
drawgl.clear()
drawgl( vo )
## draw all atoms which are in "vo"
for n, ats in u_exp:
r, col = UCell.data[ n ]
col = [ x/255.0 for x in col ]
for v in vo.has( ats ):
drawgl( v, r = r, color = col, invis = False )
## now draw all cloned Voronoi cells
#import reper2dots
#for v in vo.cut( u.rep.to_dots( 1, 1, 1 ) ):
# drawgl( Voron( *u.rep, pos = v ) )
drawgl( Voron( *u.rep ) )
## usual minimization process
else:
u = u.to_min()
print '------------'
print 'sort of minimized cell: ', u.rep.to_zell().to_sort().name
print 'zell of minimized cell: ', u.rep.to_zell().norm()
draw_with( drawgl )
def cubic(*args):
## old cube
vc = Vec(-0.5, -0.707106781187, 0.244948974278)
v1 = Vec(-0.7, 0.282842712476, 0.489897948556)
v2 = Vec(-0.3, -0.424264068713, -0.734846922836)
v3 = Vec(0.5, -0.565685424949, 0.489897948556)
v1, v2, v3 = v1 - vc, v2 - vc, v3 - vc
## new cube
vc = Vec(0.8, -0.141421356235, 1.22474487139)
v1 = Vec(-0.2, -0.282842712473, 0.979795897112)
v2 = Vec(1.0, 0.141421356238, 0.244948974278)
v3 = Vec(1.0, -1.1313708499, 0.979795897112)
v1, v2, v3 = v1 - vc, v2 - vc, v3 - vc
drawgl.clear()
## -- draw cube
vc = Voron(v1, v2, v3, pos=0.5 * (v1 + v2 + v3))
for v in vc.has(ds1):
drawgl(v, color=(0, 1, 0))
for v in vc.has(ds2):
drawgl(v, r=0.04, color=(1, 0, 0))
#drawgl( vc )
drawgl(vo1)
drawgl(vo2)
basisA = vc.has(ds1)
basisA = vc.rep.dec2frac(basisA)
basisA = map(lambda v: v.z2o(), basisA)
basisB = [Vec(0.0, 0.0, 0.0), Vec(0.5, 0.5, 0.5)]
basisA = set(basisA)
basisB = set(basisB)
print 'len( basisA ) = ', len(basisA)
print 'len( basisB ) = ', len(basisB)
basisA = basisA - basisB
print 'len( basisA ) = ', len(basisA)
print 'len( basisB ) = ', len(basisB)
## -- output basis to file
f = open('/tmp/basis_ock_ock.txt', 'w')
r = vc.rep
print r.v3 * r.v1.vcross(r.v2)
f.write("rprim %s %s %s\n %s %s %s\n %s %s %s\n" %
(tuple(r[0]) + tuple(r[1]) + tuple(r[2])))
f.write("vc.rep\t%s\n\t\t%s\n\t\t%s\n" % (vc.rep[0], vc.rep[1], vc.rep[2]))
for v in (vc.rep[0], vc.rep[1], vc.rep[2]):
drawgl(v, style='line')
f.write('-----------\n')
for v in basisA:
f.write("%s %s %s\n" % tuple(v))
f.write('-----------\n')
for v in basisB:
f.write("%s %s %s\n" % tuple(v))
f.close()
## -- test space groups
for i in xrange(1, 231):
for j in SpGrp.subs(i):
s = SpGrp(i, j)
f = True
for p in basisA:
for v in s * p:
if v not in basisA:
f = False
break
if not f:
break
if f:
for p in basisB:
for v in s * p:
if v not in basisB:
f = False
if f:
print '---', s, 'YES'
#if f:
# print '---', s, 'YES'
return
## -- output other basis
v1, v2, v3 = v1, v2, 0.5 * (v1 + v2 + v3)
vc = Voron(v1, v2, v3)
drawgl(vc)
f = open('/tmp/basis_ock_ock2.txt', 'w')
r = vc.rep
print r.v3 * r.v1.vcross(r.v2)
for v in r:
drawgl(v, style="line", color=(1, 0, 0))
basisA = vc.has(ds1)
basisA = vc.rep.dec2frac(basisA)
basisA = map(lambda v: v.z2o(), basisA)
basisB = [Vec(0.0, 0.0, 0.0)]
basisA = set(basisA)
basisB = set(basisB)
print 'len( basisA ) = ', len(basisA)
print 'len( basisB ) = ', len(basisB)
basisA = basisA - basisB
print 'len( basisA ) = ', len(basisA)
print 'len( basisB ) = ', len(basisB)
f.write("rprim %s %s %s\n %s %s %s\n %s %s %s\n" %
(tuple(r[0]) + tuple(r[1]) + tuple(r[2])))
f.write('-----------\n')
for v in basisA:
