def test_project_mo_nr2nr(self):
nao = mol.nao_nr()
c = numpy.random.random((nao, nao))
c1 = addons.project_mo_nr2nr(mol, c, mol)
self.assertAlmostEqual(abs(c - c1).max(), 0, 12)
numpy.random.seed(15)
nao = mol.nao_nr()
mo1 = numpy.random.random((nao, nao))
mo2 = addons.project_mo_nr2nr(mol, [mo1, mo1], mol_dz)
self.assertAlmostEqual(abs(mo2[0]).sum(), 83.436359425591888, 11)
self.assertAlmostEqual(abs(mo2[1]).sum(), 83.436359425591888, 11)
def test_project_mo_nr2nr(self):
nao = mol.nao_nr()
c = numpy.random.random((nao,nao))
c1 = addons.project_mo_nr2nr(mol, c, mol)
self.assertAlmostEqual(abs(c-c1).max(), 0, 12)
numpy.random.seed(15)
nao = mol.nao_nr()
mo1 = numpy.random.random((nao,nao))
mo2 = addons.project_mo_nr2nr(mol, [mo1,mo1], mol_dz)
self.assertAlmostEqual(abs(mo2[0]).sum(), 83.436359425591888, 11)
self.assertAlmostEqual(abs(mo2[1]).sum(), 83.436359425591888, 11)
def init_guess_by_minao(mol):
'''Generate initial guess density matrix based on ANO basis, then project
the density matrix to the basis set defined by ``mol``
Returns:
Density matrix, 2D ndarray
Examples:
>>> from pyscf import gto, scf
>>> mol = gto.M(atom='H 0 0 0; H 0 0 1.1')
>>> scf.hf.init_guess_by_minao(mol)
array([[ 0.94758917, 0.09227308],
[ 0.09227308, 0.94758917]])
'''
from pyscf.scf import atom_hf
from pyscf.scf import addons
def minao_basis(symb):
basis_add = pyscf.gto.basis.load('ano', symb)
occ = []
basis_new = []
for l in range(4):
ndocc, nfrac = atom_hf.frac_occ(symb, l)
if ndocc > 0:
occ.extend([2]*ndocc*(2*l+1))
if nfrac > 1e-15:
occ.extend([nfrac]*(2*l+1))
ndocc += 1
if ndocc > 0:
basis_new.append([l] + [b[:ndocc+1] for b in basis_add[l][1:]])
return occ, basis_new
atmlst = set([pyscf.gto.mole._rm_digit(pyscf.gto.mole._symbol(k))
for k in mol._basis.keys()])
basis = {}
occdic = {}
for symb in atmlst:
if symb != 'GHOST':
occ_add, basis_add = minao_basis(symb)
occdic[symb] = occ_add
basis[symb] = basis_add
occ = []
new_atom = []
for ia in range(mol.natm):
symb = mol.atom_pure_symbol(ia)
if symb != 'GHOST':
occ.append(occdic[symb])
new_atom.append(mol._atom[ia])
occ = numpy.hstack(occ)
pmol = pyscf.gto.Mole()
pmol._atm, pmol._bas, pmol._env = pmol.make_env(new_atom, basis, [])
c = addons.project_mo_nr2nr(pmol, 1, mol)
dm = numpy.dot(c*occ, c.T)
# normalize eletron number
# s = mol.intor_symmetric('cint1e_ovlp_sph')
# dm *= mol.nelectron / (dm*s).sum()
return dm
def init_guess_by_atom(mol):
'''Generate initial guess density matrix from superposition of atomic HF
density matrix. The atomic HF is occupancy averaged RHF
Returns:
Density matrix, 2D ndarray
'''
import copy
from pyscf.scf import atom_hf
from pyscf.scf import addons
atm_scf = atom_hf.get_atm_nrhf(mol)
mo = []
mo_occ = []
for ia in range(mol.natm):
symb = mol.atom_symbol(ia)
if symb != 'GHOST':
if symb in atm_scf:
e_hf, e, c, occ = atm_scf[symb]
else:
symb = mol.atom_pure_symbol(ia)
e_hf, e, c, occ = atm_scf[symb]
mo.append(c)
mo_occ.append(occ)
mo = scipy.linalg.block_diag(*mo)
mo_occ = numpy.hstack(mo_occ)
pmol = copy.copy(mol)
pmol.cart = False
c = addons.project_mo_nr2nr(pmol, mo, mol)
dm = numpy.dot(c * mo_occ, c.T)
for k, v in atm_scf.items():
logger.debug1(mol, 'Atom %s, E = %.12g', k, v[0])
return dm
def gen_g_hop_rhf(mf, mo_coeff, mo_occ, fock_ao=None, h1e=None):
mol = mf.mol
occidx = numpy.where(mo_occ == 2)[0]
viridx = numpy.where(mo_occ == 0)[0]
nocc = len(occidx)
nvir = len(viridx)
if fock_ao is None:
if h1e is None: h1e = mf.get_hcore()
dm0 = mf.make_rdm1(mo_coeff, mo_occ)
fock_ao = h1e + mf.get_veff(mol, dm0)
fock = reduce(numpy.dot, (mo_coeff.T, fock_ao, mo_coeff))
g = fock[viridx[:, None], occidx] * 2
foo = fock[occidx[:, None], occidx]
fvv = fock[viridx[:, None], viridx]
h_diag = (fvv.diagonal().reshape(-1, 1) - foo.diagonal()) * 2
# To project Hessians from another basis if different basis sets are used
# in newton solver and underlying mean-filed solver.
if hasattr(mf, '_scf') and id(mf._scf.mol) != id(mol):
mo_coeff = addons.project_mo_nr2nr(mf._scf.mol, mo_coeff, mol)
if hasattr(mf, 'xc') and hasattr(mf, '_numint'):
if mf.grids.coords is None:
mf.grids.build()
hyb = mf._numint.hybrid_coeff(mf.xc, spin=(mol.spin > 0) + 1)
rho0, vxc, fxc = mf._numint.cache_xc_kernel(mol, mf.grids, mf.xc,
mo_coeff, mo_occ, 0)
dm0 = None #mf.make_rdm1(mo_coeff, mo_occ)
else:
hyb = None
def h_op(x):
x = x.reshape(nvir, nocc)
x2 = numpy.einsum('sp,sq->pq', fvv, x) * 2
x2 -= numpy.einsum('sp,rp->rs', foo, x) * 2
d1 = reduce(numpy.dot, (mo_coeff[:, viridx], x, mo_coeff[:, occidx].T))
dm1 = d1 + d1.T
if hyb is None:
vj, vk = mf.get_jk(mol, dm1)
v1 = vj - vk * .5
else:
v1 = mf._numint.nr_rks_fxc(mol, mf.grids, mf.xc, dm0, dm1, 0, 1,
rho0, vxc, fxc)
if abs(hyb) < 1e-10:
v1 += mf.get_j(mol, dm1)
else:
vj, vk = mf.get_jk(mol, dm1)
v1 += vj - vk * (hyb * .5)
x2 += reduce(numpy.dot,
(mo_coeff[:, viridx].T, v1, mo_coeff[:, occidx])) * 4
return x2.reshape(-1)
return g.reshape(-1), h_op, h_diag.reshape(-1)
def gen_g_hop_rhf(mf, mo_coeff, mo_occ, fock_ao=None, h1e=None):
mol = mf.mol
occidx = numpy.where(mo_occ==2)[0]
viridx = numpy.where(mo_occ==0)[0]
nocc = len(occidx)
nvir = len(viridx)
if fock_ao is None:
if h1e is None: h1e = mf.get_hcore()
dm0 = mf.make_rdm1(mo_coeff, mo_occ)
fock_ao = h1e + mf.get_veff(mol, dm0)
fock = reduce(numpy.dot, (mo_coeff.T, fock_ao, mo_coeff))
g = fock[viridx[:,None],occidx] * 2
foo = fock[occidx[:,None],occidx]
fvv = fock[viridx[:,None],viridx]
