#!/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>
#
'''
RCCSD
Ref: JCP 90, 1752 (1989); DOI:10.1063/1.456069
'''
from functools import reduce
import numpy
import scipy.linalg
from pyscf import lib
from pyscf import ao2mo
from pyscf.cc import ccsd_rdm
from pyscf.grad import ccsd as ccsd_grad
[docs]
def kernel(cc, t1, t2, l1, l2, eris=None):
if eris is None:
eris = _ERIS(cc, cc.mo_coeff)
mol = cc.mol
mo_coeff = cc.mo_coeff
mo_energy = cc._scf.mo_energy
nao, nmo = mo_coeff.shape
nocc = numpy.count_nonzero(cc.mo_occ > 0)
mo_e_o = mo_energy[:nocc]
mo_e_v = mo_energy[nocc:]
with_frozen = not ((cc.frozen is None)
or (isinstance(cc.frozen, (int, numpy.integer)) and cc.frozen == 0)
or (len(cc.frozen) == 0))
d1 = _gamma1_intermediates(cc, t1, t2, l1, l2)
d2 = _gamma2_intermediates(cc, t1, t2, l1, l2)
dm2 = ccsd_rdm._make_rdm2(cc, d1, d2, with_dm1=False, with_frozen=False)
eri = ao2mo.restore(1, ao2mo.full(cc.mol, mo_coeff), nmo)
Imat = numpy.einsum('jqrs,iqrs->ij', dm2, eri) * -1
Ioo = Imat[:nocc,:nocc]
Ivv = Imat[nocc:,nocc:]
doo, dov, dvo, dvv = d1
if with_frozen:
OA, VA, OF, VF = index_frozen_active(cc)
doo[OF[:,None],OA] = Ioo[OF[:,None],OA] / lib.direct_sum('i-j->ij', mo_e_o[OF], mo_e_o[OA])
doo[OA[:,None],OF] = Ioo[OA[:,None],OF] / lib.direct_sum('i-j->ij', mo_e_o[OA], mo_e_o[OF])
dvv[VF[:,None],VA] = Ivv[VF[:,None],VA] / lib.direct_sum('a-b->ab', mo_e_v[VF], mo_e_v[VA])
dvv[VA[:,None],VF] = Ivv[VA[:,None],VF] / lib.direct_sum('a-b->ab', mo_e_v[VA], mo_e_v[VF])
dm1 = scipy.linalg.block_diag(doo+doo.T, dvv+dvv.T)
dm1ao = reduce(numpy.dot, (mo_coeff, dm1, mo_coeff.T))
vj, vk = cc._scf.get_jk(cc.mol, dm1ao)
Xvo = reduce(numpy.dot, (mo_coeff[:,nocc:].T, vj*2-vk, mo_coeff[:,:nocc]))
Xvo += Imat[:nocc,nocc:].T - Imat[nocc:,:nocc]
dm1 += ccsd_grad._response_dm1(cc, Xvo, eris)
Imat[nocc:,:nocc] = Imat[:nocc,nocc:].T
h1 =-(mol.intor('int1e_ipkin', comp=3) +
mol.intor('int1e_ipnuc', comp=3))
s1 =-mol.intor('int1e_ipovlp', comp=3)
#zeta = lib.direct_sum('i-j->ij', mo_energy, mo_energy)
eri1 = mol.intor('int2e_ip1', comp=3).reshape(3,nao,nao,nao,nao)
eri1 = numpy.einsum('xipkl,pj->xijkl', eri1, mo_coeff)
eri1 = numpy.einsum('xijpl,pk->xijkl', eri1, mo_coeff)
eri1 = numpy.einsum('xijkp,pl->xijkl', eri1, mo_coeff)
g0 = ao2mo.restore(1, ao2mo.full(mol, mo_coeff), nmo)
de = numpy.empty((mol.natm,3))
for k,(sh0, sh1, p0, p1) in enumerate(mol.offset_nr_by_atom()):
mol.set_rinv_origin(mol.atom_coord(k))
vrinv = -mol.atom_charge(k) * mol.intor('int1e_iprinv', comp=3)
# 2e AO integrals dot 2pdm
de2 = numpy.zeros(3)
for i in range(3):
g1 = numpy.einsum('pjkl,pi->ijkl', eri1[i,p0:p1], mo_coeff[p0:p1])
