#!/usr/bin/env python
# Copyright 2017-2021 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.
#
# Authors: James D. McClain <jmcclain@princeton.edu>
#
"""Module for running restricted closed-shell k-point ccsd(t)"""
import ctypes
import h5py
import numpy as np
import pyscf.pbc.cc.kccsd_rhf
from itertools import product
from pyscf import lib
from pyscf.cc import _ccsd
from pyscf.lib import logger
from pyscf.lib.parameters import LARGE_DENOM
from pyscf.pbc.lib import kpts_helper
from pyscf.pbc.mp.kmp2 import (get_frozen_mask, get_nocc, get_nmo,
padded_mo_coeff, padding_k_idx) # noqa
#einsum = np.einsum
einsum = lib.einsum
# CCSD(T) equations taken from Scuseria, JCP (94), 1991
#
# NOTE: As pointed out in cc/ccsd_t_slow.py, there is an error in this paper
# and the equation should read [ia] >= [jb] >= [kc] (since the only
# symmetry in spin-less operators is the exchange of a column of excitation
# ooperators).
[docs]
def kernel(mycc, eris, t1=None, t2=None, max_memory=2000, verbose=logger.INFO):
'''Returns the CCSD(T) for restricted closed-shell systems with k-points.
Note:
Returns real part of the CCSD(T) energy, raises warning if there is
a complex part.
Args:
mycc (:class:`RCCSD`): Coupled-cluster object storing results of
a coupled-cluster calculation.
eris (:class:`_ERIS`): Integral object holding the relevant electron-
repulsion integrals and Fock matrix elements
t1 (:obj:`ndarray`): t1 coupled-cluster amplitudes
t2 (:obj:`ndarray`): t2 coupled-cluster amplitudes
max_memory (float): Maximum memory used in calculation (NOT USED)
verbose (int, :class:`Logger`): verbosity of calculation
Returns:
energy_t (float): The real-part of the k-point CCSD(T) energy.
'''
assert isinstance(mycc, pyscf.pbc.cc.kccsd_rhf.RCCSD)
cpu1 = cpu0 = (logger.process_clock(), logger.perf_counter())
if isinstance(verbose, logger.Logger):
log = verbose
else:
log = logger.Logger(mycc.stdout, verbose)
if t1 is None: t1 = mycc.t1
if t2 is None: t2 = mycc.t2
if eris is None:
raise TypeError('Electron repulsion integrals, `eris`, must be passed in '
'to the CCSD(T) kernel or created in the cc object for '
'the k-point CCSD(T) to run!')
if t1 is None or t2 is None:
raise TypeError('Must pass in t1/t2 amplitudes to k-point CCSD(T)! (Maybe '
'need to run `.ccsd()` on the ccsd object?)')
cell = mycc._scf.cell
kpts = mycc.kpts
# The dtype of any local arrays that will be created
dtype = t1.dtype
nkpts, nocc, nvir = t1.shape
mo_energy_occ = [eris.mo_energy[ki][:nocc] for ki in range(nkpts)]
mo_energy_vir = [eris.mo_energy[ki][nocc:] for ki in range(nkpts)]
mo_energy = np.asarray([eris.mo_energy[ki] for ki in range(nkpts)],
dtype=np.double, order='C')
fov = eris.fock[:, :nocc, nocc:]
mo_e = mo_energy
mo_e_o = mo_energy_occ
mo_e_v = mo_energy_vir
# Set up class for k-point conservation
kconserv = kpts_helper.get_kconserv(cell, kpts)
# Create necessary temporary eris for fast read
feri_tmp, t2T, eris_vvop, eris_vooo_C = create_t3_eris(mycc, kconserv, [eris.vovv, eris.oovv, eris.ooov, t2])
t1T = np.array([x.T for x in t1], dtype=np.complex128, order='C')
fvo = np.array([x.T for x in fov], dtype=np.complex128, order='C')
cpu1 = log.timer_debug1('CCSD(T) tmp eri creation', *cpu1)
#def get_w_old(ki, kj, kk, ka, kb, kc, a0, a1, b0, b1, c0, c1, out=None):
# '''Wijkabc intermediate as described in Scuseria paper before Pijkabc acts'''
# km = kconserv[kc, kk, kb]
# kf = kconserv[kk, kc, kj]
# ret = einsum('kjcf,fiba->abcijk', t2[kk,kj,kc,:,:,c0:c1,:], eris.vovv[kf,ki,kb,:,:,b0:b1,a0:a1].conj())
# ret = ret - einsum('mkbc,jima->abcijk', t2[km,kk,kb,:,:,b0:b1,c0:c1], eris.ooov[kj,ki,km,:,:,:,a0:a1].conj())
# return ret
def get_w(ki, kj, kk, ka, kb, kc, a0, a1, b0, b1, c0, c1):
'''Wijkabc intermediate as described in Scuseria paper before Pijkabc acts
Uses tranposed eris for fast data access.'''
