#!/usr/bin/env python
# Copyright 2014-2020 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
import scipy.linalg
from pyscf import lib
from pyscf.lib import logger
from pyscf import gto
from pyscf.df import addons
from pyscf.gto.moleintor import getints
from pyscf import __config__
MAX_MEMORY = getattr(__config__, 'df_outcore_max_memory', 2000) # 2GB
LINEAR_DEP_THR = getattr(__config__, 'df_df_DF_lindep', 1e-12)
# This function is aliased for backward compatibility.
format_aux_basis = addons.make_auxmol
[docs]
def aux_e2(mol, auxmol_or_auxbasis, intor='int3c2e', aosym='s1', comp=None, out=None,
cintopt=None):
'''3-center AO integrals (ij|L), where L is the auxiliary basis.
Kwargs:
cintopt : Libcint-3.14 and newer version support to compute int3c2e
without the opt for the 3rd index. It can be precomputed to
reduce the overhead of cintopt initialization repeatedly.
cintopt = gto.moleintor.make_cintopt(mol._atm, mol._bas, mol._env, 'int3c2e')
'''
if isinstance(auxmol_or_auxbasis, gto.MoleBase):
auxmol = auxmol_or_auxbasis
else:
auxbasis = auxmol_or_auxbasis
auxmol = addons.make_auxmol(mol, auxbasis)
shls_slice = (0, mol.nbas, 0, mol.nbas, mol.nbas, mol.nbas+auxmol.nbas)
# Extract the call of the two lines below
# pmol = gto.mole.conc_mol(mol, auxmol)
# return pmol.intor(intor, comp, aosym=aosym, shls_slice=shls_slice, out=out)
intor = mol._add_suffix(intor)
hermi = 0
ao_loc = None
atm, bas, env = gto.mole.conc_env(mol._atm, mol._bas, mol._env,
auxmol._atm, auxmol._bas, auxmol._env)
return getints(intor, atm, bas, env, shls_slice, comp, hermi, aosym,
ao_loc, cintopt, out)
[docs]
def aux_e1(mol, auxmol_or_auxbasis, intor='int3c2e', aosym='s1', comp=None, out=None):
'''3-center 2-electron AO integrals (L|ij), where L is the auxiliary basis.
Note aux_e1 is basically analogous to aux_e2 function. It can be viewed as
the version of transposed aux_e2 tensor:
if comp == 1:
aux_e1 = aux_e2().T
else:
aux_e1 = aux_e2().transpose(0,2,1)
The same arguments as function aux_e2 can be input to aux_e1.
'''
if isinstance(auxmol_or_auxbasis, gto.MoleBase):
auxmol = auxmol_or_auxbasis
else:
auxbasis = auxmol_or_auxbasis
auxmol = addons.make_auxmol(mol, auxbasis)
out = aux_e2(mol, auxmol, intor, aosym, comp, out)
if out.ndim == 2: # comp == 1, aosym == s2
out = out.T
elif out.ndim == 3: # aosym == s1
assert aosym == 's1', ''
out = out.transpose(1, 2, 0)
else: # comp > 1 and aosym == s1
out = out.transpose(0, 2, 3, 1)
return out
[docs]
def fill_2c2e(mol, auxmol_or_auxbasis, intor='int2c2e', comp=None, hermi=1, out=None):
'''2-center 2-electron AO integrals for auxiliary basis (auxmol)
'''
if isinstance(auxmol_or_auxbasis, gto.MoleBase):
auxmol = auxmol_or_auxbasis
else:
auxbasis = auxmol_or_auxbasis
auxmol = addons.make_auxmol(mol, auxbasis)
return auxmol.intor(intor, comp=comp, hermi=hermi, out=out)
# Note the temporary memory usage is about twice as large as the return cderi
# array
[docs]
def cholesky_eri(mol, auxbasis='weigend+etb', auxmol=None,