g1 = g1 + g1.transpose(1,0,2,3)
g1 = g1 + g1.transpose(2,3,0,1)
g1 *= -1
hx =(numpy.einsum('pq,pi,qj->ij', h1[i,p0:p1], mo_coeff[p0:p1], mo_coeff) +
reduce(numpy.dot, (mo_coeff.T, vrinv[i], mo_coeff)))
hx = hx + hx.T
sx = numpy.einsum('pq,pi,qj->ij', s1[i,p0:p1], mo_coeff[p0:p1], mo_coeff)
sx = sx + sx.T
fij =(hx[:nocc,:nocc]
- numpy.einsum('ij,j->ij', sx[:nocc,:nocc], mo_e_o) * .5
- numpy.einsum('ij,i->ij', sx[:nocc,:nocc], mo_e_o) * .5
- numpy.einsum('kl,ijlk->ij', sx[:nocc,:nocc],
g0[:nocc,:nocc,:nocc,:nocc]) * 2
+ numpy.einsum('kl,iklj->ij', sx[:nocc,:nocc],
g0[:nocc,:nocc,:nocc,:nocc])
+ numpy.einsum('ijkk->ij', g1[:nocc,:nocc,:nocc,:nocc]) * 2
- numpy.einsum('ikkj->ij', g1[:nocc,:nocc,:nocc,:nocc]))
fab =(hx[nocc:,nocc:]
- numpy.einsum('ij,j->ij', sx[nocc:,nocc:], mo_e_v) * .5
- numpy.einsum('ij,i->ij', sx[nocc:,nocc:], mo_e_v) * .5
- numpy.einsum('kl,ijlk->ij', sx[:nocc,:nocc],
g0[nocc:,nocc:,:nocc,:nocc]) * 2
+ numpy.einsum('kl,iklj->ij', sx[:nocc,:nocc],
g0[nocc:,:nocc,:nocc,nocc:])
+ numpy.einsum('ijkk->ij', g1[nocc:,nocc:,:nocc,:nocc]) * 2
- numpy.einsum('ikkj->ij', g1[nocc:,:nocc,:nocc,nocc:]))
if with_frozen:
fij[OA[:,None],OF] -= numpy.einsum('ij,j->ij', sx[OA[:,None],OF], mo_e_o[OF]) * .5
fij[OA[:,None],OF] += numpy.einsum('ij,i->ij', sx[OA[:,None],OF], mo_e_o[OA]) * .5
fij[OF[:,None],OA] -= numpy.einsum('ij,j->ij', sx[OF[:,None],OA], mo_e_o[OA]) * .5
fij[OF[:,None],OA] += numpy.einsum('ij,i->ij', sx[OF[:,None],OA], mo_e_o[OF]) * .5
fab[VA[:,None],VF] -= numpy.einsum('ij,j->ij', sx[VA[:,None],VF], mo_e_v[VF]) * .5
fab[VA[:,None],VF] += numpy.einsum('ij,i->ij', sx[VA[:,None],VF], mo_e_v[VA]) * .5
fab[VF[:,None],VA] -= numpy.einsum('ij,j->ij', sx[VF[:,None],VA], mo_e_v[VA]) * .5
fab[VF[:,None],VA] += numpy.einsum('ij,i->ij', sx[VF[:,None],VA], mo_e_v[VF]) * .5
fai =(hx[nocc:,:nocc]
- numpy.einsum('ai,i->ai', sx[nocc:,:nocc], mo_e_o)
- numpy.einsum('kl,ijlk->ij', sx[:nocc,:nocc],
g0[nocc:,:nocc,:nocc,:nocc]) * 2
+ numpy.einsum('kl,iklj->ij', sx[:nocc,:nocc],
g0[nocc:,:nocc,:nocc,:nocc])
+ numpy.einsum('ijkk->ij', g1[nocc:,:nocc,:nocc,:nocc]) * 2
- numpy.einsum('ikkj->ij', g1[nocc:,:nocc,:nocc,:nocc]))
f1 = numpy.zeros((nmo,nmo))
f1[:nocc,:nocc] = fij
f1[nocc:,nocc:] = fab
f1[nocc:,:nocc] = fai
f1[:nocc,nocc:] = fai.T
de2[i] += numpy.einsum('ij,ji', f1, dm1)
de2[i] += numpy.einsum('ij,ji', sx, Imat)
de2[i] += numpy.einsum('iajb,iajb', dm2, g1) * .5
de[k] = de2
return de
class _ERIS:
def __init__(self, cc, mo_coeff):
nocc = numpy.count_nonzero(cc.mo_occ > 0)
eri0 = ao2mo.full(cc._scf._eri, mo_coeff)
eri0 = ao2mo.restore(1, eri0, mo_coeff.shape[1])