km = kconserv[kc, kk, kb]
kf = kconserv[kk, kc, kj]
out = einsum('cfjk,abif->abcijk', t2T[kc,kf,kj,c0:c1,:,:,:], eris_vvop[ka,kb,ki,a0:a1,b0:b1,:,nocc:])
out = out - einsum('cbmk,aijm->abcijk', t2T[kc,kb,km,c0:c1,b0:b1,:,:], eris_vooo_C[ka,ki,kj,a0:a1,:,:,:])
return out
def get_permuted_w(ki, kj, kk, ka, kb, kc, orb_indices):
'''Pijkabc operating on Wijkabc intermediate as described in Scuseria paper'''
a0, a1, b0, b1, c0, c1 = orb_indices
out = get_w(ki, kj, kk, ka, kb, kc, a0, a1, b0, b1, c0, c1)
out = out + get_w(kj, kk, ki, kb, kc, ka, b0, b1, c0, c1, a0, a1).transpose(2,0,1,5,3,4)
out = out + get_w(kk, ki, kj, kc, ka, kb, c0, c1, a0, a1, b0, b1).transpose(1,2,0,4,5,3)
out = out + get_w(ki, kk, kj, ka, kc, kb, a0, a1, c0, c1, b0, b1).transpose(0,2,1,3,5,4)
out = out + get_w(kk, kj, ki, kc, kb, ka, c0, c1, b0, b1, a0, a1).transpose(2,1,0,5,4,3)
out = out + get_w(kj, ki, kk, kb, ka, kc, b0, b1, a0, a1, c0, c1).transpose(1,0,2,4,3,5)
return out
def get_rw(ki, kj, kk, ka, kb, kc, orb_indices):
'''R operating on Wijkabc intermediate as described in Scuseria paper'''
a0, a1, b0, b1, c0, c1 = orb_indices
ret = (4. * get_permuted_w(ki,kj,kk,ka,kb,kc,orb_indices) +
1. * get_permuted_w(kj,kk,ki,ka,kb,kc,orb_indices).transpose(0,1,2,5,3,4) +
1. * get_permuted_w(kk,ki,kj,ka,kb,kc,orb_indices).transpose(0,1,2,4,5,3) -
2. * get_permuted_w(ki,kk,kj,ka,kb,kc,orb_indices).transpose(0,1,2,3,5,4) -
2. * get_permuted_w(kk,kj,ki,ka,kb,kc,orb_indices).transpose(0,1,2,5,4,3) -
2. * get_permuted_w(kj,ki,kk,ka,kb,kc,orb_indices).transpose(0,1,2,4,3,5))
return ret
#def get_v_old(ki, kj, kk, ka, kb, kc, a0, a1, b0, b1, c0, c1):
# '''Vijkabc intermediate as described in Scuseria paper'''
# km = kconserv[ki,ka,kj]
# kf = kconserv[ki,ka,kj]
# out = np.zeros((a1-a0,b1-b0,c1-c0) + (nocc,)*3, dtype=dtype)
# if kk == kc:
# out = out + einsum('kc,ijab->abcijk', 0.5*t1[kk,:,c0:c1], eris.oovv[ki,kj,ka,:,:,a0:a1,b0:b1].conj())
# out = out + einsum('kc,ijab->abcijk', 0.5*fov[kk,:,c0:c1], t2[ki,kj,ka,:,:,a0:a1,b0:b1])
# return out
def get_v(ki, kj, kk, ka, kb, kc, a0, a1, b0, b1, c0, c1):
'''Vijkabc intermediate as described in Scuseria paper'''
#km = kconserv[ki,ka,kj]
#kf = kconserv[ki,ka,kj]
out = np.zeros((a1-a0,b1-b0,c1-c0) + (nocc,)*3, dtype=dtype)
if kk == kc:
out = out + einsum('ck,baji->abcijk', 0.5*t1T[kk,c0:c1,:], eris_vvop[kb,ka,kj,b0:b1,a0:a1,:,:nocc])
