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 draw_with(eng):
eng.clear()
vo = Voron(*u.rep)
eng(vo)
u.to_decart()
if args.atoms:
for n, vs in u * 1: ## for each atoms in extended unitcell
r, col = UCell.data[n]
col = [x / 255.0 for x in col]
for v in vo.touch(vs):
eng(v, r=r, color=col, invis=False)
eng(n, pos=v)
for v in vo.has(
vs): ## only draw atoms which are in Voron cell
if not vo.touch(v):
eng(v, r=r, color=col, invis=False)
eng(n, pos=v)
if args.wycksub:
u.to_fract()
Z = u.to_min().rep.minimize().to_zell().norm()
for wname, ws in zip('abcdefghijklmnopqrstuvwxyz',
c.spgrp.wyckpos()):
for n, vs in u_basis:
for v in vs:
if v in ws:
print '--(%s)-->' % wname, n, v, c.spgrp * v,
u4min = UCell(u_basis.rep)
u4min.add('A', ws)
u4min = u4min.to_min()
z = u4min.rep.minimize().to_zell().norm()
if Z != z:
print 'FOUND %s' % z.to_sort()
vo = Voron(*u4min.rep)
eng(vo)
else:
print 'not wyck sublattice'
def draw_with(eng):
eng.clear()
vo = Voron(*u.rep)
eng(vo)
u.to_decart()
for n, vs in u * 1: ## for each atoms in extended unitcell
r, col = UCell.data[n]
col = [x / 255.0 for x in col]
for v in vo.touch(vs):
eng(v, r=r, color=col, invis=False)
eng(n, pos=v)
for v in vo.has(vs): ## only draw atoms which are in Voron cell
if not vo.touch(v):
eng(v, r=r, color=col, invis=False)
eng(n, pos=v)