h_diag = (fvv.diagonal().reshape(-1,1)-foo.diagonal()) * 2
# To project Hessians from another basis if different basis sets are used
# in newton solver and underlying mean-filed solver.
if hasattr(mf, '_scf') and id(mf._scf.mol) != id(mol):
mo_coeff = addons.project_mo_nr2nr(mf._scf.mol, mo_coeff, mol)
if hasattr(mf, 'xc') and hasattr(mf, '_numint'):
if mf.grids.coords is None:
mf.grids.build()
hyb = mf._numint.hybrid_coeff(mf.xc, spin=(mol.spin>0)+1)
rho0, vxc, fxc = mf._numint.cache_xc_kernel(mol, mf.grids, mf.xc,
mo_coeff, mo_occ, 0)
dm0 = None #mf.make_rdm1(mo_coeff, mo_occ)
else:
hyb = None
def h_op(x):
x = x.reshape(nvir,nocc)
x2 = numpy.einsum('sp,sq->pq', fvv, x) * 2
x2-= numpy.einsum('sp,rp->rs', foo, x) * 2
d1 = reduce(numpy.dot, (mo_coeff[:,viridx], x, mo_coeff[:,occidx].T))
dm1 = d1 + d1.T
if hyb is None:
v1 = mf.get_veff(mol, dm1)
else:
v1 = mf._numint.nr_rks_fxc(mol, mf.grids, mf.xc, dm0, dm1,
0, 1, rho0, vxc, fxc)
if abs(hyb) < 1e-10:
v1 += mf.get_j(mol, dm1)
else:
vj, vk = mf.get_jk(mol, dm1)
v1 += vj - vk * hyb * .5
x2 += reduce(numpy.dot, (mo_coeff[:,viridx].T, v1,
mo_coeff[:,occidx])) * 4
return x2.reshape(-1)
return g.reshape(-1), h_op, h_diag.reshape(-1)
def gen_g_hop_rhf(mf, mo_coeff, mo_occ, fock_ao=None, h1e=None,
with_symmetry=True):
mol = mf.mol
occidx = numpy.where(mo_occ==2)[0]
viridx = numpy.where(mo_occ==0)[0]
nocc = len(occidx)
nvir = len(viridx)
orbo = mo_coeff[:,occidx]
orbv = mo_coeff[:,viridx]
if with_symmetry and mol.symmetry:
orbsym = hf_symm.get_orbsym(mol, mo_coeff)
sym_forbid = orbsym[viridx].reshape(-1,1) != orbsym[occidx]
if fock_ao is None:
if h1e is None: h1e = mf.get_hcore()
dm0 = mf.make_rdm1(mo_coeff, mo_occ)
fock_ao = h1e + mf.get_veff(mol, dm0)
fock = reduce(numpy.dot, (mo_coeff.T, fock_ao, mo_coeff))
g = fock[viridx[:,None],occidx] * 2
foo = fock[occidx[:,None],occidx]
fvv = fock[viridx[:,None],viridx]
h_diag = (fvv.diagonal().reshape(-1,1)-foo.diagonal()) * 2
if with_symmetry and mol.symmetry:
g[sym_forbid] = 0
h_diag[sym_forbid] = 0
# To project Hessians from another basis if different basis sets are used
# in newton solver and underlying mean-filed solver.
if hasattr(mf, '_scf') and id(mf._scf.mol) != id(mol):
mo_coeff = addons.project_mo_nr2nr(mf._scf.mol, mo_coeff, mol)
vind = _gen_rhf_response(mf, mo_coeff, mo_occ, singlet=None, hermi=1)
def h_op(x):
x = x.reshape(nvir,nocc)
if with_symmetry and mol.symmetry:
x = x.copy()
x[sym_forbid] = 0
x2 = numpy.einsum('ps,sq->pq', fvv, x)
#x2-= .5*numpy.einsum('ps,rp->rs', foo, x)
#x2-= .5*numpy.einsum('sp,rp->rs', foo, x)
x2-= numpy.einsum('ps,rp->rs', foo, x)
# *2 for double occupancy
d1 = reduce(numpy.dot, (orbv, x*2, orbo.T.conj()))
dm1 = d1 + d1.T.conj()
v1 = vind(dm1)
x2 += reduce(numpy.dot, (orbv.T.conj(), v1, orbo))
if with_symmetry and mol.symmetry:
x2[sym_forbid] = 0
return x2.reshape(-1) * 2
return g.reshape(-1), h_op, h_diag.reshape(-1)
def test_project_dm_nr2nr(self):
nao = mol.nao_nr()
dm = numpy.random.random((nao, nao))
dm = dm + dm.T
x1 = addons.project_dm_nr2nr(mol, dm, mol)
self.assertAlmostEqual(abs(dm - x1).max(), 0, 12)
numpy.random.seed(15)
mo = numpy.random.random((nao, 10))
mo1 = addons.project_mo_nr2nr(mol, mo, mol_dz)
dm = numpy.dot(mo, mo.T)
dmref = numpy.dot(mo1, mo1.T)
dm1 = addons.project_dm_nr2nr(mol, [dm, dm], mol_dz)
self.assertAlmostEqual(abs(dmref - dm1[0]).max(), 0, 11)
self.assertAlmostEqual(abs(dmref - dm1[1]).max(), 0, 11)
self.assertAlmostEqual(lib.finger(dm1[0]), 73.603267455214876, 11)
def test_project_dm_nr2nr(self):
nao = mol.nao_nr()
dm = numpy.random.random((nao,nao))
dm = dm + dm.T
x1 = addons.project_dm_nr2nr(mol, dm, mol)
self.assertAlmostEqual(abs(dm-x1).max(), 0, 12)
numpy.random.seed(15)
mo = numpy.random.random((nao,10))
mo1 = addons.project_mo_nr2nr(mol, mo, mol_dz)
dm = numpy.dot(mo, mo.T)
dmref = numpy.dot(mo1, mo1.T)
dm1 = addons.project_dm_nr2nr(mol, [dm,dm], mol_dz)
self.assertAlmostEqual(abs(dmref-dm1[0]).max(), 0, 11)
self.assertAlmostEqual(abs(dmref-dm1[1]).max(), 0, 11)
self.assertAlmostEqual(lib.finger(dm1[0]), 73.603267455214876, 11)
def gen_g_hop_uhf(mf, mo_coeff, mo_occ, fock_ao=None, h1e=None):
mol = mf.mol
occidxa = numpy.where(mo_occ[0] > 0)[0]
occidxb = numpy.where(mo_occ[1] > 0)[0]
viridxa = numpy.where(mo_occ[0] == 0)[0]
viridxb = numpy.where(mo_occ[1] == 0)[0]
nocca = len(occidxa)
noccb = len(occidxb)
nvira = len(viridxa)
nvirb = len(viridxb)
if fock_ao is None:
if h1e is None: h1e = mf.get_hcore()
dm0 = mf.make_rdm1(mo_coeff, mo_occ)
fock_ao = h1e + mf.get_veff(mol, dm0)
focka = reduce(numpy.dot, (mo_coeff[0].T, fock_ao[0], mo_coeff[0]))
fockb = reduce(numpy.dot, (mo_coeff[1].T, fock_ao[1], mo_coeff[1]))
g = numpy.hstack((focka[viridxa[:, None],
occidxa].reshape(-1), fockb[viridxb[:, None],
occidxb].reshape(-1)))
h_diaga = (focka[viridxa, viridxa].reshape(-1, 1) -
focka[occidxa, occidxa])
h_diagb = (fockb[viridxb, viridxb].reshape(-1, 1) -
fockb[occidxb, occidxb])
h_diag = numpy.hstack((h_diaga.reshape(-1), h_diagb.reshape(-1)))
if hasattr(mf, '_scf') and id(mf._scf.mol) != id(mol):
mo_coeff = (addons.project_mo_nr2nr(mf._scf.mol, mo_coeff[0], mol),
addons.project_mo_nr2nr(mf._scf.mol, mo_coeff[1], mol))
if hasattr(mf, 'xc') and hasattr(mf, '_numint'):
if mf.grids.coords is None:
mf.grids.build()
hyb = mf._numint.hybrid_coeff(mf.xc, spin=(mol.spin > 0) + 1)
rho0, vxc, fxc = mf._numint.cache_xc_kernel(mol, mf.grids, mf.xc,
mo_coeff, mo_occ, 1)
#dm0 =(numpy.dot(mo_coeff[0]*mo_occ[0], mo_coeff[0].T),
# numpy.dot(mo_coeff[1]*mo_occ[1], mo_coeff[1].T))
dm0 = None
else:
hyb = None
def h_op(x):
x1a = x[:nvira * nocca].reshape(nvira, nocca)
x1b = x[nvira * nocca:].reshape(nvirb, noccb)
x2a = numpy.einsum('rp,rq->pq', focka[viridxa[:, None], viridxa], x1a)
x2a -= numpy.einsum('sq,ps->pq', focka[occidxa[:, None], occidxa], x1a)
x2b = numpy.einsum('rp,rq->pq', fockb[viridxb[:, None], viridxb], x1b)
x2b -= numpy.einsum('sq,ps->pq', fockb[occidxb[:, None], occidxb], x1b)
d1a = reduce(numpy.dot,
(mo_coeff[0][:, viridxa], x1a, mo_coeff[0][:, occidxa].T))
d1b = reduce(numpy.dot,
(mo_coeff[1][:, viridxb], x1b, mo_coeff[1][:, occidxb].T))
dm1 = numpy.array((d1a + d1a.T, d1b + d1b.T))
if hyb is None:
vj, vk = mf.get_jk(mol, dm1)
v1 = vj[0] + vj[1] - vk
else:
v1 = mf._numint.nr_uks_fxc(mol, mf.grids, mf.xc, dm0, dm1, 0, 1,
rho0, vxc, fxc)
if abs(hyb) < 1e-10:
vj = mf.get_j(mol, dm1)
v1 += vj[0] + vj[1]
else:
vj, vk = mf.get_jk(mol, dm1)
v1 += vj[0] + vj[1] - vk * hyb
x2a += reduce(
numpy.dot,
(mo_coeff[0][:, viridxa].T, v1[0], mo_coeff[0][:, occidxa]))