# We see this is the same t2T term needed for the `w` contraction:
# einsum('cbmk,aijm->abcijk', t2T[kc,kb,km,c0:c1,b0:b1], eris_vooo_C[ka,ki,kj,a0:a1])
#
# For the kpoint indices [kk,ki,kj,kc,ka,kb] we have that we need
# t2T[kb,ka,km], where km = kconserv[kb,kj,ka]
# The remaining k-point not used in t2T, i.e. kc, has the condition kc == kk in the case of
# get_v. So, we have from 3-particle conservation
# (kk-kc) + ki + kj - ka - kb = 0,
# i.e. ki = km.
out = out + einsum('ck,baij->abcijk', 0.5*fvo[kk,c0:c1,:], t2T[kb,ka,ki,b0:b1,a0:a1,:,:])
return out
def get_permuted_v(ki, kj, kk, ka, kb, kc, orb_indices):
'''Pijkabc operating on Vijkabc intermediate as described in Scuseria paper'''
a0, a1, b0, b1, c0, c1 = orb_indices
ret = get_v(ki, kj, kk, ka, kb, kc, a0, a1, b0, b1, c0, c1)
ret = ret + get_v(kj, kk, ki, kb, kc, ka, b0, b1, c0, c1, a0, a1).transpose(2,0,1,5,3,4)
ret = ret + get_v(kk, ki, kj, kc, ka, kb, c0, c1, a0, a1, b0, b1).transpose(1,2,0,4,5,3)
ret = ret + get_v(ki, kk, kj, ka, kc, kb, a0, a1, c0, c1, b0, b1).transpose(0,2,1,3,5,4)
ret = ret + get_v(kk, kj, ki, kc, kb, ka, c0, c1, b0, b1, a0, a1).transpose(2,1,0,5,4,3)
ret = ret + get_v(kj, ki, kk, kb, ka, kc, b0, b1, a0, a1, c0, c1).transpose(1,0,2,4,3,5)
return ret
def contract_t3Tv(kpt_indices, orb_indices, data):
'''Calculate t3T(ransposed) array using C driver.'''
ki, kj, kk, ka, kb, kc = kpt_indices
a0, a1, b0, b1, c0, c1 = orb_indices
slices = np.array([a0, a1, b0, b1, c0, c1], dtype=np.int32)
mo_offset = np.array([ki,kj,kk,ka,kb,kc], dtype=np.int32)
vvop_ab = np.asarray(data[0][0], dtype=np.complex128, order='C')
vvop_ac = np.asarray(data[0][1], dtype=np.complex128, order='C')
vvop_ba = np.asarray(data[0][2], dtype=np.complex128, order='C')
vvop_bc = np.asarray(data[0][3], dtype=np.complex128, order='C')
vvop_ca = np.asarray(data[0][4], dtype=np.complex128, order='C')
vvop_cb = np.asarray(data[0][5], dtype=np.complex128, order='C')
vooo_aj = np.asarray(data[1][0], dtype=np.complex128, order='C')
vooo_ak = np.asarray(data[1][1], dtype=np.complex128, order='C')
vooo_bi = np.asarray(data[1][2], dtype=np.complex128, order='C')
vooo_bk = np.asarray(data[1][3], dtype=np.complex128, order='C')
vooo_ci = np.asarray(data[1][4], dtype=np.complex128, order='C')
vooo_cj = np.asarray(data[1][5], dtype=np.complex128, order='C')
t2T_cj = np.asarray(data[2][0], dtype=np.complex128, order='C')
t2T_bk = np.asarray(data[2][1], dtype=np.complex128, order='C')
t2T_ci = np.asarray(data[2][2], dtype=np.complex128, order='C')
t2T_ak = np.asarray(data[2][3], dtype=np.complex128, order='C')
t2T_bi = np.asarray(data[2][4], dtype=np.complex128, order='C')
t2T_aj = np.asarray(data[2][5], dtype=np.complex128, order='C')
t2T_cb = np.asarray(data[3][0], dtype=np.complex128, order='C')
t2T_bc = np.asarray(data[3][1], dtype=np.complex128, order='C')
t2T_ca = np.asarray(data[3][2], dtype=np.complex128, order='C')
t2T_ac = np.asarray(data[3][3], dtype=np.complex128, order='C')
t2T_ba = np.asarray(data[3][4], dtype=np.complex128, order='C')
t2T_ab = np.asarray(data[3][5], dtype=np.complex128, order='C')
data = [vvop_ab, vvop_ac, vvop_ba, vvop_bc, vvop_ca, vvop_cb,
vooo_aj, vooo_ak, vooo_bi, vooo_bk, vooo_ci, vooo_cj,
