def submodel_vp_colored(m,sm,rotated=None):
""" m is the full model with the VP's already calculated
sm is the submodel that we will save. it is modified and
likely otherwise unusable - be careful """
if( rotated == None ):
vpcoloredmodel = Model('vp colored atoms',m.lx,m.ly,m.lz,sm.atoms)
else:
vpcoloredmodel = Model('vp colored atoms',m.lx,m.ly,m.lz,rotated.atoms)
for i,atom in enumerate(vpcoloredmodel.atoms):
atomi = m.atoms[m.atoms.index(sm.atoms[i])]
if(atomi.vp.type == 'Full-icosahedra'):
sm.atoms[i].vp = atomi.vp.copy()
if( rotated != None ): rotated.atoms[i].vp = atomi.vp.copy()
atom.z = 1 # Dark blue
elif(atomi.vp.type == 'Icosahedra-like'):
sm.atoms[i].vp = atomi.vp.copy()
if( rotated != None ): rotated.atoms[i].vp = atomi.vp.copy()
atom.z = 2 # Light blue
elif(atomi.vp.type == 'Mixed'):
sm.atoms[i].vp = atomi.vp.copy()
if( rotated != None ): rotated.atoms[i].vp = atomi.vp.copy()
atom.z = 3 # Orange
elif(atomi.vp.type == 'Crystal-like'):
sm.atoms[i].vp = atomi.vp.copy()
if( rotated != None ): rotated.atoms[i].vp = atomi.vp.copy()
atom.z = 4 # Red
elif(atomi.vp.type == 'Undef'):
sm.atoms[i].vp = atomi.vp.copy()
if( rotated != None ): rotated.atoms[i].vp = atomi.vp.copy()
atom.z = 5 # Grey
vpcoloredmodel.write_real_xyz('vpcolored.xyz')
