#!/usr/bin/env python
# Copyright 2014-2019 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
# Author: Qiming Sun <osirpt.sun@gmail.com>
#
import numpy
from pyscf import gto
from pyscf.lib import logger
from pyscf.lib import param
from pyscf.data import elements
from pyscf.scf import hf, rohf, addons
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def get_atm_nrhf(mol, atomic_configuration=elements.NRSRHF_CONFIGURATION):
elements = {a[0] for a in mol._atom}
logger.info(mol, 'Spherically averaged atomic HF for %s', elements)
atm_template = mol.copy(deep=False)
atm_template.charge = 0
atm_template.enuc = 0
atm_template.symmetry = False # TODO: enable SO3 symmetry here
atm_template.atom = atm_template._atom = []
atm_template.cart = False # AtomSphAverageRHF does not support cartesian basis
atm_scf_result = {}
for ia, a in enumerate(mol._atom):
element = a[0]
if element in atm_scf_result:
continue
atm = atm_template
atm._atom = [a]
atm._atm = mol._atm[ia:ia+1]
atm._bas = mol._bas[mol._bas[:,0] == ia].copy()
atm._ecpbas = mol._ecpbas[mol._ecpbas[:,0] == ia].copy()
# Point to the only atom
atm._bas[:,0] = 0
atm._ecpbas[:,0] = 0
if element in mol._pseudo:
atm._pseudo = {element: mol._pseudo.get(element)}
atm.spin = atm.nelectron % 2
nao = atm.nao
# nao == 0 for the case that no basis was assigned to an atom
if nao == 0 or atm.nelectron == 0: # GHOST
mo_occ = mo_energy = numpy.zeros(nao)
mo_coeff = numpy.zeros((nao,nao))
atm_scf_result[element] = (0, mo_energy, mo_coeff, mo_occ)
elif atm._pseudo:
from pyscf.scf import atom_hf_pp
atm.a = None
if atm.nelectron == 1:
atm_hf = atom_hf_pp.AtomHF1ePP(atm)
else:
atm_hf = atom_hf_pp.AtomSCFPP(atm)
atm_hf.atomic_configuration = atomic_configuration
atm_hf.verbose = mol.verbose
atm_hf.run()
atm_scf_result[element] = (atm_hf.e_tot, atm_hf.mo_energy,
atm_hf.mo_coeff, atm_hf.mo_occ)
else:
if atm.nelectron == 1:
atm_hf = AtomHF1e(atm)
else:
atm_hf = AtomSphAverageRHF(atm)
atm_hf.atomic_configuration = atomic_configuration
atm_hf.verbose = mol.verbose
atm_hf.run()
atm_scf_result[element] = (atm_hf.e_tot, atm_hf.mo_energy,
atm_hf.mo_coeff, atm_hf.mo_occ)
return atm_scf_result
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class AtomSphAverageRHF(hf.RHF):
def __init__(self, mol):
self._eri = None
self.atomic_configuration = elements.NRSRHF_CONFIGURATION
hf.SCF.__init__(self, mol)
# The default initial guess minao does not have super-heavy elements
if gto.charge(mol.atom_symbol(0)) > 96:
self.init_guess = '1e'
self = self.apply(addons.remove_linear_dep_)
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def check_sanity(self):
pass
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def dump_flags(self, verbose=None):
log = logger.new_logger(self, verbose)
hf.RHF.dump_flags(self, log)
log.info('atom = %s', self.mol.atom_symbol(0))
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def eig(self, f, s):
mol = self.mol
ao_ang = _angular_momentum_for_each_ao(mol)
nao = mol.nao
mo_coeff = []
mo_energy = []
for l in range(param.L_MAX):
degen = 2 * l + 1
idx = numpy.where(ao_ang == l)[0]
nao_l = len(idx)
if nao_l > 0:
nsh = nao_l // degen
f_l = f[idx[:,None],idx].reshape(nsh, degen, nsh, degen)
s_l = s[idx[:,None],idx].reshape(nsh, degen, nsh, degen)
# Average over angular parts
f_l = numpy.einsum('piqi->pq', f_l) / degen
s_l = numpy.einsum('piqi->pq', s_l) / degen
e, c = self._eigh(f_l, s_l)
for i, ei in enumerate(e):
logger.debug1(self, 'l = %d e_%d = %.9g', l, i, ei)
mo_energy.append(numpy.repeat(e, degen))
mo = numpy.zeros((nao, nsh, degen))
for i in range(degen):
mo[idx[i::degen],:,i] = c
mo_coeff.append(mo.reshape(nao, nao_l))
return numpy.hstack(mo_energy), numpy.hstack(mo_coeff)
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def get_occ(self, mo_energy=None, mo_coeff=None):
'''spherically averaged fractional occupancy'''
mol = self.mol
symb = mol.atom_symbol(0)
nelec_ecp = mol.atom_nelec_core(0)
coreshl = gto.ecp.core_configuration(nelec_ecp, atom_symbol=gto.mole._std_symbol(symb))
occ = []
for l in range(param.L_MAX):
n2occ, frac = frac_occ(symb, l, self.atomic_configuration)
degen = 2 * l + 1
idx = mol._bas[:,gto.ANG_OF] == l
nbas_l = mol._bas[idx,gto.NCTR_OF].sum()
if l < 4:
n2occ -= coreshl[l]
assert n2occ <= nbas_l
logger.debug1(self, 'l = %d occ = %d + %.4g', l, n2occ, frac)
if nbas_l > 0:
occ_l = numpy.zeros(nbas_l)
occ_l[:n2occ] = 2
if frac > 0:
occ_l[n2occ] = frac
occ.append(numpy.repeat(occ_l, degen))
else:
occ.append(numpy.zeros(nbas_l * degen))
return numpy.hstack(occ)
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def get_grad(self, mo_coeff, mo_occ, fock=None):
return 0
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def scf(self, *args, **kwargs):
kwargs['dump_chk'] = False
return hf.RHF.scf(self, *args, **kwargs)
def _finalize(self):
if self.converged:
logger.info(self, 'Atomic HF for atom %s converged. SCF energy = %.15g\n',
self.mol.atom_symbol(0), self.e_tot)
else:
logger.info(self, 'Atomic HF for atom %s not converged. SCF energy = %.15g\n',
self.mol.atom_symbol(0), self.e_tot)
return self
AtomSphericAverageRHF = AtomSphAverageRHF
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class AtomHF1e(rohf.HF1e, AtomSphAverageRHF):
eig = AtomSphAverageRHF.eig
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def frac_occ(symb, l, atomic_configuration=elements.NRSRHF_CONFIGURATION):
nuc = gto.charge(symb)
if l < 4 and atomic_configuration[nuc][l] > 0:
ne = atomic_configuration[nuc][l]
nd = (l * 2 + 1) * 2
ndocc = ne.__floordiv__(nd)
frac = (float(ne) / nd - ndocc) * 2
else:
ndocc = frac = 0
return ndocc, frac
def _angular_momentum_for_each_ao(mol):
ao_ang = numpy.zeros(mol.nao, dtype=int)
ao_loc = mol.ao_loc_nr()
for i in range(mol.nbas):
p0, p1 = ao_loc[i], ao_loc[i+1]
ao_ang[p0:p1] = mol.bas_angular(i)
return ao_ang