t2T_cj, t2T_cb, t2T_bk, t2T_bc, t2T_ci, t2T_ca, t2T_ak,
t2T_ac, t2T_bi, t2T_ba, t2T_aj, t2T_ab]
data_ptrs = [x.ctypes.data_as(ctypes.c_void_p) for x in data]
data_ptrs = (ctypes.c_void_p*24)(*data_ptrs)
a0, a1, b0, b1, c0, c1 = task
t3Tw = np.empty((a1-a0,b1-b0,c1-c0) + (nocc,)*3, dtype=np.complex128, order='C')
t3Tv = np.empty((a1-a0,b1-b0,c1-c0) + (nocc,)*3, dtype=np.complex128, order='C')
drv = _ccsd.libcc.CCsd_zcontract_t3T
drv(t3Tw.ctypes.data_as(ctypes.c_void_p),
t3Tv.ctypes.data_as(ctypes.c_void_p),
mo_e.ctypes.data_as(ctypes.c_void_p),
t1T.ctypes.data_as(ctypes.c_void_p),
fvo.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(nocc), ctypes.c_int(nvir),
ctypes.c_int(nkpts),
mo_offset.ctypes.data_as(ctypes.c_void_p),
slices.ctypes.data_as(ctypes.c_void_p),
data_ptrs)
return t3Tw, t3Tv
def get_data(kpt_indices):
idx_args = get_data_slices(kpt_indices, task, kconserv)
vvop_indices, vooo_indices, t2T_vvop_indices, t2T_vooo_indices = idx_args
vvop_data = [eris_vvop[tuple(x)] for x in vvop_indices]
vooo_data = [eris_vooo_C[tuple(x)] for x in vooo_indices]
t2T_vvop_data = [t2T[tuple(x)] for x in t2T_vvop_indices]
t2T_vooo_data = [t2T[tuple(x)] for x in t2T_vooo_indices]
data = [vvop_data, vooo_data, t2T_vvop_data, t2T_vooo_data]
return data
energy_t = 0.0
# Get location of padded elements in occupied and virtual space
nonzero_opadding, nonzero_vpadding = padding_k_idx(mycc, kind="split")
mem_now = lib.current_memory()[0]
max_memory = max(0, mycc.max_memory - mem_now)
blkmin = 4
# temporary t3 array is size: 2 * nkpts**3 * blksize**3 * nocc**3 * 16
vir_blksize = min(nvir, max(blkmin, int((max_memory*.9e6/16/nocc**3/nkpts**3/2)**(1./3))))
tasks = []
log.debug('max_memory %d MB (%d MB in use)', max_memory, mem_now)
log.debug('virtual blksize = %d (nvir = %d)', nvir, vir_blksize)
for a0, a1 in lib.prange(0, nvir, vir_blksize):
for b0, b1 in lib.prange(0, nvir, vir_blksize):
for c0, c1 in lib.prange(0, nvir, vir_blksize):
tasks.append((a0,a1,b0,b1,c0,c1))
for ka in range(nkpts):
for kb in range(ka+1):
for task_id, task in enumerate(tasks):
a0,a1,b0,b1,c0,c1 = task
my_permuted_w = np.zeros((nkpts,)*3 + (a1-a0,b1-b0,c1-c0) + (nocc,)*3, dtype=dtype)
my_permuted_v = np.zeros((nkpts,)*3 + (a1-a0,b1-b0,c1-c0) + (nocc,)*3, dtype=dtype)
for ki, kj, kk in product(range(nkpts), repeat=3):
# Find momentum conservation condition for triples
# amplitude t3ijkabc
kc = kpts_helper.get_kconserv3(cell, kpts, [ki, kj, kk, ka, kb])
if not (ka >= kb and kb >= kc):
continue
kpt_indices = [ki,kj,kk,ka,kb,kc]
data = get_data(kpt_indices)
t3Tw, t3Tv = contract_t3Tv(kpt_indices, task, data)
my_permuted_w[ki,kj,kk] = t3Tw
my_permuted_v[ki,kj,kk] = t3Tv
#my_permuted_w[ki,kj,kk] = get_permuted_w(ki,kj,kk,ka,kb,kc,task)
#my_permuted_v[ki,kj,kk] = get_permuted_v(ki,kj,kk,ka,kb,kc,task)
for ki, kj, kk in product(range(nkpts), repeat=3):
# eigenvalue denominator: e(i) + e(j) + e(k)
eijk = _get_epqr([0,nocc,ki,mo_e_o,nonzero_opadding],
[0,nocc,kj,mo_e_o,nonzero_opadding],
[0,nocc,kk,mo_e_o,nonzero_opadding])
# Find momentum conservation condition for triples
# amplitude t3ijkabc
kc = kpts_helper.get_kconserv3(cell, kpts, [ki, kj, kk, ka, kb])
if not (ka >= kb and kb >= kc):
continue
if ka == kb and kb == kc:
symm_kpt = 1.
