'''
generates IBOs
'''
mo_occ = mf.mo_coeff[:,mf.mo_occ>0]
a = lo.iao.iao(cell, mo_occ)
# Orthogonalize IAO
a = lo.vec_lowdin(a, mf.get_ovlp())
#ibo must take the orthonormalized IAOs
ibo = lo.ibo.ibo(cell, mo_occ, a)
'''
Generates IBO files as VASP Chgcars
'''
for i in range(ibo.shape[1]):
chgcar.orbital(cell, 'diamond_ibo{:02d}.chgcar'.format(i+1), ibo[:,i])
print("wrote cube {:02d}".format(i+1))
'''
Makes Population Analysis with IAOs
'''
# transform mo_occ to IAO representation. Note the AO dimension is reduced
mo_occ = reduce(numpy.dot, (a.T, mf.get_ovlp(), mo_occ))
dm = numpy.dot(mo_occ, mo_occ.T) * 2
iao_mol = cell.copy()
iao_mol.build(False, False, basis='minao')
mullic = mf.mulliken_pop(iao_mol, dm, s=numpy.eye(iao_mol.nao_nr()))
f.write(''.join(['%5.3s' % atomN[0]
for atomN in vaspAtomicInfo]) + '\n')
f.write(''.join(['%5d' % atomN[1]
for atomN in vaspAtomicInfo]) + '\n')
f.write('Cartesian \n')
for ia in range(cell.natm):
f.write(' %14.8f %14.8f %14.8f\n' % tuple(swappedCoords[ia]))
f.write('\n')
f.write('%6.5s %6.5s %6.5s \n' % (self.nx, self.ny, self.nz))
fmt = ' %14.8e '
for iz in range(self.nz):
for iy in range(self.ny):
f.write('\n')
for ix in range(self.nx):
f.write(fmt % field[ix, iy, iz])
def read(self, chgcar_file):
raise NotImplementedError
if __name__ == '__main__':
from pyscf.pbc import scf
from pyscf.tools import chgcar
cell = gto.M(atom='H 0 0 0; H 0 0 1', a=numpy.eye(3) * 3)
mf = scf.RHF(cell).run()
chgcar.density(cell, 'h2.CHGCAR', mf.make_rdm1()) #makes total density
chgcar.orbital(cell, 'h2_mo1.CHGCAR', mf.mo_coeff[:,
0]) # makes mo#1 (sigma)
chgcar.orbital(cell, 'h2_mo2.CHGCAR',
mf.mo_coeff[:, 1]) # makes mo#2 (sigma*)
import numpy as np from pyscf.pbc import gto, scf from pyscf.tools import chgcar # # Regular CHGCAR file for crystal cell # cell = gto.M(atom='H 0 0 0; H 0 0 1', a=np.eye(3)*3) mf = scf.RHF(cell).run() # electron density chgcar.density(cell, 'cell_h2.CHGCAR', mf.make_rdm1()) # 1st MO chgcar.orbital(cell, 'cell_h2_mo1.CHGCAR', mf.mo_coeff[:,0]) # # Extended mode to support molecular system. In this mode, a lattic was # generated and the molecule was placed in the center of the unit cell. # from pyscf import gto, scf mol = gto.M(atom='H 0 0 0; H 0 0 1') mf = scf.RHF(mol).run() # electron density chgcar.density(mol, 'mole_h2.CHGCAR', mf.make_rdm1()) # 2nd MO chgcar.orbital(mol, 'mole_h2_mo2.CHGCAR', mf.mo_coeff[:,1])