x2b += reduce(
numpy.dot,
(mo_coeff[1][:, viridxb].T, v1[1], mo_coeff[1][:, occidxb]))
return numpy.hstack((x2a.ravel(), x2b.ravel()))
return g, h_op, h_diag
def fproj(mo):
if project:
return addons.project_mo_nr2nr(chk_mol, mo, mol)
else:
return mo
def init_guess_by_minao(mol):
'''Generate initial guess density matrix based on ANO basis, then project
the density matrix to the basis set defined by ``mol``
Returns:
Density matrix, 2D ndarray
Examples:
>>> from pyscf import gto, scf
>>> mol = gto.M(atom='H 0 0 0; H 0 0 1.1')
>>> scf.hf.init_guess_by_minao(mol)
array([[ 0.94758917, 0.09227308],
[ 0.09227308, 0.94758917]])
'''
from pyscf.scf import atom_hf
from pyscf.scf import addons
def minao_basis(symb, nelec_ecp):
basis_add = pyscf.gto.basis.load('ano', symb)
occ = []
basis_new = []
# coreshl defines the core shells to be removed in the initial guess
coreshl = pyscf.gto.ecp.core_configuration(nelec_ecp)
#coreshl = (0,0,0,0) # it keeps all core electrons in the initial guess
for l in range(4):
ndocc, nfrac = atom_hf.frac_occ(symb, l)
if coreshl[l] > 0:
occ.extend([0]*coreshl[l]*(2*l+1))
if ndocc > coreshl[l]:
occ.extend([2]*(ndocc-coreshl[l])*(2*l+1))
if nfrac > 1e-15:
occ.extend([nfrac]*(2*l+1))
ndocc += 1
if ndocc > 0:
basis_new.append([l] + [b[:ndocc+1] for b in basis_add[l][1:]])
return occ, basis_new
atmlst = set([mol.atom_symbol(ia) for ia in range(mol.natm)])
nelec_ecp_dic = {}
for ia in range(mol.natm):
symb = mol.atom_symbol(ia)
if symb not in nelec_ecp_dic:
nelec_ecp_dic[symb] = mol.atom_nelec_core(ia)
basis = {}
occdic = {}
for symb in atmlst:
if symb != 'GHOST':
nelec_ecp = nelec_ecp_dic[symb]
stdsymb = pyscf.gto.mole._std_symbol(symb)
occ_add, basis_add = minao_basis(stdsymb, nelec_ecp)
occdic[symb] = occ_add
basis[symb] = basis_add
occ = []
new_atom = []
for ia in range(mol.natm):
symb = mol.atom_symbol(ia)
if symb != 'GHOST':
occ.append(occdic[symb])
new_atom.append(mol._atom[ia])
occ = numpy.hstack(occ)
pmol = pyscf.gto.Mole()
pmol._atm, pmol._bas, pmol._env = pmol.make_env(new_atom, basis, [])
c = addons.project_mo_nr2nr(pmol, 1, mol)
dm = numpy.dot(c*occ, c.T)
# normalize eletron number
# s = mol.intor_symmetric('cint1e_ovlp_sph')
# dm *= mol.nelectron / (dm*s).sum()
return dm
def gen_g_hop_rhf(mf, mo_coeff, mo_occ, fock_ao=None, h1e=None,
with_symmetry=True):
mo_coeff0 = mo_coeff
mol = mf.mol
if getattr(mf, '_scf', None) and mf._scf.mol != mol:
#TODO: construct vind with dual-basis treatment, (see also JCP, 118, 9497)
# To project Hessians from another basis if different basis sets are used
# in newton solver and underlying mean-filed solver.
mo_coeff = addons.project_mo_nr2nr(mf._scf.mol, mo_coeff, mol)
occidx = numpy.where(mo_occ==2)[0]
viridx = numpy.where(mo_occ==0)[0]
nocc = len(occidx)
nvir = len(viridx)
orbo = mo_coeff[:,occidx]
orbv = mo_coeff[:,viridx]
if with_symmetry and mol.symmetry:
orbsym = hf_symm.get_orbsym(mol, mo_coeff)
sym_forbid = orbsym[viridx,None] != orbsym[occidx]
if fock_ao is None:
# dm0 is the density matrix in projected basis. Computing fock in
# projected basis.
dm0 = mf.make_rdm1(mo_coeff, mo_occ)
fock_ao = mf.get_fock(h1e, dm=dm0)
fock = reduce(numpy.dot, (mo_coeff.conj().T, fock_ao, mo_coeff))
else:
# If fock is given, it corresponds to main basis. It needs to be
# diagonalized with the mo_coeff of the main basis.
fock = reduce(numpy.dot, (mo_coeff0.conj().T, fock_ao, mo_coeff0))
g = fock[viridx[:,None],occidx] * 2
foo = fock[occidx[:,None],occidx]
fvv = fock[viridx[:,None],viridx]
h_diag = (fvv.diagonal().real[:,None] - foo.diagonal().real) * 2
if with_symmetry and mol.symmetry:
g[sym_forbid] = 0
h_diag[sym_forbid] = 0
vind = _gen_rhf_response(mf, mo_coeff, mo_occ, singlet=None, hermi=1)
def h_op(x):
x = x.reshape(nvir,nocc)
if with_symmetry and mol.symmetry:
x = x.copy()
x[sym_forbid] = 0
x2 = numpy.einsum('ps,sq->pq', fvv, x)
#x2-= .5*numpy.einsum('ps,rp->rs', foo, x)
#x2-= .5*numpy.einsum('sp,rp->rs', foo, x)
x2-= numpy.einsum('ps,rp->rs', foo, x)
# *2 for double occupancy
d1 = reduce(numpy.dot, (orbv, x*2, orbo.conj().T))
dm1 = d1 + d1.conj().T
v1 = vind(dm1)
x2 += reduce(numpy.dot, (orbv.conj().T, v1, orbo))
if with_symmetry and mol.symmetry:
x2[sym_forbid] = 0
return x2.ravel() * 2
return g.reshape(-1), h_op, h_diag.reshape(-1)
def fproj(mo):
if project:
mo = addons.project_mo_nr2nr(chk_mol, mo, mol)
norm = numpy.einsum('pi,pi->i', mo.conj(), s.dot(mo))
mo /= numpy.sqrt(norm)
return mo
def project_to_atomic_orbitals(mol, basname):
'''projected AO = |bas><bas|ANO>
'''
from pyscf.scf.addons import project_mo_nr2nr
from pyscf.scf import atom_hf
from pyscf.gto.ecp import core_configuration
def search_atm_l(atm, l):
bas_ang = atm._bas[:, gto.ANG_OF]
ao_loc = atm.ao_loc_nr()
idx = []
for ib in numpy.where(bas_ang == l)[0]:
idx.extend(range(ao_loc[ib], ao_loc[ib + 1]))
return idx
# Overlap of ANO and ECP basis
def ecp_ano_det_ovlp(atm_ecp, atm_ano, ecpcore):
ecp_ao_loc = atm_ecp.ao_loc_nr()
ano_ao_loc = atm_ano.ao_loc_nr()
ecp_ao_dim = ecp_ao_loc[1:] - ecp_ao_loc[:-1]
ano_ao_dim = ano_ao_loc[1:] - ano_ao_loc[:-1]
ecp_bas_l = [[atm_ecp.bas_angular(i)] * d
for i, d in enumerate(ecp_ao_dim)]
ano_bas_l = [[atm_ano.bas_angular(i)] * d
for i, d in enumerate(ano_ao_dim)]
ecp_bas_l = numpy.hstack(ecp_bas_l)
ano_bas_l = numpy.hstack(ano_bas_l)
ecp_idx = []
ano_idx = []
for l in range(4):
nocc, nfrac = atom_hf.frac_occ(stdsymb, l)
if nfrac > 1e-15:
nocc += 1
if nocc == 0:
break
i0 = ecpcore[l] * (2 * l + 1)
i1 = nocc * (2 * l + 1)
ecp_idx.append(numpy.where(ecp_bas_l == l)[0][:i1 - i0])
ano_idx.append(numpy.where(ano_bas_l == l)[0][i0:i1])
ecp_idx = numpy.hstack(ecp_idx)
ano_idx = numpy.hstack(ano_idx)
s12 = gto.intor_cross('int1e_ovlp', atm_ecp, atm_ano)[ecp_idx][:,
ano_idx]
return numpy.linalg.det(s12)
nelec_ecp_dic = {}
for ia in range(mol.natm):
symb = mol.atom_symbol(ia)
if symb not in nelec_ecp_dic:
nelec_ecp_dic[symb] = mol.atom_nelec_core(ia)
aos = {}
atm = gto.Mole()
atmp = gto.Mole()
for symb in mol._basis.keys():
stdsymb = gto.mole._std_symbol(symb)
atm._atm, atm._bas, atm._env = \
atm.make_env([[stdsymb,(0,0,0)]], {stdsymb:mol._basis[symb]}, [])
atm.cart = mol.cart
s0 = atm.intor_symmetric('int1e_ovlp')
if 'GHOST' in symb.upper():
aos[symb] = numpy.diag(1. / numpy.sqrt(s0.diagonal()))
continue
basis_add = gto.basis.load(basname, stdsymb)
atmp._atm, atmp._bas, atmp._env = \
atmp.make_env([[stdsymb,(0,0,0)]], {stdsymb:basis_add}, [])
atmp.cart = mol.cart
nelec_ecp = nelec_ecp_dic[symb]
if nelec_ecp > 0:
ecpcore = core_configuration(nelec_ecp)