int3c='int3c2e', aosym='s2ij', int2c='int2c2e', comp=1,
max_memory=MAX_MEMORY, decompose_j2c='cd',
lindep=LINEAR_DEP_THR, verbose=0, fauxe2=aux_e2):
'''
Returns:
2D array of (naux,nao*(nao+1)/2) in C-contiguous
'''
from pyscf.df.outcore import _guess_shell_ranges
assert (comp == 1)
t0 = (logger.process_clock(), logger.perf_counter())
log = logger.new_logger(mol, verbose)
if auxmol is None:
auxmol = addons.make_auxmol(mol, auxbasis)
j2c = auxmol.intor(int2c, hermi=1)
if decompose_j2c == 'eig':
low = _eig_decompose(mol, j2c, lindep)
else:
try:
low = scipy.linalg.cholesky(j2c, lower=True)
decompose_j2c = 'cd'
except scipy.linalg.LinAlgError:
low = _eig_decompose(mol, j2c, lindep)
decompose_j2c = 'eig'
j2c = None
naux, naoaux = low.shape
log.debug('size of aux basis %d', naux)
log.timer_debug1('2c2e', *t0)
int3c = gto.moleintor.ascint3(mol._add_suffix(int3c))
atm, bas, env = gto.mole.conc_env(mol._atm, mol._bas, mol._env,
auxmol._atm, auxmol._bas, auxmol._env)
ao_loc = gto.moleintor.make_loc(bas, int3c)
nao = ao_loc[mol.nbas]
if aosym == 's1':
nao_pair = nao * nao
else:
nao_pair = nao * (nao+1) // 2
cderi = numpy.empty((naux, nao_pair))
max_words = max_memory*.98e6/8 - low.size - cderi.size
# Divide by 3 because scipy.linalg.solve may create a temporary copy for
# ints and return another copy for results
buflen = min(max(int(max_words/naoaux/comp/3), 8), nao_pair)
shranges = _guess_shell_ranges(mol, buflen, aosym)
log.debug1('shranges = %s', shranges)
cintopt = gto.moleintor.make_cintopt(atm, bas, env, int3c)
bufs1 = numpy.empty((comp*max([x[2] for x in shranges]),naoaux))
bufs2 = numpy.empty_like(bufs1)
p1 = 0
for istep, sh_range in enumerate(shranges):
log.debug('int3c2e [%d/%d], AO [%d:%d], nrow = %d',
istep+1, len(shranges), *sh_range)
bstart, bend, nrow = sh_range
shls_slice = (bstart, bend, 0, mol.nbas, mol.nbas, mol.nbas+auxmol.nbas)
ints = gto.moleintor.getints3c(int3c, atm, bas, env, shls_slice, comp,
aosym, ao_loc, cintopt, out=bufs1)
if ints.ndim == 3 and ints.flags.f_contiguous:
ints = lib.transpose(ints.T, axes=(0,2,1), out=bufs2).reshape(naoaux,-1)
bufs1, bufs2 = bufs2, bufs1
else:
ints = ints.reshape((-1,naoaux)).T
p0, p1 = p1, p1 + nrow
if decompose_j2c == 'cd':
if ints.flags.c_contiguous:
ints = lib.transpose(ints, out=bufs2).T
bufs1, bufs2 = bufs2, bufs1
dat = scipy.linalg.solve_triangular(low, ints, lower=True,
overwrite_b=True, check_finite=False)
if dat.flags.f_contiguous:
dat = lib.transpose(dat.T, out=bufs2)
cderi[:,p0:p1] = dat
else:
dat = numpy.ndarray((naux, ints.shape[1]), buffer=bufs2)
cderi[:,p0:p1] = lib.dot(low, ints, c=dat)
dat = ints = None
log.timer('cholesky_eri', *t0)
return cderi
# Debug version of cholesky_eri. Note the temporary memory usage is about
# twice as large as the return cderi array
[docs]
def cholesky_eri_debug(mol, auxbasis='weigend+etb', auxmol=None,
int3c='int3c2e', aosym='s2ij', int2c='int2c2e', comp=1,
verbose=0, fauxe2=aux_e2):
'''
Returns:
2D array of (naux,nao*(nao+1)/2) in C-contiguous