eri0 = eri0.reshape((mo_coeff.shape[1],)*4)
self.oooo = eri0[:nocc,:nocc,:nocc,:nocc].copy()
self.ooov = eri0[:nocc,:nocc,:nocc,nocc:].copy()
self.ovoo = eri0[:nocc,nocc:,:nocc,:nocc].copy()
self.oovo = eri0[:nocc,:nocc,nocc:,:nocc].copy()
self.oovv = eri0[:nocc,:nocc,nocc:,nocc:].copy()
self.ovov = eri0[:nocc,nocc:,:nocc,nocc:].copy()
self.ovvo = eri0[:nocc,nocc:,nocc:,:nocc].copy()
self.ovvv = eri0[:nocc,nocc:,nocc:,nocc:].copy()
self.vvvv = eri0[nocc:,nocc:,nocc:,nocc:].copy()
self.vvvo = eri0[nocc:,nocc:,nocc:,:nocc].copy()
self.vovv = eri0[nocc:,:nocc,nocc:,nocc:].copy()
self.vvov = eri0[nocc:,nocc:,:nocc,nocc:].copy()
self.vvoo = eri0[nocc:,nocc:,:nocc,:nocc].copy()
self.voov = eri0[nocc:,:nocc,:nocc,nocc:].copy()
self.vooo = eri0[nocc:,:nocc,:nocc,:nocc].copy()
self.mo_coeff = mo_coeff
self.fock = numpy.diag(cc._scf.mo_energy)
[docs]
def index_frozen_active(cc):
nocc = numpy.count_nonzero(cc.mo_occ > 0)
moidx = cc.get_frozen_mask()
OA = numpy.where( moidx[:nocc])[0] # occupied active orbitals
OF = numpy.where(~moidx[:nocc])[0] # occupied frozen orbitals
VA = numpy.where( moidx[nocc:])[0] # virtual active orbitals
VF = numpy.where(~moidx[nocc:])[0] # virtual frozen orbitals
return OA, VA, OF, VF
def _gamma1_intermediates(cc, t1, t2, l1, l2):
d1 = ccsd_rdm._gamma1_intermediates(cc, t1, t2, l1, l2)
if cc.frozen is None:
return d1
nocc = numpy.count_nonzero(cc.mo_occ>0)
nvir = cc.mo_occ.size - nocc
OA, VA, OF, VF = index_frozen_active(cc)
doo = numpy.zeros((nocc,nocc))
dov = numpy.zeros((nocc,nvir))
dvo = numpy.zeros((nvir,nocc))
dvv = numpy.zeros((nvir,nvir))
doo[OA[:,None],OA] = d1[0]
dov[OA[:,None],VA] = d1[1]
dvo[VA[:,None],OA] = d1[2]
dvv[VA[:,None],VA] = d1[3]
return doo, dov, dvo, dvv
def _gamma2_intermediates(cc, t1, t2, l1, l2):
d2 = ccsd_rdm._gamma2_intermediates(cc, t1, t2, l1, l2)
nocc, nvir = t1.shape
if cc.frozen is None:
dovov, dvvvv, doooo, doovv, dovvo, dvvov, dovvv, dooov = d2
dvvov = dovvv.transpose(2,3,0,1)
dvvvv = ao2mo.restore(1, d2[1], nvir)
return dovov, dvvvv, doooo, doovv, dovvo, dvvov, dovvv, dooov
nocc0 = numpy.count_nonzero(cc.mo_occ>0)
nvir0 = cc.mo_occ.size - nocc0
OA, VA, OF, VF = index_frozen_active(cc)
dovov = numpy.zeros((nocc0,nvir0,nocc0,nvir0))
dvvvv = numpy.zeros((nvir0,nvir0,nvir0,nvir0))
doooo = numpy.zeros((nocc0,nocc0,nocc0,nocc0))
doovv = numpy.zeros((nocc0,nocc0,nvir0,nvir0))
dovvo = numpy.zeros((nocc0,nvir0,nvir0,nocc0))
dovvv = numpy.zeros((nocc0,nvir0,nvir0,nvir0))
dooov = numpy.zeros((nocc0,nocc0,nocc0,nvir0))
dovov[OA[:,None,None,None],VA[:,None,None],OA[:,None],VA] = d2[0]
