def test_pp_int(self):
L = 2.
n = 20
cell = pbcgto.Cell()
cell.atom = 'He 1. .1 .3; He .0 .8 1.1'
cell.a = np.eye(3) * L
cell.mesh = [n] * 3
cell.basis = {'He': [[0, (0.8, 1.0)], [1, (1.2, 1.0)]]}
cell.pseudo = {
'He':
pbcgto.pseudo.parse('''
He
2
0.40000000 3 -1.98934751 -0.75604821 0.95604821
2
0.29482550 3 1.23870466 .855 .3
.71 -1.1
.9
0.32235865 2 2.25670239 -0.39677748
0.93894690
''')
}
cell.build()
np.random.seed(9)
kpt = np.random.random(3)
ref = get_pp_nl(cell)
dat = pp_int.get_pp_nl(cell)
self.assertTrue(dat.dtype == np.double)
self.assertAlmostEqual(np.linalg.norm(ref - dat), 0, 11)
ref = get_pp_nl(cell, kpt)
dat = pp_int.get_pp_nl(cell, (kpt, kpt))
self.assertTrue(dat.dtype == np.complex128)
self.assertAlmostEqual(np.linalg.norm(ref - dat[0]), 0, 11)
self.assertAlmostEqual(np.linalg.norm(ref - dat[1]), 0, 11)
ref = get_pp_loc_part2(cell)
dat = pp_int.get_pp_loc_part2(cell)
self.assertAlmostEqual(np.linalg.norm(ref - dat), 0, 11)
ref = get_pp_loc_part2(cell, kpt)
dat = pp_int.get_pp_loc_part2(cell, kpt)
self.assertAlmostEqual(np.linalg.norm(ref - dat), 0, 11)
def test_pp_loc_part2(self):
cell = pbcgto.Cell()
cell.atom = 'He 1. .5 .5; C .1 1.3 2.1'
cell.basis = {'He': [(0, (2.5, 1)), (0, (1., 1))],
'C' :'gth-szv',}
cell.pseudo = {'C':'gth-pade'}
cell.h = np.eye(3) * 2.5
cell.gs = [15] * 3
cell.build()
np.random.seed(1)
kpt = np.random.random(3)
ref = get_pp_loc_part2(cell)
dat = pp_int.get_pp_loc_part2(cell)
self.assertAlmostEqual(np.linalg.norm(ref-dat), 0, 12)
ref = get_pp_loc_part2(cell, kpt)
dat = pp_int.get_pp_loc_part2(cell, kpt)
self.assertAlmostEqual(np.linalg.norm(ref-dat), 0, 12)
def test_pp_int(self):
L = 2.
n = 20
cell = pbcgto.Cell()
cell.atom = 'He 1. .1 .3; He .0 .8 1.1'
cell.a = np.eye(3) * L
cell.mesh = [n] * 3
cell.basis = { 'He': [[0, (0.8, 1.0)],
[1, (1.2, 1.0)]
]}
cell.pseudo = {'He': pbcgto.pseudo.parse('''
He
2
0.40000000 3 -1.98934751 -0.75604821 0.95604821
2
0.29482550 3 1.23870466 .855 .3
.71 -1.1
.9
0.32235865 2 2.25670239 -0.39677748
0.93894690
''')}
cell.build()
np.random.seed(9)
kpt = np.random.random(3)
ref = get_pp_nl(cell)
dat = pp_int.get_pp_nl(cell)
self.assertTrue(dat.dtype == np.double)
self.assertAlmostEqual(np.linalg.norm(ref-dat), 0, 11)
ref = get_pp_nl(cell, kpt)
dat = pp_int.get_pp_nl(cell, (kpt,kpt))
self.assertTrue(dat.dtype == np.complex128)
self.assertAlmostEqual(np.linalg.norm(ref-dat[0]), 0, 11)
self.assertAlmostEqual(np.linalg.norm(ref-dat[1]), 0, 11)
ref = get_pp_loc_part2(cell)
dat = pp_int.get_pp_loc_part2(cell)
self.assertAlmostEqual(np.linalg.norm(ref-dat), 0, 11)
ref = get_pp_loc_part2(cell, kpt)
dat = pp_int.get_pp_loc_part2(cell, kpt)
self.assertAlmostEqual(np.linalg.norm(ref-dat), 0, 11)
def test_pp_loc_part2(self):
cell = pbcgto.Cell()
cell.atom = 'He 1. .5 .5; C .1 1.3 2.1'
cell.basis = {'He': [(0, (2.5, 1)), (0, (1., 1))],
'C' :'gth-szv',}
cell.pseudo = {'C':'gth-pade'}
cell.a = np.eye(3) * 2.5
cell.gs = [15] * 3
cell.build()
np.random.seed(1)
kpt = np.random.random(3)
ref = get_pp_loc_part2(cell)
dat = pp_int.get_pp_loc_part2(cell)
self.assertAlmostEqual(np.linalg.norm(ref-dat), 0, 12)
ref = get_pp_loc_part2(cell, kpt)
dat = pp_int.get_pp_loc_part2(cell, kpt)
self.assertAlmostEqual(np.linalg.norm(ref-dat), 0, 12)
def get_gth_pp(mol):
from pyscf.gto import ATOM_OF
from pyscf.pbc.gto import Cell
from pyscf.pbc.gto.pseudo import pp_int
from pyscf.df import incore
# Analytical integration for get_pp_loc_part1(cell).
fakemol = pp_int.fake_cell_vloc(mol, 0)
vpploc = 0
if fakemol.nbas > 0:
charges = fakemol.atom_charges()
atmlst = fakemol._bas[:, ATOM_OF]
v = incore.aux_e2(mol, fakemol, 'int3c2e', aosym='s2', comp=1)
v = numpy.einsum('...i,i->...', v, -charges[atmlst])
vpploc += lib.unpack_tril(v)
# To compute the rest part of GTH PP, mimic the mol with a 0D cell.
cell_0D = mol.view(Cell)
cell_0D.dimension = 0
cell_0D.a = numpy.eye(3)
vpploc += pp_int.get_pp_loc_part2(cell_0D).real
vpploc += pp_int.get_pp_nl(cell_0D).real
return vpploc
def get_gth_pp(mol):
from pyscf.gto import ATOM_OF
from pyscf.pbc.gto import Cell
from pyscf.pbc.gto.pseudo import pp_int
from pyscf.df import incore
# Analytical integration for get_pp_loc_part1(cell).
fakemol = pp_int.fake_cell_vloc(mol, 0)
vpploc = 0
if fakemol.nbas > 0:
charges = fakemol.atom_charges()
atmlst = fakemol._bas[:,ATOM_OF]
v = incore.aux_e2(mol, fakemol, 'int3c2e', aosym='s2', comp=1)
v = numpy.einsum('...i,i->...', v, -charges[atmlst])
vpploc += lib.unpack_tril(v)
# To compute the rest part of GTH PP, mimic the mol with a 0D cell.
cell_0D = mol.view(Cell)
cell_0D.dimension = 0
cell_0D.a = numpy.eye(3)
vpploc += pp_int.get_pp_loc_part2(cell_0D).real
vpploc += pp_int.get_pp_nl(cell_0D).real
return vpploc