# Comparing to ANO valence basis, to check whether the ECP basis set has
# reasonable AO-character contraction. The ANO valence AO should have
# significant overlap to ECP basis if the ECP basis has AO-character.
if abs(ecp_ano_det_ovlp(atm, atmp, ecpcore)) > .1:
aos[symb] = numpy.diag(1. / numpy.sqrt(s0.diagonal()))
continue
else:
ecpcore = [0] * 4
ano = project_mo_nr2nr(atmp, 1, atm)
rm_ano = numpy.eye(ano.shape[0]) - reduce(numpy.dot, (ano, ano.T, s0))
c = rm_ano.copy()
for l in range(param.L_MAX):
idx = numpy.asarray(search_atm_l(atm, l))
nbf_atm_l = len(idx)
if nbf_atm_l == 0:
break
idxp = numpy.asarray(search_atm_l(atmp, l))
if l < 4:
idxp = idxp[ecpcore[l]:]
nbf_ano_l = len(idxp)
if mol.cart:
degen = (l + 1) * (l + 2) // 2
else:
degen = l * 2 + 1
if nbf_atm_l > nbf_ano_l > 0:
# For angular l, first place the projected ANO, then the rest AOs.
sdiag = reduce(
numpy.dot,
(rm_ano[:, idx].T, s0, rm_ano[:, idx])).diagonal()
nleft = (nbf_atm_l - nbf_ano_l) // degen
shell_average = numpy.einsum('ij->i', sdiag.reshape(-1, degen))
shell_rest = numpy.argsort(-shell_average)[:nleft]
idx_rest = []
for k in shell_rest:
idx_rest.extend(idx[k * degen:(k + 1) * degen])
c[:, idx[:nbf_ano_l]] = ano[:, idxp]
c[:, idx[nbf_ano_l:]] = rm_ano[:, idx_rest]
elif nbf_ano_l >= nbf_atm_l > 0: # More ANOs than the mol basis functions
c[:, idx] = ano[:, idxp[:nbf_atm_l]]
sdiag = numpy.einsum('pi,pq,qi->i', c, s0, c)
c *= 1. / numpy.sqrt(sdiag)
aos[symb] = c
nao = mol.nao_nr()
c = numpy.zeros((nao, nao))
p1 = 0
for ia in range(mol.natm):
symb = mol.atom_symbol(ia)
if symb in mol._basis:
ano = aos[symb]
else:
ano = aos[mol.atom_pure_symbol(ia)]
p0, p1 = p1, p1 + ano.shape[1]
c[p0:p1, p0:p1] = ano
return c
def gen_g_hop_uhf(mf, mo_coeff, mo_occ, fock_ao=None, h1e=None,
with_symmetry=True):
mol = mf.mol
mo_coeff0 = mo_coeff
if getattr(mf, '_scf', None) and mf._scf.mol != mol:
#TODO: construct vind with dual-basis treatment, (see also JCP, 118, 9497)
mo_coeff = (addons.project_mo_nr2nr(mf._scf.mol, mo_coeff[0], mol),
addons.project_mo_nr2nr(mf._scf.mol, mo_coeff[1], mol))
occidxa = numpy.where(mo_occ[0]>0)[0]
occidxb = numpy.where(mo_occ[1]>0)[0]
viridxa = numpy.where(mo_occ[0]==0)[0]
viridxb = numpy.where(mo_occ[1]==0)[0]
nocca = len(occidxa)
noccb = len(occidxb)
nvira = len(viridxa)
nvirb = len(viridxb)
orboa = mo_coeff[0][:,occidxa]
orbob = mo_coeff[1][:,occidxb]
orbva = mo_coeff[0][:,viridxa]
orbvb = mo_coeff[1][:,viridxb]
if with_symmetry and mol.symmetry:
orbsyma, orbsymb = uhf_symm.get_orbsym(mol, mo_coeff)
sym_forbida = orbsyma[viridxa,None] != orbsyma[occidxa]
sym_forbidb = orbsymb[viridxb,None] != orbsymb[occidxb]
sym_forbid = numpy.hstack((sym_forbida.ravel(), sym_forbidb.ravel()))
if fock_ao is None:
dm0 = mf.make_rdm1(mo_coeff, mo_occ)
fock_ao = mf.get_fock(h1e, dm=dm0)
focka = reduce(numpy.dot, (mo_coeff[0].conj().T, fock_ao[0], mo_coeff[0]))
fockb = reduce(numpy.dot, (mo_coeff[1].conj().T, fock_ao[1], mo_coeff[1]))
else:
focka = reduce(numpy.dot, (mo_coeff0[0].conj().T, fock_ao[0], mo_coeff0[0]))
fockb = reduce(numpy.dot, (mo_coeff0[1].conj().T, fock_ao[1], mo_coeff0[1]))
fooa = focka[occidxa[:,None],occidxa]
fvva = focka[viridxa[:,None],viridxa]
foob = fockb[occidxb[:,None],occidxb]
fvvb = fockb[viridxb[:,None],viridxb]
g = numpy.hstack((focka[viridxa[:,None],occidxa].ravel(),
fockb[viridxb[:,None],occidxb].ravel()))
h_diaga = fvva.diagonal().real[:,None] - fooa.diagonal().real
h_diagb = fvvb.diagonal().real[:,None] - foob.diagonal().real
h_diag = numpy.hstack((h_diaga.reshape(-1), h_diagb.reshape(-1)))
if with_symmetry and mol.symmetry:
g[sym_forbid] = 0
h_diag[sym_forbid] = 0
vind = _gen_uhf_response(mf, mo_coeff, mo_occ, hermi=1)
def h_op(x):
if with_symmetry and mol.symmetry:
x = x.copy()
x[sym_forbid] = 0
x1a = x[:nvira*nocca].reshape(nvira,nocca)
x1b = x[nvira*nocca:].reshape(nvirb,noccb)
x2a = numpy.einsum('pr,rq->pq', fvva, x1a)
x2a-= numpy.einsum('sq,ps->pq', fooa, x1a)
x2b = numpy.einsum('pr,rq->pq', fvvb, x1b)
x2b-= numpy.einsum('sq,ps->pq', foob, x1b)
d1a = reduce(numpy.dot, (orbva, x1a, orboa.conj().T))
d1b = reduce(numpy.dot, (orbvb, x1b, orbob.conj().T))
dm1 = numpy.array((d1a+d1a.conj().T,d1b+d1b.conj().T))
v1 = vind(dm1)
x2a += reduce(numpy.dot, (orbva.conj().T, v1[0], orboa))
x2b += reduce(numpy.dot, (orbvb.conj().T, v1[1], orbob))
x2 = numpy.hstack((x2a.ravel(), x2b.ravel()))
if with_symmetry and mol.symmetry:
x2[sym_forbid] = 0
return x2
return g, h_op, h_diag
def fproj(mo):
if project:
return addons.project_mo_nr2nr(chk_mol, mo, mol)
else:
return mo
def gen_g_hop_uhf(mf,
mo_coeff,
mo_occ,
fock_ao=None,
h1e=None,
with_symmetry=True):
mol = mf.mol
mo_coeff0 = mo_coeff
if getattr(mf, '_scf', None) and mf._scf.mol != mol:
#TODO: construct vind with dual-basis treatment, (see also JCP, 118, 9497)
mo_coeff = (addons.project_mo_nr2nr(mf._scf.mol, mo_coeff[0], mol),
addons.project_mo_nr2nr(mf._scf.mol, mo_coeff[1], mol))
occidxa = numpy.where(mo_occ[0] > 0)[0]
occidxb = numpy.where(mo_occ[1] > 0)[0]
viridxa = numpy.where(mo_occ[0] == 0)[0]
viridxb = numpy.where(mo_occ[1] == 0)[0]
nocca = len(occidxa)
noccb = len(occidxb)
nvira = len(viridxa)
nvirb = len(viridxb)
orboa = mo_coeff[0][:, occidxa]
orbob = mo_coeff[1][:, occidxb]
orbva = mo_coeff[0][:, viridxa]
orbvb = mo_coeff[1][:, viridxb]
if with_symmetry and mol.symmetry:
orbsyma, orbsymb = uhf_symm.get_orbsym(mol, mo_coeff)
sym_forbida = orbsyma[viridxa, None] != orbsyma[occidxa]
sym_forbidb = orbsymb[viridxb, None] != orbsymb[occidxb]
sym_forbid = numpy.hstack((sym_forbida.ravel(), sym_forbidb.ravel()))
if fock_ao is None:
if getattr(mf, '_scf', None) and mf._scf.mol != mol:
h1e = mf.get_hcore(mol)
dm0 = mf.make_rdm1(mo_coeff, mo_occ)
fock_ao = mf.get_fock(h1e, dm=dm0)
focka = reduce(numpy.dot,
(mo_coeff[0].conj().T, fock_ao[0], mo_coeff[0]))
fockb = reduce(numpy.dot,
(mo_coeff[1].conj().T, fock_ao[1], mo_coeff[1]))
else:
focka = reduce(numpy.dot,
(mo_coeff0[0].conj().T, fock_ao[0], mo_coeff0[0]))
fockb = reduce(numpy.dot,
(mo_coeff0[1].conj().T, fock_ao[1], mo_coeff0[1]))
fooa = focka[occidxa[:, None], occidxa]
fvva = focka[viridxa[:, None], viridxa]
foob = fockb[occidxb[:, None], occidxb]
fvvb = fockb[viridxb[:, None], viridxb]
g = numpy.hstack((focka[viridxa[:, None],
occidxa].ravel(), fockb[viridxb[:, None],
occidxb].ravel()))
h_diaga = fvva.diagonal().real[:, None] - fooa.diagonal().real
h_diagb = fvvb.diagonal().real[:, None] - foob.diagonal().real
h_diag = numpy.hstack((h_diaga.reshape(-1), h_diagb.reshape(-1)))
if with_symmetry and mol.symmetry:
g[sym_forbid] = 0
h_diag[sym_forbid] = 0
vind = _gen_uhf_response(mf, mo_coeff, mo_occ, hermi=1)
def h_op(x):
if with_symmetry and mol.symmetry:
x = x.copy()
x[sym_forbid] = 0
x1a = x[:nvira * nocca].reshape(nvira, nocca)
x1b = x[nvira * nocca:].reshape(nvirb, noccb)
x2a = numpy.einsum('pr,rq->pq', fvva, x1a)
x2a -= numpy.einsum('sq,ps->pq', fooa, x1a)
x2b = numpy.einsum('pr,rq->pq', fvvb, x1b)
x2b -= numpy.einsum('sq,ps->pq', foob, x1b)
d1a = reduce(numpy.dot, (orbva, x1a, orboa.conj().T))
d1b = reduce(numpy.dot, (orbvb, x1b, orbob.conj().T))
dm1 = numpy.array((d1a + d1a.conj().T, d1b + d1b.conj().T))
v1 = vind(dm1)
x2a += reduce(numpy.dot, (orbva.conj().T, v1[0], orboa))
x2b += reduce(numpy.dot, (orbvb.conj().T, v1[1], orbob))
x2 = numpy.hstack((x2a.ravel(), x2b.ravel()))
if with_symmetry and mol.symmetry:
x2[sym_forbid] = 0
return x2
return g, h_op, h_diag
def gen_g_hop_uhf(mf, mo_coeff, mo_occ, fock_ao=None, h1e=None):
mol = mf.mol
occidxa = numpy.where(mo_occ[0]>0)[0]
occidxb = numpy.where(mo_occ[1]>0)[0]
viridxa = numpy.where(mo_occ[0]==0)[0]
viridxb = numpy.where(mo_occ[1]==0)[0]
nocca = len(occidxa)
noccb = len(occidxb)
nvira = len(viridxa)
nvirb = len(viridxb)
if fock_ao is None:
if h1e is None: h1e = mf.get_hcore()
dm0 = mf.make_rdm1(mo_coeff, mo_occ)
fock_ao = h1e + mf.get_veff(mol, dm0)
focka = reduce(numpy.dot, (mo_coeff[0].T, fock_ao[0], mo_coeff[0]))
fockb = reduce(numpy.dot, (mo_coeff[1].T, fock_ao[1], mo_coeff[1]))
g = numpy.hstack((focka[viridxa[:,None],occidxa].reshape(-1),
fockb[viridxb[:,None],occidxb].reshape(-1)))
h_diaga =(focka[viridxa,viridxa].reshape(-1,1) - focka[occidxa,occidxa])
h_diagb =(fockb[viridxb,viridxb].reshape(-1,1) - fockb[occidxb,occidxb])
h_diag = numpy.hstack((h_diaga.reshape(-1), h_diagb.reshape(-1)))
if hasattr(mf, '_scf') and id(mf._scf.mol) != id(mol):
mo_coeff = (addons.project_mo_nr2nr(mf._scf.mol, mo_coeff[0], mol),
addons.project_mo_nr2nr(mf._scf.mol, mo_coeff[1], mol))
if hasattr(mf, 'xc') and hasattr(mf, '_numint'):
if mf.grids.coords is None:
mf.grids.build()
hyb = mf._numint.hybrid_coeff(mf.xc, spin=(mol.spin>0)+1)
rho0, vxc, fxc = mf._numint.cache_xc_kernel(mol, mf.grids, mf.xc,
mo_coeff, mo_occ, 1)
#dm0 =(numpy.dot(mo_coeff[0]*mo_occ[0], mo_coeff[0].T),
# numpy.dot(mo_coeff[1]*mo_occ[1], mo_coeff[1].T))
dm0 = None
else:
hyb = None
def h_op(x):
x1a = x[:nvira*nocca].reshape(nvira,nocca)
x1b = x[nvira*nocca:].reshape(nvirb,noccb)
x2a = numpy.einsum('rp,rq->pq', focka[viridxa[:,None],viridxa], x1a)
x2a -= numpy.einsum('sq,ps->pq', focka[occidxa[:,None],occidxa], x1a)
x2b = numpy.einsum('rp,rq->pq', fockb[viridxb[:,None],viridxb], x1b)
x2b -= numpy.einsum('sq,ps->pq', fockb[occidxb[:,None],occidxb], x1b)
d1a = reduce(numpy.dot, (mo_coeff[0][:,viridxa], x1a,
mo_coeff[0][:,occidxa].T))
d1b = reduce(numpy.dot, (mo_coeff[1][:,viridxb], x1b,
mo_coeff[1][:,occidxb].T))
dm1 = numpy.array((d1a+d1a.T,d1b+d1b.T))
if hyb is None:
v1 = mf.get_veff(mol, dm1)
else:
v1 = mf._numint.nr_uks_fxc(mol, mf.grids, mf.xc, dm0, dm1,
0, 1, rho0, vxc, fxc)
if abs(hyb) < 1e-10:
vj = mf.get_j(mol, dm1)
v1 += vj[0] + vj[1]
else:
vj, vk = mf.get_jk(mol, dm1)
v1 += vj[0]+vj[1] - vk * hyb * .5
x2a += reduce(numpy.dot, (mo_coeff[0][:,viridxa].T, v1[0],
mo_coeff[0][:,occidxa]))
x2b += reduce(numpy.dot, (mo_coeff[1][:,viridxb].T, v1[1],
mo_coeff[1][:,occidxb]))
return numpy.hstack((x2a.ravel(), x2b.ravel()))
return g, h_op, h_diag
def gen_g_hop_uhf(mf,
mo_coeff,
mo_occ,
fock_ao=None,
h1e=None,
with_symmetry=True):
mol = mf.mol
if hasattr(mf, '_scf') and id(mf._scf.mol) != id(mol):
mo_coeff = (addons.project_mo_nr2nr(mf._scf.mol, mo_coeff[0], mol),
addons.project_mo_nr2nr(mf._scf.mol, mo_coeff[1], mol))
occidxa = numpy.where(mo_occ[0] > 0)[0]
occidxb = numpy.where(mo_occ[1] > 0)[0]
viridxa = numpy.where(mo_occ[0] == 0)[0]
viridxb = numpy.where(mo_occ[1] == 0)[0]
nocca = len(occidxa)
noccb = len(occidxb)
nvira = len(viridxa)
nvirb = len(viridxb)
orboa = mo_coeff[0][:, occidxa]
orbob = mo_coeff[1][:, occidxb]
orbva = mo_coeff[0][:, viridxa]
orbvb = mo_coeff[1][:, viridxb]
if with_symmetry and mol.symmetry:
orbsyma, orbsymb = uhf_symm.get_orbsym(mol, mo_coeff)
sym_forbida = orbsyma[viridxa].reshape(-1, 1) != orbsyma[occidxa]
sym_forbidb = orbsymb[viridxb].reshape(-1, 1) != orbsymb[occidxb]
sym_forbid = numpy.hstack((sym_forbida.ravel(), sym_forbidb.ravel()))
if fock_ao is None:
if h1e is None: h1e = mf.get_hcore()
dm0 = mf.make_rdm1(mo_coeff, mo_occ)
fock_ao = h1e + mf.get_veff(mol, dm0)
focka = reduce(numpy.dot, (mo_coeff[0].T, fock_ao[0], mo_coeff[0]))
fockb = reduce(numpy.dot, (mo_coeff[1].T, fock_ao[1], mo_coeff[1]))
fooa = focka[occidxa[:, None], occidxa]
fvva = focka[viridxa[:, None], viridxa]
foob = fockb[occidxb[:, None], occidxb]
fvvb = fockb[viridxb[:, None], viridxb]
g = numpy.hstack((focka[occidxa[:, None],
viridxa].T.ravel(), fockb[occidxb[:, None],
viridxb].T.ravel()))
h_diaga = focka[viridxa, viridxa].reshape(-1, 1) - focka[occidxa, occidxa]
h_diagb = fockb[viridxb, viridxb].reshape(-1, 1) - fockb[occidxb, occidxb]
h_diag = numpy.hstack((h_diaga.reshape(-1), h_diagb.reshape(-1)))
if with_symmetry and mol.symmetry:
g[sym_forbid] = 0
h_diag[sym_forbid] = 0
vind = _gen_uhf_response(mf, mo_coeff, mo_occ, hermi=1)
def h_op(x):
if with_symmetry and mol.symmetry:
x = x.copy()
x[sym_forbid] = 0
x1a = x[:nvira * nocca].reshape(nvira, nocca)
x1b = x[nvira * nocca:].reshape(nvirb, noccb)
x2a = numpy.einsum('pr,rq->pq', fvva, x1a)
x2a -= numpy.einsum('sq,ps->pq', fooa, x1a)
x2b = numpy.einsum('pr,rq->pq', fvvb, x1b)
x2b -= numpy.einsum('sq,ps->pq', foob, x1b)
d1a = reduce(numpy.dot, (orbva, x1a, orboa.T.conj()))
d1b = reduce(numpy.dot, (orbvb, x1b, orbob.T.conj()))
dm1 = numpy.array((d1a + d1a.T.conj(), d1b + d1b.T.conj()))
v1 = vind(dm1)
x2a += reduce(numpy.dot, (orbva.T.conj(), v1[0], orboa))
x2b += reduce(numpy.dot, (orbvb.T.conj(), v1[1], orbob))
x2 = numpy.hstack((x2a.ravel(), x2b.ravel()))
if with_symmetry and mol.symmetry:
x2[sym_forbid] = 0
return x2
return g, h_op, h_diag
def init_guess_by_minao(mol):
'''Generate initial guess density matrix based on ANO basis, then project
the density matrix to the basis set defined by ``mol``
Returns:
Density matrix, 2D ndarray
Examples:
>>> from pyscf import gto, scf
>>> mol = gto.M(atom='H 0 0 0; H 0 0 1.1')
>>> scf.hf.init_guess_by_minao(mol)
array([[ 0.94758917, 0.09227308],
[ 0.09227308, 0.94758917]])
'''
from pyscf.scf import atom_hf
from pyscf.scf import addons
def minao_basis(symb, nelec_ecp):
basis_add = gto.basis.load('ano', symb)
occ = []
basis_new = []