elif ka == kb or kb == kc:
symm_kpt = 3.
else:
symm_kpt = 6.
eabc = _get_epqr([a0,a1,ka,mo_e_v,nonzero_vpadding],
[b0,b1,kb,mo_e_v,nonzero_vpadding],
[c0,c1,kc,mo_e_v,nonzero_vpadding],
fac=[-1.,-1.,-1.])
eijkabc = (eijk[None,None,None,:,:,:] + eabc[:,:,:,None,None,None])
pwijk = my_permuted_w[ki,kj,kk] + my_permuted_v[ki,kj,kk]
rwijk = (4. * my_permuted_w[ki,kj,kk] +
1. * my_permuted_w[kj,kk,ki].transpose(0,1,2,5,3,4) +
1. * my_permuted_w[kk,ki,kj].transpose(0,1,2,4,5,3) -
2. * my_permuted_w[ki,kk,kj].transpose(0,1,2,3,5,4) -
2. * my_permuted_w[kk,kj,ki].transpose(0,1,2,5,4,3) -
2. * my_permuted_w[kj,ki,kk].transpose(0,1,2,4,3,5))
rwijk = rwijk / eijkabc
energy_t += symm_kpt * einsum('abcijk,abcijk', rwijk, pwijk.conj())
energy_t *= (1. / 3)
energy_t /= nkpts
if abs(energy_t.imag) > 1e-4:
log.warn('Non-zero imaginary part of CCSD(T) energy was found %s', energy_t.imag)
log.timer('CCSD(T)', *cpu0)
log.note('CCSD(T) correction per cell = %.15g', energy_t.real)
log.note('CCSD(T) correction per cell (imag) = %.15g', energy_t.imag)
return energy_t.real
###################################
# Helper function for t3 creation
###################################
[docs]
def check_read_success(filename, **kwargs):
'''Determine criterion for successfully reading a dataset based on its
meta values.
For now, returns False.'''
def check_write_complete(filename, **kwargs):
'''Check for `completed` attr in file.'''
import os
mode = kwargs.get('mode', 'r')
if not os.path.isfile(filename):
return False
f = h5py.File(filename, mode=mode, **kwargs)
return f.attrs.get('completed', False)
write_complete = check_write_complete(filename, **kwargs)
return False and write_complete
[docs]
def transpose_t2(t2, nkpts, nocc, nvir, kconserv, out=None):
'''Creates t2.transpose(2,3,1,0).'''