'''
assert (comp == 1)
t0 = (logger.process_clock(), logger.perf_counter())
log = logger.new_logger(mol, verbose)
if auxmol is None:
auxmol = addons.make_auxmol(mol, auxbasis)
j2c = auxmol.intor(int2c, hermi=1)
naux = j2c.shape[0]
log.debug('size of aux basis %d', naux)
t1 = log.timer('2c2e', *t0)
j3c = fauxe2(mol, auxmol, intor=int3c, aosym=aosym).reshape(-1,naux)
t1 = log.timer('3c2e', *t1)
try:
low = scipy.linalg.cholesky(j2c, lower=True)
j2c = None
t1 = log.timer('Cholesky 2c2e', *t1)
cderi = scipy.linalg.solve_triangular(low, j3c.T, lower=True,
overwrite_b=True)
except scipy.linalg.LinAlgError:
w, v = scipy.linalg.eigh(j2c)
idx = w > LINEAR_DEP_THR
v = (v[:,idx] / numpy.sqrt(w[idx]))
cderi = lib.dot(v.conj().T, j3c.T)
j3c = None
if cderi.flags.f_contiguous:
cderi = lib.transpose(cderi.T)
log.timer('cholesky_eri', *t0)
return cderi
def _eig_decompose(dev, j2c, lindep=LINEAR_DEP_THR):
w, v = scipy.linalg.eigh(j2c)
mask = w > lindep
v = v[:,mask]
v /= numpy.sqrt(w[mask])
logger.debug(dev, 'cond = %.4g, drop %d bfns',
w[-1]/w[0], w.size-numpy.count_nonzero(mask))
return v.conj().T
if __name__ == '__main__':
from pyscf import scf
from pyscf import ao2mo
mol = gto.Mole()
mol.verbose = 0
mol.output = None
mol.atom.extend([
["H", (0, 0, 0 )],
["H", (0, 0, 1 )],
])
mol.basis = 'cc-pvdz'
mol.build()
auxmol = format_aux_basis(mol)
j3c = aux_e2(mol, auxmol, intor='int3c2e_sph', aosym='s1')
nao = mol.nao_nr()
naoaux = auxmol.nao_nr()
j3c = j3c.reshape(nao,nao,naoaux)
atm, bas, env = \
gto.mole.conc_env(mol._atm, mol._bas, mol._env,
auxmol._atm, auxmol._bas, auxmol._env)
eri0 = numpy.empty((nao,nao,naoaux))
pi = 0
for i in range(mol.nbas):
pj = 0
for j in range(mol.nbas):
pk = 0
for k in range(mol.nbas, mol.nbas+auxmol.nbas):
shls = (i, j, k)
buf = gto.moleintor.getints_by_shell('int3c2e_sph',
shls, atm, bas, env)
di, dj, dk = buf.shape
eri0[pi:pi+di,pj:pj+dj,pk:pk+dk] = buf
pk += dk
pj += dj
pi += di
print(numpy.allclose(eri0, j3c))
j2c = fill_2c2e(mol, auxmol)
eri0 = numpy.empty_like(j2c)
pi = 0
for i in range(mol.nbas, len(bas)):
pj = 0
for j in range(mol.nbas, len(bas)):
shls = (i, j)
buf = gto.moleintor.getints_by_shell('int2c2e_sph',
shls, atm, bas, env)
di, dj = buf.shape
eri0[pi:pi+di,pj:pj+dj] = buf
pj += dj
pi += di
print(numpy.allclose(eri0, j2c))
j3c = aux_e2(mol, auxmol, intor='int3c2e_sph', aosym='s2ij')
cderi = cholesky_eri(mol, auxmol=auxmol)
eri0 = numpy.einsum('pi,pk->ik', cderi, cderi)
eri1 = numpy.einsum('ik,kl->il', j3c, numpy.linalg.inv(j2c))
eri1 = numpy.einsum('ip,kp->ik', eri1, j3c)
print(abs(eri1 - eri0).max())
eri0 = ao2mo.restore(1, eri0, nao)
mf = scf.RHF(mol)
ehf0 = mf.scf()
nao = mf.mo_energy.size
eri1 = ao2mo.restore(1, mf._eri, nao)
print(abs(eri1-eri0).max() - 0.0022142583265513105)
mf._eri = ao2mo.restore(8, eri0, nao)
ehf1 = mf.scf()
mf = scf.RHF(mol).density_fit(auxbasis='weigend')
ehf2 = mf.scf()
mf = mf.density_fit(auxbasis='weigend')
ehf3 = mf.scf()
print(ehf0, ehf1, ehf2, ehf3)