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*)
''' Write orbitals, electron density in VASP CHGCAR format. ''' 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())