if out is None:
out = np.empty((nkpts,nkpts,nkpts,nvir,nvir,nocc,nocc), dtype=t2.dtype)
# Check if it's stored in lower triangular form
if len(t2.shape) == 7 and t2.shape[:2] == (nkpts, nkpts):
for ki, kj, ka in product(range(nkpts), repeat=3):
kb = kconserv[ki,ka,kj]
out[ka,kb,kj] = t2[ki,kj,ka].transpose(2,3,1,0)
elif len(t2.shape) == 6 and t2.shape[:2] == (nkpts*(nkpts+1)//2, nkpts):
for ki, kj, ka in product(range(nkpts), repeat=3):
kb = kconserv[ki,ka,kj]
# t2[ki,kj,ka] = t2[tril_index(ki,kj),ka] ki<kj
# t2[kj,ki,kb] = t2[ki,kj,ka].transpose(1,0,3,2) ki<kj
# = t2[tril_index(ki,kj),ka].transpose(1,0,3,2)
if ki <= kj:
tril_idx = (kj*(kj+1))//2 + ki
out[ka,kb,kj] = t2[tril_idx,ka].transpose(2,3,1,0).copy()
out[kb,ka,ki] = out[ka,kb,kj].transpose(1,0,3,2)
else:
raise ValueError('No known conversion for t2 shape %s' % t2.shape)
return out
[docs]
def create_eris_vvop(vovv, oovv, nkpts, nocc, nvir, kconserv, out=None):
'''Creates vvop from vovv and oovv array (physicist notation).'''
nmo = nocc + nvir
assert (vovv.shape == (nkpts,nkpts,nkpts,nvir,nocc,nvir,nvir))
if out is None:
out = np.empty((nkpts,nkpts,nkpts,nvir,nvir,nocc,nmo), dtype=vovv.dtype)
else:
assert (out.shape == (nkpts,nkpts,nkpts,nvir,nvir,nocc,nmo))
for ki, kj, ka in product(range(nkpts), repeat=3):
kb = kconserv[ki,ka,kj]
out[ki,kj,ka,:,:,:,nocc:] = vovv[kb,ka,kj].conj().transpose(3,2,1,0)
if oovv is not None:
out[ki,kj,ka,:,:,:,:nocc] = oovv[kb,ka,kj].conj().transpose(3,2,1,0)
return out
[docs]
def create_eris_vooo(ooov, nkpts, nocc, nvir, kconserv, out=None):
'''Creates vooo from ooov array.
This is not exactly chemist's notation, but close. Here a chemist notation vooo
is created from physicist ooov, and then the last two indices of vooo are swapped.
'''
assert (ooov.shape == (nkpts,nkpts,nkpts,nocc,nocc,nocc,nvir))
if out is None:
out = np.empty((nkpts,nkpts,nkpts,nvir,nocc,nocc,nocc), dtype=ooov.dtype)
for ki, kj, ka in product(range(nkpts), repeat=3):
kb = kconserv[ki,kj,ka]
# <bj|ai> -> (ba|ji) (Physicist->Chemist)
# (ij|ab) = (ba|ij)* (Permutational symmetry)
# out = (ij|ab).transpose(0,1,3,2)
out[ki,kj,kb] = ooov[kb,kj,ka].conj().transpose(3,1,0,2)
return out
[docs]
def create_t3_eris(mycc, kconserv, eris, tmpfile='tmp_t3_eris.h5'):
'''Create/transpose necessary eri integrals needed for fast read-in by CCSD(T).'''
eris_vovv, eris_oovv, eris_ooov, t2 = eris
nkpts = mycc.nkpts
nocc = mycc.nocc
nmo = mycc.nmo
nvir = nmo - nocc
nmo = nocc + nvir
feri_tmp = None
h5py_kwargs = {}
feri_tmp_filename = tmpfile
dtype = np.result_type(eris_vovv, eris_oovv, eris_ooov, t2)
if not check_read_success(feri_tmp_filename):
feri_tmp = lib.H5TmpFile(feri_tmp_filename, 'w', **h5py_kwargs)
t2T_out = feri_tmp.create_dataset('t2T', (nkpts,nkpts,nkpts,nvir,nvir,nocc,nocc), dtype=dtype) # noqa: E501
eris_vvop_out = feri_tmp.create_dataset('vvop', (nkpts,nkpts,nkpts,nvir,nvir,nocc,nmo), dtype=dtype) # noqa: E501
eris_vooo_C_out = feri_tmp.create_dataset('vooo_C', (nkpts,nkpts,nkpts,nvir,nocc,nocc,nocc), dtype=dtype) # noqa: E501
transpose_t2(t2, nkpts, nocc, nvir, kconserv, out=t2T_out)
create_eris_vvop(eris_vovv, eris_oovv, nkpts, nocc, nvir, kconserv, out=eris_vvop_out)
create_eris_vooo(eris_ooov, nkpts, nocc, nvir, kconserv, out=eris_vooo_C_out)
feri_tmp.attrs['completed'] = True
feri_tmp.close()
feri_tmp = lib.H5TmpFile(feri_tmp_filename, 'r', **h5py_kwargs)
t2T = feri_tmp['t2T']
eris_vvop = feri_tmp['vvop']
eris_vooo_C = feri_tmp['vooo_C']
mem_now = lib.current_memory()[0]
max_memory = max(0, mycc.max_memory - mem_now)
unit = nkpts**3 * (nvir**2 * nocc**2 + nvir**2 * nmo * nocc + nvir * nocc**3)
if (unit*16 < max_memory): # Store all in memory
t2T = t2T[:]
eris_vvop = eris_vvop[:]
eris_vooo_C = eris_vooo_C[:]
return feri_tmp, t2T, eris_vvop, eris_vooo_C
def _convert_to_int(kpt_indices):
'''Convert all kpoint indices for 3-particle operator to integers.'''