# coreshl defines the core shells to be removed in the initial guess
coreshl = gto.ecp.core_configuration(nelec_ecp)
#coreshl = (0,0,0,0) # it keeps all core electrons in the initial guess
for l in range(4):
ndocc, nfrac = atom_hf.frac_occ(symb, l)
if coreshl[l] > 0:
occ.extend([0] * coreshl[l] * (2 * l + 1))
if ndocc > coreshl[l]:
occ.extend([2] * (ndocc - coreshl[l]) * (2 * l + 1))
if nfrac > 1e-15:
occ.extend([nfrac] * (2 * l + 1))
ndocc += 1
if ndocc > 0:
basis_new.append([l] +
[b[:ndocc + 1] for b in basis_add[l][1:]])
return occ, basis_new
atmlst = set([mol.atom_symbol(ia) for ia in range(mol.natm)])
nelec_ecp_dic = {}
for ia in range(mol.natm):
symb = mol.atom_symbol(ia)
if symb not in nelec_ecp_dic:
nelec_ecp_dic[symb] = mol.atom_nelec_core(ia)
basis = {}
occdic = {}
for symb in atmlst:
if symb != 'GHOST':
nelec_ecp = nelec_ecp_dic[symb]
stdsymb = gto.mole._std_symbol(symb)
occ_add, basis_add = minao_basis(stdsymb, nelec_ecp)
occdic[symb] = occ_add
basis[symb] = basis_add
occ = []
new_atom = []
for ia in range(mol.natm):
symb = mol.atom_symbol(ia)
if symb != 'GHOST':
occ.append(occdic[symb])
new_atom.append(mol._atom[ia])
occ = numpy.hstack(occ)
pmol = gto.Mole()
pmol._atm, pmol._bas, pmol._env = pmol.make_env(new_atom, basis, [])
c = addons.project_mo_nr2nr(pmol, 1, mol)
dm = numpy.dot(c * occ, c.T)
# normalize eletron number
# s = mol.intor_symmetric('int1e_ovlp')
# dm *= mol.nelectron / (dm*s).sum()
return dm
def project_to_atomic_orbitals(mol, basname):
'''projected AO = |bas><bas|ANO>
'''
from pyscf.scf.addons import project_mo_nr2nr
from pyscf.gto.ecp import core_configuration
def search_atm_l(atm, l):
idx = []
p0 = 0
for ib, b in enumerate(atm._bas):
l0 = atm.bas_angular(ib)
nctr = atm.bas_nctr(ib)
if l0 == l:
idx.extend(range(p0,p0+(2*l+1)*nctr))
p0 += (2*l0+1) * nctr
return idx
aos = {}
atm = gto.Mole()
atmp = gto.Mole()
for symb in mol._basis.keys():
stdsymb = gto.mole._std_symbol(symb)
atm._atm, atm._bas, atm._env = \
atm.make_env([[stdsymb,(0,0,0)]], {stdsymb:mol._basis[symb]}, [])
if 'GHOST' in symb.upper():
aos[symb] = numpy.eye(atm.nao_nr())
continue
s0 = atm.intor_symmetric('cint1e_ovlp_sph')
basis_add = gto.basis.load(basname, stdsymb)
atmp._atm, atmp._bas, atmp._env = \
atmp.make_env([[stdsymb,(0,0,0)]], {stdsymb:basis_add}, [])
ano = project_mo_nr2nr(atmp, 1, atm)
rm_ano = numpy.eye(ano.shape[0]) - reduce(numpy.dot, (ano, ano.T, s0))
nelec_ecp = 0
if mol._ecp:
if symb in mol._ecp:
nelec_ecp = mol._ecp[symb][0]
elif stdsymb in mol._ecp:
nelec_ecp = mol._ecp[stdsymb][0]
ecpcore = core_configuration(nelec_ecp)
c = rm_ano.copy()
for l in range(param.L_MAX):
idx = numpy.asarray(search_atm_l(atm, l))
if len(idx) == 0:
break
idxp = numpy.asarray(search_atm_l(atmp, l))
if l < 4:
idxp = idxp[ecpcore[l]:]
if len(idx) > len(idxp) > 0:
# For angular l, first place the projected ANO, then the rest AOs.
sdiag = reduce(numpy.dot, (rm_ano[:,idx].T, s0, rm_ano[:,idx])).diagonal()
nleft = (len(idx) - len(idxp)) // (2*l+1)
shell_average = numpy.einsum('ij->i', sdiag.reshape(-1,l*2+1))
shell_rest = numpy.argsort(-shell_average)[:nleft]
idx_rest = []
for k in shell_rest:
idx_rest.extend(idx[k*(2*l+1):(k+1)*(2*l+1)])
c[:,idx[:len(idxp)]] = ano[:,idxp]
c[:,idx[len(idxp):]] = rm_ano[:,idx_rest]
elif len(idxp) >= len(idx) > 0: # More ANOs than the mol basis functions
c[:,idx] = ano[:,idxp[:len(idx)]]
aos[symb] = c
nao = mol.nao_nr()
c = numpy.zeros((nao,nao))
p0 = 0
for ia in range(mol.natm):
symb = mol.atom_symbol(ia)
if symb in mol._basis:
ano = aos[symb]
else:
symb = mol.atom_pure_symbol(ia)
ano = aos[symb]
p1 = p0 + ano.shape[1]
c[p0:p1,p0:p1] = ano
p0 = p1
return c
def project_to_atomic_orbitals(mol, basname):
'''projected AO = |bas><bas|ANO>
'''
from pyscf.scf.addons import project_mo_nr2nr
from pyscf.scf import atom_hf
from pyscf.gto.ecp import core_configuration
def search_atm_l(atm, l):
bas_ang = atm._bas[:,gto.ANG_OF]
ao_loc = atm.ao_loc_nr()
idx = []
for ib in numpy.where(bas_ang == l)[0]:
idx.extend(range(ao_loc[ib], ao_loc[ib+1]))
return idx
# Overlap of ANO and ECP basis
def ecp_ano_det_ovlp(atm_ecp, atm_ano, ecpcore):
ecp_ao_loc = atm_ecp.ao_loc_nr()
ano_ao_loc = atm_ano.ao_loc_nr()
ecp_ao_dim = ecp_ao_loc[1:] - ecp_ao_loc[:-1]
ano_ao_dim = ano_ao_loc[1:] - ano_ao_loc[:-1]
ecp_bas_l = [[atm_ecp.bas_angular(i)]*d for i,d in enumerate(ecp_ao_dim)]
ano_bas_l = [[atm_ano.bas_angular(i)]*d for i,d in enumerate(ano_ao_dim)]
ecp_bas_l = numpy.hstack(ecp_bas_l)
ano_bas_l = numpy.hstack(ano_bas_l)
nelec_core = 0
ecp_occ_tmp = []
ecp_idx = []
ano_idx = []
for l in range(4):
nocc, frac = atom_hf.frac_occ(stdsymb, l)
l_occ = [2] * ((nocc-ecpcore[l])*(2*l+1))
if frac > 1e-15:
l_occ.extend([frac] * (2*l+1))
nocc += 1
if nocc == 0:
break
nelec_core += 2 * ecpcore[l] * (2*l+1)
i0 = ecpcore[l] * (2*l+1)
i1 = nocc * (2*l+1)
ecp_idx.append(numpy.where(ecp_bas_l==l)[0][:i1-i0])
ano_idx.append(numpy.where(ano_bas_l==l)[0][i0:i1])
ecp_occ_tmp.append(l_occ[:i1-i0])
ecp_idx = numpy.hstack(ecp_idx)
ano_idx = numpy.hstack(ano_idx)
ecp_occ = numpy.zeros(atm_ecp.nao_nr())
ecp_occ[ecp_idx] = numpy.hstack(ecp_occ_tmp)
nelec_valence_left = int(gto.mole.charge(stdsymb) - nelec_core
- sum(ecp_occ[ecp_idx]))
if nelec_valence_left > 0:
logger.warn(mol, 'Characters of %d valence electrons are not identified.\n'
'It can affect the "meta-lowdin" localization method '
'and the population analysis of SCF method.\n'
'Adjustment to the core/valence partition may be needed '
'(see function lo.nao.set_atom_conf)\nto get reasonable '
'local orbitals or Mulliken population.\n',
nelec_valence_left)
# Return 0 to force the projection to ANO basis
return 0
else:
s12 = gto.intor_cross('int1e_ovlp', atm_ecp, atm_ano)[ecp_idx][:,ano_idx]
return numpy.linalg.det(s12)
nelec_ecp_dic = {}
for ia in range(mol.natm):
symb = mol.atom_symbol(ia)
if symb not in nelec_ecp_dic:
nelec_ecp_dic[symb] = mol.atom_nelec_core(ia)
aos = {}
atm = gto.Mole()
atmp = gto.Mole()
for symb in mol._basis.keys():
stdsymb = gto.mole._std_symbol(symb)
atm._atm, atm._bas, atm._env = \
atm.make_env([[stdsymb,(0,0,0)]], {stdsymb:mol._basis[symb]}, [])
atm.cart = mol.cart
atm._built = True
s0 = atm.intor_symmetric('int1e_ovlp')
if gto.is_ghost_atom(symb):
aos[symb] = numpy.diag(1./numpy.sqrt(s0.diagonal()))
continue
basis_add = gto.basis.load(basname, stdsymb)
atmp._atm, atmp._bas, atmp._env = \
atmp.make_env([[stdsymb,(0,0,0)]], {stdsymb:basis_add}, [])
atmp.cart = mol.cart
atmp._built = True
if symb in nelec_ecp_dic and nelec_ecp_dic[symb] > 0:
if not PROJECT_ECP_BASIS:
# If ECP basis has good atomic character, ECP basis can be used in the
# localization/population analysis directly. Otherwise project ECP basis to
# ANO basis.
continue
ecpcore = core_configuration(nelec_ecp_dic[symb])
# Comparing to ANO valence basis, to check whether the ECP basis set has
# reasonable AO-character contraction. The ANO valence AO should have
# significant overlap to ECP basis if the ECP basis has AO-character.
if abs(ecp_ano_det_ovlp(atm, atmp, ecpcore)) > .1:
aos[symb] = numpy.diag(1./numpy.sqrt(s0.diagonal()))
continue
else:
ecpcore = [0] * 4
ano = project_mo_nr2nr(atmp, numpy.eye(atmp.nao_nr()), atm)
rm_ano = numpy.eye(ano.shape[0]) - reduce(numpy.dot, (ano, ano.T, s0))
c = rm_ano.copy()
for l in range(param.L_MAX):
idx = numpy.asarray(search_atm_l(atm, l))
nbf_atm_l = len(idx)
if nbf_atm_l == 0:
break
idxp = numpy.asarray(search_atm_l(atmp, l))
if l < 4:
idxp = idxp[ecpcore[l]:]
nbf_ano_l = len(idxp)
if mol.cart:
degen = (l + 1) * (l + 2) // 2
else:
degen = l * 2 + 1
if nbf_atm_l > nbf_ano_l > 0:
# For angular l, first place the projected ANO, then the rest AOs.
sdiag = reduce(numpy.dot, (rm_ano[:,idx].T, s0, rm_ano[:,idx])).diagonal()
nleft = (nbf_atm_l - nbf_ano_l) // degen
shell_average = numpy.einsum('ij->i', sdiag.reshape(-1,degen))
shell_rest = numpy.argsort(-shell_average)[:nleft]
idx_rest = []
for k in shell_rest:
idx_rest.extend(idx[k*degen:(k+1)*degen])
c[:,idx[:nbf_ano_l]] = ano[:,idxp]
c[:,idx[nbf_ano_l:]] = rm_ano[:,idx_rest]
elif nbf_ano_l >= nbf_atm_l > 0: # More ANOs than the mol basis functions
c[:,idx] = ano[:,idxp[:nbf_atm_l]]
sdiag = numpy.einsum('pi,pq,qi->i', c, s0, c)
c *= 1./numpy.sqrt(sdiag)
aos[symb] = c
nao = mol.nao_nr()
c = numpy.zeros((nao,nao))
p1 = 0
for ia in range(mol.natm):
symb = mol.atom_symbol(ia)
if symb in mol._basis:
ano = aos[symb]
else:
ano = aos[mol.atom_pure_symbol(ia)]
p0, p1 = p1, p1 + ano.shape[1]
c[p0:p1,p0:p1] = ano
return c
def gen_g_hop_rhf(mf,
mo_coeff,
mo_occ,
fock_ao=None,
h1e=None,
with_symmetry=True):
mo_coeff0 = mo_coeff
mol = mf.mol
if getattr(mf, '_scf', None) and mf._scf.mol != mol:
#TODO: construct vind with dual-basis treatment, (see also JCP, 118, 9497)
# To project Hessians from another basis if different basis sets are used
# in newton solver and underlying mean-filed solver.
mo_coeff = addons.project_mo_nr2nr(mf._scf.mol, mo_coeff, mol)
occidx = numpy.where(mo_occ == 2)[0]
viridx = numpy.where(mo_occ == 0)[0]
nocc = len(occidx)
nvir = len(viridx)
orbo = mo_coeff[:, occidx]
orbv = mo_coeff[:, viridx]
if with_symmetry and mol.symmetry:
orbsym = hf_symm.get_orbsym(mol, mo_coeff)
sym_forbid = orbsym[viridx, None] != orbsym[occidx]
if fock_ao is None:
# dm0 is the density matrix in projected basis. Computing fock in
# projected basis.
if getattr(mf, '_scf', None) and mf._scf.mol != mol:
h1e = mf.get_hcore(mol)
dm0 = mf.make_rdm1(mo_coeff, mo_occ)
fock_ao = mf.get_fock(h1e, dm=dm0)
fock = reduce(numpy.dot, (mo_coeff.conj().T, fock_ao, mo_coeff))
else:
# If fock is given, it corresponds to main basis. It needs to be
# diagonalized with the mo_coeff of the main basis.
fock = reduce(numpy.dot, (mo_coeff0.conj().T, fock_ao, mo_coeff0))
g = fock[viridx[:, None], occidx] * 2
foo = fock[occidx[:, None], occidx]
fvv = fock[viridx[:, None], viridx]
h_diag = (fvv.diagonal().real[:, None] - foo.diagonal().real) * 2
if with_symmetry and mol.symmetry:
g[sym_forbid] = 0
h_diag[sym_forbid] = 0
vind = _gen_rhf_response(mf, mo_coeff, mo_occ, singlet=None, hermi=1)
def h_op(x):
x = x.reshape(nvir, nocc)
if with_symmetry and mol.symmetry:
x = x.copy()
x[sym_forbid] = 0
x2 = numpy.einsum('ps,sq->pq', fvv, x)
#x2-= .5*numpy.einsum('ps,rp->rs', foo, x)
#x2-= .5*numpy.einsum('sp,rp->rs', foo, x)
x2 -= numpy.einsum('ps,rp->rs', foo, x)
# *2 for double occupancy
d1 = reduce(numpy.dot, (orbv, x * 2, orbo.conj().T))
dm1 = d1 + d1.conj().T
v1 = vind(dm1)
x2 += reduce(numpy.dot, (orbv.conj().T, v1, orbo))
if with_symmetry and mol.symmetry:
x2[sym_forbid] = 0
return x2.ravel() * 2
return g.reshape(-1), h_op, h_diag.reshape(-1)
def project_to_atomic_orbitals(mol, basname):
'''projected AO = |bas><bas|ANO>
'''
from pyscf.scf.addons import project_mo_nr2nr
from pyscf.scf import atom_hf
from pyscf.gto.ecp import core_configuration
def search_atm_l(atm, l):
bas_ang = atm._bas[:, gto.ANG_OF]
ao_loc = atm.ao_loc_nr()
idx = []
for ib in numpy.where(bas_ang == l)[0]:
idx.extend(range(ao_loc[ib], ao_loc[ib + 1]))
return idx
# Overlap of ANO and ECP basis
def ecp_ano_det_ovlp(atm_ecp, atm_ano, ecpcore):
ecp_ao_loc = atm_ecp.ao_loc_nr()
ano_ao_loc = atm_ano.ao_loc_nr()
ecp_ao_dim = ecp_ao_loc[1:] - ecp_ao_loc[:-1]
ano_ao_dim = ano_ao_loc[1:] - ano_ao_loc[:-1]
ecp_bas_l = [[atm_ecp.bas_angular(i)] * d
for i, d in enumerate(ecp_ao_dim)]
ano_bas_l = [[atm_ano.bas_angular(i)] * d
for i, d in enumerate(ano_ao_dim)]
ecp_bas_l = numpy.hstack(ecp_bas_l)
ano_bas_l = numpy.hstack(ano_bas_l)
nelec_core = 0
ecp_occ_tmp = []
ecp_idx = []
ano_idx = []
for l in range(4):
nocc, frac = atom_hf.frac_occ(stdsymb, l)
l_occ = [2] * ((nocc - ecpcore[l]) * (2 * l + 1))
if frac > 1e-15:
l_occ.extend([frac] * (2 * l + 1))
nocc += 1
if nocc == 0:
break
nelec_core += 2 * ecpcore[l] * (2 * l + 1)
i0 = ecpcore[l] * (2 * l + 1)
i1 = nocc * (2 * l + 1)
ecp_idx.append(numpy.where(ecp_bas_l == l)[0][:i1 - i0])
ano_idx.append(numpy.where(ano_bas_l == l)[0][i0:i1])
ecp_occ_tmp.append(l_occ[:i1 - i0])
ecp_idx = numpy.hstack(ecp_idx)
ano_idx = numpy.hstack(ano_idx)
ecp_occ = numpy.zeros(atm_ecp.nao_nr())
ecp_occ[ecp_idx] = numpy.hstack(ecp_occ_tmp)
nelec_valence_left = int(
gto.charge(stdsymb) - nelec_core - sum(ecp_occ[ecp_idx]))
if nelec_valence_left > 0:
logger.warn(
mol, 'Characters of %d valence electrons are not identified.\n'
'It can affect the "meta-lowdin" localization method '
'and the population analysis of SCF method.\n'
'Adjustment to the core/valence partition may be needed '
'(see function lo.nao.set_atom_conf)\nto get reasonable '
'local orbitals or Mulliken population.\n', nelec_valence_left)
# Return 0 to force the projection to ANO basis
return 0
else:
s12 = gto.intor_cross('int1e_ovlp', atm_ecp,
atm_ano)[ecp_idx][:, ano_idx]
return numpy.linalg.det(s12)
nelec_ecp_dic = {}
for ia in range(mol.natm):
symb = mol.atom_symbol(ia)
if symb not in nelec_ecp_dic:
nelec_ecp_dic[symb] = mol.atom_nelec_core(ia)
aos = {}
atm = gto.Mole()
atmp = gto.Mole()
for symb in mol._basis.keys():
stdsymb = gto.mole._std_symbol(symb)
atm._atm, atm._bas, atm._env = \
atm.make_env([[stdsymb,(0,0,0)]], {stdsymb:mol._basis[symb]}, [])
atm.cart = mol.cart
atm._built = True
s0 = atm.intor_symmetric('int1e_ovlp')
if gto.is_ghost_atom(symb):
aos[symb] = numpy.diag(1. / numpy.sqrt(s0.diagonal()))
continue
basis_add = gto.basis.load(basname, stdsymb)
atmp._atm, atmp._bas, atmp._env = \
atmp.make_env([[stdsymb,(0,0,0)]], {stdsymb:basis_add}, [])
atmp.cart = mol.cart
atmp._built = True
if symb in nelec_ecp_dic and nelec_ecp_dic[symb] > 0:
# If ECP basis has good atomic character, ECP basis can be used in the
# localization/population analysis directly. Otherwise project ECP
# basis to ANO basis.
if not PROJECT_ECP_BASIS:
continue
ecpcore = core_configuration(nelec_ecp_dic[symb])
# Comparing to ANO valence basis, to check whether the ECP basis set has
# reasonable AO-character contraction. The ANO valence AO should have
# significant overlap to ECP basis if the ECP basis has AO-character.
if abs(ecp_ano_det_ovlp(atm, atmp, ecpcore)) > .1:
aos[symb] = numpy.diag(1. / numpy.sqrt(s0.diagonal()))
continue
else:
ecpcore = [0] * 4
# MINAO for heavier elements needs to be used with pseudo potential
if (basname.upper() == 'MINAO' and gto.charge(stdsymb) > 36
and symb not in nelec_ecp_dic):
raise RuntimeError(
'Basis MINAO has to be used with ecp for heavy elements')
ano = project_mo_nr2nr(atmp, numpy.eye(atmp.nao_nr()), atm)
rm_ano = numpy.eye(ano.shape[0]) - reduce(numpy.dot, (ano, ano.T, s0))
c = rm_ano.copy()
for l in range(param.L_MAX):
idx = numpy.asarray(search_atm_l(atm, l))
nbf_atm_l = len(idx)
if nbf_atm_l == 0:
break
idxp = numpy.asarray(search_atm_l(atmp, l))
if l < 4:
idxp = idxp[ecpcore[l]:]
nbf_ano_l = len(idxp)
if mol.cart:
degen = (l + 1) * (l + 2) // 2
else:
degen = l * 2 + 1
if nbf_atm_l > nbf_ano_l > 0:
# For angular l, first place the projected ANO, then the rest AOs.
sdiag = reduce(
numpy.dot,
(rm_ano[:, idx].T, s0, rm_ano[:, idx])).diagonal()
nleft = (nbf_atm_l - nbf_ano_l) // degen
shell_average = numpy.einsum('ij->i', sdiag.reshape(-1, degen))
shell_rest = numpy.argsort(-shell_average)[:nleft]
idx_rest = []
for k in shell_rest:
idx_rest.extend(idx[k * degen:(k + 1) * degen])
c[:, idx[:nbf_ano_l]] = ano[:, idxp]
c[:, idx[nbf_ano_l:]] = rm_ano[:, idx_rest]
elif nbf_ano_l >= nbf_atm_l > 0: # More ANOs than the mol basis functions
c[:, idx] = ano[:, idxp[:nbf_atm_l]]
sdiag = numpy.einsum('pi,pq,qi->i', c, s0, c)
c *= 1. / numpy.sqrt(sdiag)
aos[symb] = c
nao = mol.nao_nr()
c = numpy.zeros((nao, nao))
p1 = 0
for ia in range(mol.natm):
symb = mol.atom_symbol(ia)
if symb in mol._basis:
ano = aos[symb]
else:
ano = aos[mol.atom_pure_symbol(ia)]
p0, p1 = p1, p1 + ano.shape[1]
c[p0:p1, p0:p1] = ano
return c
def fproj(mo):
if project:
mo = addons.project_mo_nr2nr(chk_mol, mo, mol)
norm = numpy.einsum('pi,pi->i', mo.conj(), s.dot(mo))
mo /= numpy.sqrt(norm)
return mo
def project_to_atomic_orbitals(mol, basname):
'''projected AO = |bas><bas|ANO>
'''
from pyscf.scf.addons import project_mo_nr2nr
from pyscf.gto.ecp import core_configuration
def search_atm_l(atm, l):
idx = []
p0 = 0
for ib, b in enumerate(atm._bas):
l0 = atm.bas_angular(ib)
nctr = atm.bas_nctr(ib)
if l0 == l:
idx.extend(range(p0, p0 + (2 * l + 1) * nctr))
p0 += (2 * l0 + 1) * nctr
return idx
aos = {}
atm = gto.Mole()
atmp = gto.Mole()
for symb in mol._basis.keys():
stdsymb = gto.mole._std_symbol(symb)
atm._atm, atm._bas, atm._env = \
atm.make_env([[stdsymb,(0,0,0)]], {stdsymb:mol._basis[symb]}, [])
if 'GHOST' in symb.upper():
aos[symb] = numpy.eye(atm.nao_nr())
continue
s0 = atm.intor_symmetric('cint1e_ovlp_sph')
basis_add = gto.basis.load(basname, stdsymb)
atmp._atm, atmp._bas, atmp._env = \
atmp.make_env([[stdsymb,(0,0,0)]], {stdsymb:basis_add}, [])
ano = project_mo_nr2nr(atmp, 1, atm)
rm_ano = numpy.eye(ano.shape[0]) - reduce(numpy.dot, (ano, ano.T, s0))
nelec_ecp = 0
if mol._ecp:
if symb in mol._ecp:
nelec_ecp = mol._ecp[symb][0]
elif stdsymb in mol._ecp:
nelec_ecp = mol._ecp[stdsymb][0]
ecpcore = core_configuration(nelec_ecp)
c = rm_ano.copy()
for l in range(param.L_MAX):
idx = numpy.asarray(search_atm_l(atm, l))
if len(idx) == 0:
break
idxp = numpy.asarray(search_atm_l(atmp, l))
if l < 4:
idxp = idxp[ecpcore[l]:]
if len(idx) > len(idxp) > 0:
# For angular l, first place the projected ANO, then the rest AOs.
sdiag = reduce(
numpy.dot,
(rm_ano[:, idx].T, s0, rm_ano[:, idx])).diagonal()
nleft = (len(idx) - len(idxp)) // (2 * l + 1)
shell_average = numpy.einsum('ij->i',
sdiag.reshape(-1, l * 2 + 1))
shell_rest = numpy.argsort(-shell_average)[:nleft]
idx_rest = []
for k in shell_rest:
idx_rest.extend(idx[k * (2 * l + 1):(k + 1) * (2 * l + 1)])
c[:, idx[:len(idxp)]] = ano[:, idxp]
c[:, idx[len(idxp):]] = rm_ano[:, idx_rest]
elif len(idxp) >= len(
idx) > 0: # More ANOs than the mol basis functions
c[:, idx] = ano[:, idxp[:len(idx)]]
aos[symb] = c
nao = mol.nao_nr()
c = numpy.zeros((nao, nao))
p0 = 0
for ia in range(mol.natm):
symb = mol.atom_symbol(ia)
if symb in mol._basis:
ano = aos[symb]
else:
symb = mol.atom_pure_symbol(ia)
ano = aos[symb]
p1 = p0 + ano.shape[1]
c[p0:p1, p0:p1] = ano
p0 = p1
return c