dvvvv[VA[:,None,None,None],VA[:,None,None],VA[:,None],VA] = ao2mo.restore(1, d2[1], nvir)
doooo[OA[:,None,None,None],OA[:,None,None],OA[:,None],OA] = d2[2]
doovv[OA[:,None,None,None],OA[:,None,None],VA[:,None],VA] = d2[3]
dovvo[OA[:,None,None,None],VA[:,None,None],VA[:,None],OA] = d2[4]
dovvv[OA[:,None,None,None],VA[:,None,None],VA[:,None],VA] = d2[6]
dooov[OA[:,None,None,None],OA[:,None,None],OA[:,None],VA] = d2[7]
dvvov = dovvv.transpose(2,3,0,1)
return dovov, dvvvv, doooo, doovv, dovvo, dvvov, dovvv, dooov
if __name__ == '__main__':
from pyscf import gto
from pyscf import scf
from pyscf.cc import ccsd
from pyscf import grad
mol = gto.M(
verbose = 0,
atom = [
["O" , (0. , 0. , 0.)],
[1 , (0. ,-0.757 , 0.587)],
[1 , (0. , 0.757 , 0.587)]],
basis = '631g'
)
mf = scf.RHF(mol).run()
mycc = ccsd.CCSD(mf)
ecc, t1, t2 = mycc.kernel()
l1, l2 = mycc.solve_lambda()
g1 = kernel(mycc, t1, t2, l1, l2)
ghf = grad.RHF(mf).grad()
print('gcc')
print(ghf+g1)
print(lib.fp(g1) - -0.042511000925747583)
#[[ 0 0 1.00950969e-02]
# [ 0 2.28063353e-02 -5.04754844e-03]
# [ 0 -2.28063353e-02 -5.04754844e-03]]
print('-----------------------------------')
mol = gto.M(
verbose = 0,
atom = [
["O" , (0. , 0. , 0.)],
[1 , (0. ,-0.757 , 0.587)],
[1 , (0. , 0.757 , 0.587)]],
basis = '631g'
)
mf = scf.RHF(mol).run()
mycc = ccsd.CCSD(mf)
mycc.frozen = [0,1,10,11,12]
ecc, t1, t2 = mycc.kernel()
l1, l2 = mycc.solve_lambda()
g1 = kernel(mycc, t1, t2, l1, l2)
ghf = grad.RHF(mf).grad()
print('gcc')
print(ghf+g1)
print(lib.fp(g1) - 0.10048468674687236)
#[[ -7.81105940e-17 3.81840540e-15 1.20415540e-02]
# [ 1.73095055e-16 -7.94568837e-02 -6.02077699e-03]
# [ -9.49844615e-17 7.94568837e-02 -6.02077699e-03]]
r = 1.76
mol = gto.M(
verbose = 0,
atom = '''H 0 0 0; H 0 0 %f''' % r,
basis = '631g',
unit = 'bohr')
mf = scf.RHF(mol)
mf.conv_tol = 1e-14
ehf0 = mf.scf()
ghf = grad.RHF(mf).grad()
mycc = ccsd.CCSD(mf)
ecc, t1, t2 = mycc.kernel()
l1, l2 = mycc.solve_lambda()
g1 = kernel(mycc, t1, t2, l1, l2)
ghf = grad.RHF(mf).grad()
print('ghf')
print(ghf)
print('gcc')
print(g1) # 0.015643667024
print('tot')
print(ghf+g1) # -0.0708003526454
mol = gto.M(
verbose = 0,
atom = '''H 0 0 0; H 0 0 %f''' % (r-.001),
basis = '631g',
unit = 'bohr')
mf = scf.RHF(mol)
mf.conv_tol = 1e-14
ehf0 = mf.scf()
mycc = ccsd.CCSD(mf)
ecc0 = mycc.kernel()[0]
mol = gto.M(
verbose = 0,
atom = '''H 0 0 0; H 0 0 %f''' % (r+.001),
basis = '631g',
unit = 'bohr')
mf = scf.RHF(mol)
mf.conv_tol = 1e-14
ehf1 = mf.scf()
mycc = ccsd.CCSD(mf)
ecc1 = mycc.kernel()[0]
print((ehf1-ehf0)*500 - ghf[1,2])
print('decc', (ecc1-ecc0)*500 - g1[1,2])
print('decc', (ehf1+ecc1-ehf0-ecc0)*500 - (ghf[1,2]+g1[1,2]))