out_indices = [0]*6
for ix, x in enumerate(kpt_indices):
assert isinstance(x, (int, np.integer, np.ndarray, list))
if isinstance(x, (np.ndarray)) and (x.ndim == 0):
out_indices[ix] = int(x)
else:
out_indices[ix] = x
return out_indices
def _tile_list(kpt_indices):
'''Similar to a cartesian product but for a list of kpoint indices for
a 3-particle operator.'''
max_length = 0
out_indices = [0]*6
for ix, x in enumerate(kpt_indices):
if hasattr(x, '__len__'):
max_length = max(max_length, len(x))
if max_length == 0:
return kpt_indices
else:
for ix, x in enumerate(kpt_indices):
if isinstance(x, (int, np.integer)):
out_indices[ix] = [x] * max_length
else:
out_indices[ix] = x
return map(list, zip(*out_indices))
[docs]
def zip_kpoints(kpt_indices):
'''Similar to a cartesian product but for a list of kpoint indices for
a 3-particle operator. Ensures all indices are integers.'''
out_indices = _convert_to_int(kpt_indices)
out_indices = _tile_list(out_indices)
return out_indices
[docs]
def get_data_slices(kpt_indices, orb_indices, kconserv):
kpt_indices = zip_kpoints(kpt_indices)
if isinstance(kpt_indices[0], (int, np.integer)): # Ensure we are working
kpt_indices = [kpt_indices] # with a list of lists
a0,a1,b0,b1,c0,c1 = orb_indices
length = len(kpt_indices)*6
def _vijk_indices(kpt_indices, orb_indices, transpose=(0, 1, 2)):
'''Get indices needed for t3 construction and a given transpose of (a,b,c).'''
kpt_indices = ([kpt_indices[x] for x in transpose] +
[kpt_indices[x+3] for x in transpose])
orb_indices = lib.flatten([[orb_indices[2*x], orb_indices[2*x+1]]
for x in transpose])
ki, kj, kk, ka, kb, kc = kpt_indices
a0, a1, b0, b1, c0, c1 = orb_indices
kf = kconserv[ka,ki,kb]
km = kconserv[kc,kk,kb]
sl00 = slice(None, None)
vvop_idx = [ka, kb, ki, slice(a0,a1), slice(b0,b1), sl00, sl00]
vooo_idx = [ka, ki, kj, slice(a0,a1), sl00, sl00, sl00]
t2T_vvop_idx = [kc, kf, kj, slice(c0,c1), sl00, sl00, sl00]
t2T_vooo_idx = [kc, kb, km, slice(c0,c1), sl00, sl00, sl00]
return vvop_idx, vooo_idx, t2T_vvop_idx, t2T_vooo_idx
vvop_indices = [0] * length
vooo_indices = [0] * length
t2T_vvop_indices = [0] * length
t2T_vooo_indices = [0] * length
transpose = [(0, 1, 2), (0, 2, 1), (1, 0, 2),
(1, 2, 0), (2, 0, 1), (2, 1, 0)]
count = 0
for kpt in kpt_indices:
for t in transpose:
vvop_idx, vooo_idx, t2T_vvop_idx, t2T_vooo_idx = _vijk_indices(kpt, orb_indices, t)
vvop_indices[count] = vvop_idx
vooo_indices[count] = vooo_idx
t2T_vvop_indices[count] = t2T_vvop_idx
t2T_vooo_indices[count] = t2T_vooo_idx
count += 1
return vvop_indices, vooo_indices, t2T_vvop_indices, t2T_vooo_indices
def _get_epqr(pindices,qindices,rindices,fac=[1.0,1.0,1.0],large_num=LARGE_DENOM):
'''Create a denominator
fac[0]*e[kp,p0:p1] + fac[1]*e[kq,q0:q1] + fac[2]*e[kr,r0:r1]
where padded elements have been replaced by a large number.
