# 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: Oliver J. Backhouse <olbackhouse@gmail.com>
# George H. Booth <george.booth@kcl.ac.uk>
#
'''
Functions to support chkfiles with MPI
'''
import numpy as np
import h5py
from pyscf import lib
from pyscf.lib import logger
from pyscf import __config__
from pyscf import gto
from pyscf.lib import chkfile as chkutil
from pyscf.agf2 import mpi_helper
from pyscf.agf2.aux_space import GreensFunction, SelfEnergy
[docs]
def load(chkfile, key):
''' Load array(s) from chkfile.
See pyscf.lib.chkfile
'''
if mpi_helper.rank == 0:
vals = chkutil.load(chkfile, key)
else:
vals = None
mpi_helper.barrier()
vals = mpi_helper.bcast_dict(vals)
return vals
[docs]
def load_mol(chkfile):
''' Load the mol from the chkfile.
See pyscf.lib.chkfile
'''
if mpi_helper.rank == 0:
mol = chkutil.load_mol(chkfile)
dumps = mol.dumps()
else:
dumps = None
mpi_helper.barrier()
dumps = mpi_helper.bcast_dict(dumps)
mol = gto.loads(dumps)
return mol
[docs]
def load_agf2(chkfile):
''' Load the AGF2 data from the chkfile.
'''
if mpi_helper.rank == 0:
dic = chkutil.load(chkfile, 'agf2')
else:
dic = None
mpi_helper.barrier()
dic = mpi_helper.bcast_dict(dic)
if 'gf' in dic:
gf = dic['gf']
dic['gf'] = GreensFunction(gf['energy'], gf['coupling'], chempot=gf['chempot'])
elif 'gfa' in dic:
gfa, gfb = dic['gfa'], dic['gfb']
dic['gf'] = (GreensFunction(gfa['energy'], gfa['coupling'], chempot=gfa['chempot']),
GreensFunction(gfb['energy'], gfb['coupling'], chempot=gfb['chempot']))
del (dic['gfa'], dic['gfb'])
if 'se' in dic:
se = dic['se']
dic['se'] = SelfEnergy(se['energy'], se['coupling'], chempot=se['chempot'])
elif 'sea' in dic:
sea, seb = dic['sea'], dic['seb']
dic['se'] = (SelfEnergy(sea['energy'], sea['coupling'], chempot=sea['chempot']),
SelfEnergy(seb['energy'], seb['coupling'], chempot=seb['chempot']))
del (dic['sea'], dic['seb'])
if 'ngf' in dic:
dic['nmom'] = (dic.get('ngf', None), dic.get('nse', None))
del (dic['ngf'], dic['nse'])
if 'frozena' in dic:
dic['frozen'] = (dic['frozena'], dic['frozenb'])
del (dic['frozena'], dic['frozenb'])
return load_mol(chkfile), dic
[docs]
def dump_agf2(agf2, chkfile=None, key='agf2',
gf=None, se=None, frozen=None, nmom=None,
mo_energy=None, mo_coeff=None, mo_occ=None):
''' Save the AGF2 calculatuion to a chkfile.
'''
if mpi_helper.rank != 0:
# only dump on root process
return agf2
if chkfile is None: chkfile = agf2.chkfile
if gf is None: gf = agf2.gf
if se is None: se = agf2.se
if frozen is None: frozen = agf2.frozen
if mo_energy is None: mo_energy = agf2.mo_energy
if mo_coeff is None: mo_coeff = agf2.mo_coeff
if mo_occ is None: mo_occ = agf2.mo_occ
if isinstance(gf, (tuple, list)):
if frozen is not None:
if isinstance(frozen, int) or isinstance(frozen[0], int):
frozen = [frozen, frozen]
if h5py.is_hdf5(chkfile):
fh5 = h5py.File(chkfile, 'a')
if key in fh5:
del (fh5[key])
else:
fh5 = h5py.File(chkfile, 'w')
if 'mol' not in fh5:
fh5['mol'] = agf2.mol.dumps()
def store(subkey, val):
if val is not None:
fh5[key+'/'+subkey] = val
store('e_1b', agf2.e_1b)
store('e_2b', agf2.e_2b)
store('e_init', agf2.e_init)
store('converged', agf2.converged)
store('mo_energy', mo_energy)
store('mo_coeff', mo_coeff)
store('mo_occ', mo_occ)
store('_nmo', agf2._nmo)
store('_nocc', agf2._nocc)
if gf is not None:
if isinstance(gf, (tuple, list)):
store('gfa/energy', gf[0].energy)
store('gfa/coupling', gf[0].coupling)
store('gfa/chempot', gf[0].chempot)
store('gfb/energy', gf[1].energy)
store('gfb/coupling', gf[1].coupling)
store('gfb/chempot', gf[1].chempot)
if frozen is not None:
store('frozena', frozen[0])
store('frozenb', frozen[1])
else:
store('gf/energy', gf.energy)
store('gf/coupling', gf.coupling)
store('gf/chempot', gf.chempot)
store('frozen', frozen)
if se is not None:
if isinstance(se, (tuple, list)):
store('sea/energy', se[0].energy)
store('sea/coupling', se[0].coupling)
store('sea/chempot', se[0].chempot)
store('seb/energy', se[1].energy)
store('seb/coupling', se[1].coupling)
store('seb/chempot', se[1].chempot)
else:
store('se/energy', se.energy)
store('se/coupling', se.coupling)
store('se/chempot', se.chempot)
if getattr(agf2, 'nmom', None) is not None:
if nmom is None:
nmom = agf2.nmom
ngf, nse = nmom
store('ngf', ngf)
store('nse', nse)
fh5.close()
return agf2