f.write("%s %s %s\n" % tuple(v))
drawgl(r.frac2dec(v), r=0.05, color=(0, 0, 1))
f.write('-----------\n')
for v in basisB:
f.write("%s %s %s\n" % tuple(v))
drawgl(r.frac2dec(v), r=0.05, color=(0, 1, 1))
f.close()
def cubic( *args ):
## old cube
vc = Vec( -0.5, -0.707106781187, 0.244948974278 )
v1 = Vec( -0.7, 0.282842712476, 0.489897948556 )
v2 = Vec( -0.3, -0.424264068713, -0.734846922836 )
v3 = Vec( 0.5, -0.565685424949, 0.489897948556 )
v1,v2,v3 = v1 - vc, v2 - vc, v3 - vc
## new cube
vc = Vec( 0.8, -0.141421356235, 1.22474487139 )
v1 = Vec( -0.2, -0.282842712473, 0.979795897112 )
v2 = Vec( 1.0, 0.141421356238, 0.244948974278 )
v3 = Vec( 1.0, -1.1313708499, 0.979795897112 )
v1,v2,v3 = v1 - vc, v2 - vc, v3 - vc
drawgl.clear()
## -- draw cube
vc = Voron( v1, v2, v3, pos = 0.5 * ( v1+v2+v3 ) )
for v in vc.has( ds1 ):
drawgl( v, color=(0,1,0) )
for v in vc.has( ds2 ):
drawgl( v, r=0.04, color=(1,0,0) )
#drawgl( vc )
drawgl( vo1 )
drawgl( vo2 )
basisA = vc.has( ds1 )
basisA = vc.rep.dec2frac( basisA )
basisA = map( lambda v: v.z2o(), basisA )
basisB = [ Vec( 0.0, 0.0, 0.0 ),
Vec( 0.5, 0.5, 0.5 ) ]
basisA = set( basisA )
basisB = set( basisB )
print 'len( basisA ) = ', len( basisA )
print 'len( basisB ) = ', len( basisB )
basisA = basisA - basisB
print 'len( basisA ) = ', len( basisA )
print 'len( basisB ) = ', len( basisB )
## -- output basis to file
f = open( '/tmp/basis_ock_ock.txt', 'w' )
r = vc.rep
print r.v3 * r.v1.vcross( r.v2 )
f.write( "rprim %s %s %s\n %s %s %s\n %s %s %s\n" % ( tuple( r[0] ) + tuple( r[1] ) + tuple( r[2] ) ) )
f.write( "vc.rep\t%s\n\t\t%s\n\t\t%s\n" % ( vc.rep[ 0 ], vc.rep[ 1 ], vc.rep[ 2 ] ) )
for v in ( vc.rep[ 0 ], vc.rep[ 1 ], vc.rep[ 2 ] ):
drawgl( v, style = 'line' )
f.write( '-----------\n' )
for v in basisA:
f.write( "%s %s %s\n" % tuple( v ) )
f.write( '-----------\n' )
for v in basisB:
f.write( "%s %s %s\n" % tuple( v ) )
f.close()
## -- test space groups
for i in xrange( 1, 231 ):
for j in SpGrp.subs( i ):
s = SpGrp( i, j )
f = True
for p in basisA:
for v in s * p:
if v not in basisA:
f = False
break
if not f:
break
if f:
for p in basisB:
for v in s * p:
if v not in basisB:
f = False
if f:
print '---', s, 'YES'
#if f:
# print '---', s, 'YES'
return
## -- output other basis
v1, v2, v3 = v1, v2, 0.5 * (v1 + v2 + v3)
vc = Voron( v1, v2, v3 )
drawgl( vc )
f = open( '/tmp/basis_ock_ock2.txt', 'w' )
r = vc.rep
print r.v3 * r.v1.vcross( r.v2 )
for v in r:
drawgl( v, style="line", color=( 1,0,0 ) )
basisA = vc.has( ds1 )
basisA = vc.rep.dec2frac( basisA )
basisA = map( lambda v: v.z2o(), basisA )
basisB = [ Vec( 0.0, 0.0, 0.0 ) ]
basisA = set( basisA )
basisB = set( basisB )
print 'len( basisA ) = ', len( basisA )
print 'len( basisB ) = ', len( basisB )
basisA = basisA - basisB
print 'len( basisA ) = ', len( basisA )
print 'len( basisB ) = ', len( basisB )
f.write( "rprim %s %s %s\n %s %s %s\n %s %s %s\n" % ( tuple( r[0] ) + tuple( r[1] ) + tuple( r[2] ) ) )
f.write( '-----------\n' )
for v in basisA:
f.write( "%s %s %s\n" % tuple( v ) )
drawgl( r.frac2dec( v ), r=0.05, color = (0,0,1) )
f.write( '-----------\n' )
for v in basisB:
f.write( "%s %s %s\n" % tuple( v ) )
drawgl( r.frac2dec( v ), r=0.05, color = (0,1,1) )
f.close()