Args:
pindices (5-list of object):
A list of p0, p1, kp, orbital values, and non-zero indices for the first
denominator element.
qindices (5-list of object):
A list of q0, q1, kq, orbital values, and non-zero indices for the second
denominator element.
rindices (5-list of object):
A list of r0, r1, kr, orbital values, and non-zero indices for the third
denominator element.
fac (3-list of float):
Factors to multiply the first and second denominator elements.
large_num (float):
Number to replace the padded elements.
'''
def get_idx(x0,x1,kx,n0_p):
return np.logical_and(n0_p[kx] >= x0, n0_p[kx] < x1)
assert (all([len(x) == 5 for x in [pindices,qindices]]))
p0,p1,kp,mo_e_p,nonzero_p = pindices
q0,q1,kq,mo_e_q,nonzero_q = qindices
r0,r1,kr,mo_e_r,nonzero_r = rindices
fac_p, fac_q, fac_r = fac
epqr = large_num * np.ones((p1-p0,q1-q0,r1-r0), dtype=mo_e_p[0].dtype)
idxp = get_idx(p0,p1,kp,nonzero_p)
idxq = get_idx(q0,q1,kq,nonzero_q)
idxr = get_idx(r0,r1,kr,nonzero_r)
n0_ovp_pqr = np.ix_(nonzero_p[kp][idxp]-p0, nonzero_q[kq][idxq]-q0, nonzero_r[kr][idxr]-r0)
epqr[n0_ovp_pqr] = lib.direct_sum('p,q,r->pqr', fac_p*mo_e_p[kp][p0:p1],
fac_q*mo_e_q[kq][q0:q1],
fac_r*mo_e_r[kr][r0:r1])[n0_ovp_pqr]
#epqr[n0_ovp_pqr] = temp[n0_ovp_pqr]
return epqr
if __name__ == '__main__':
from pyscf.pbc import gto
from pyscf.pbc import scf
from pyscf.pbc import cc
cell = gto.Cell()
cell.atom = '''
C 0.000000000000 0.000000000000 0.000000000000
C 1.685068664391 1.685068664391 1.685068664391
'''
cell.basis = 'gth-szv'
cell.pseudo = 'gth-pade'
cell.a = '''
0.000000000, 3.370137329, 3.370137329
3.370137329, 0.000000000, 3.370137329
3.370137329, 3.370137329, 0.000000000'''
cell.unit = 'B'
cell.verbose = 4
cell.mesh = [24, 24, 24]
cell.build()
nmp = [1,1,4]
kpts = cell.make_kpts(nmp)
kpts -= kpts[0]
kmf = scf.KRHF(cell, kpts=kpts, exxdiv=None)
kmf.conv_tol = 1e-12
kmf.conv_tol_grad = 1e-12
kmf.direct_scf_tol = 1e-16
ehf = kmf.kernel()
mycc = cc.KRCCSD(kmf)
eris = mycc.ao2mo()
ecc, t1, t2 = mycc.kernel(eris=eris)
energy_t = kernel(mycc, eris=eris, verbose=9)
# Start of supercell calculations
from pyscf.pbc.tools.pbc import super_cell
supcell = super_cell(cell, nmp)
supcell.build()
kmf = scf.RHF(supcell, exxdiv=None)
kmf.conv_tol = 1e-12
kmf.conv_tol_grad = 1e-12
kmf.direct_scf_tol = 1e-16
sup_ehf = kmf.kernel()
myscc = cc.RCCSD(kmf)
eris = myscc.ao2mo()
sup_ecc, t1, t2 = myscc.kernel(eris=eris)
sup_energy_t = myscc.ccsd_t(eris=eris)
print("Kpoint CCSD: %20.16f" % ecc)
print("Supercell CCSD: %20.16f" % (sup_ecc/np.prod(nmp)))
print("Kpoint CCSD(T): %20.16f" % energy_t)
print("Supercell CCSD(T): %20.16f" % (sup_energy_t/np.prod(nmp)))