def get_k(mol_or_mf, dm, hermi=1):
if isinstance(mol_or_mf, gto.mole.Mole):
mf = hf.SCF(mol_or_mf).view(SCF)
else:
mf = mol_or_mf
# dm may be too big for mpi4py library to serialize. Broadcast dm here.
if any(comm.allgather(isinstance(dm, str) and dm == 'SKIPPED_ARG')):
dm = mpi.bcast_tagged_array(dm)
mf.unpack_(comm.bcast(mf.pack()))
if mf.opt is None:
mf.opt = mf.init_direct_scf()
with lib.temporary_env(mf.opt._this.contents,
fprescreen=_vhf._fpointer('CVHFnrs8_vk_prescreen')):
vk = _eval_jk(mf, dm, hermi, _vk_jobs_s8)
return vk.reshape(dm.shape)
def get_k(mol_or_mf=None, dm=None, hermi=1, omega=None):
if isinstance(mol_or_mf, gto.mole.Mole):
mf = hf.SCF(mol_or_mf).view(SCF)
else:
mf = mol_or_mf
# dm may be too big for mpi4py library to serialize. Broadcast dm here.
if any(comm.allgather(dm is mpi.Message.SkippedArg)):
dm = mpi.bcast_tagged_array(dm)
mf.unpack_(comm.bcast(mf.pack()))
if mf.opt is None:
mf.opt = mf.init_direct_scf()
with lib.temporary_env(mf.opt._this.contents,
fprescreen=_vhf._fpointer('CVHFnrs8_vk_prescreen')):
if omega is None:
vk = _eval_jk(mf, dm, hermi, _vk_jobs_s8)
else:
with mf.mol.with_range_coulomb(omega):
vk = _eval_jk(mf, dm, hermi, _vk_jobs_s8)
return vk.reshape(dm.shape)
def get_jk(mol_or_mf, dm, hermi=1):
'''MPI version of scf.hf.get_jk function'''
#vj = get_j(mol_or_mf, dm, hermi)
#vk = get_k(mol_or_mf, dm, hermi)
if isinstance(mol_or_mf, gto.mole.Mole):
mf = hf.SCF(mol_or_mf).view(SCF)
else:
mf = mol_or_mf
# dm may be too big for mpi4py library to serialize. Broadcast dm here.
if any(comm.allgather(isinstance(dm, str) and dm == 'SKIPPED_ARG')):
dm = mpi.bcast_tagged_array(dm)
mf.unpack_(comm.bcast(mf.pack()))
if mf.opt is None:
mf.opt = mf.init_direct_scf()
vj, vk = _eval_jk(mf, dm, hermi, _jk_jobs_s8)
if rank == 0:
for i in range(vj.shape[0]):
lib.hermi_triu(vj[i], 1, inplace=True)
return vj.reshape(dm.shape), vk.reshape(dm.shape)
def __init__(self, **kw):
"""
Constructor a self-consistent field
"""
self.perform_scf = kw['perform_scf'] if 'perform_scf' in kw else False
self.kmat_algo = kw['kmat_algo'] if 'kmat_algo' in kw else None
self.kmat_timing = 0.0 if 'kmat_timing' in kw else None
for x in ['xc_code', 'dealloc_hsx', 'dtype']:
kw.pop(x, None)
tddft_iter.__init__(self,
dtype=np.float64,
xc_code='RPA',
dealloc_hsx=False,
**kw)
#print(__name__, ' dtype ', self.dtype)
self.xc_code_kernel = copy(self.xc_code)
self.xc_code = self.xc_code_mf
self.dm_mf = self.make_rdm1(
) # necessary to get_hcore(...) in case of pp starting point
if self.gen_pb:
self.hkernel_den = pack2den_u(self.kernel)
if self.nspin == 1:
self.pyscf_scf = hf.SCF(self)
else:
self.pyscf_scf = uhf.UHF(self)
self.pyscf_scf.direct_scf = False # overriding the attributes from hf.SCF ...
self.pyscf_scf.get_hcore = self.get_hcore
self.pyscf_scf.get_ovlp = self.get_ovlp
self.pyscf_scf.get_j = self.get_j
self.pyscf_scf.get_jk = self.get_jk
self.pyscf_scf.energy_nuc = self.energy_nuc
if self.perform_scf: self.kernel_scf(**kw)
def get_jk(mol_or_mf, dm, hermi, dmcur, *args, **kwargs):
'''MPI version of scf.hf.get_jk function'''
#vj = get_j(mol_or_mf, dm, hermi)
#vk = get_k(mol_or_mf, dm, hermi)
if isinstance(mol_or_mf, gto.mole.Mole):
mf = hf.SCF(mol_or_mf).view(SCF)
else:
mf = mol_or_mf
# dm may be too big for mpi4py library to serialize. Broadcast dm here.
if any(comm.allgather(isinstance(dm, str) and dm == 'SKIPPED_ARG')):
dm = mpi.bcast_tagged_array_occdf(dm)
mf.unpack_(comm.bcast(mf.pack()))
# initial and final grids level
grdlvl_i = 0
grdlvl_f = 1
# norm_ddm threshold for grids change
thrd_nddm = 0.2
# set block size to adapt memory
sblk = 200
# interspace betweeen v shell
intsp = 1
# threshold for u and v
gthrdu = 1e-10
gthrdvs = 1e-10
gthrdvd = 1e-10
global cond, wao_vx, ngridsx, coordsx, gridatm
dms = numpy.asarray(dm)
dm_shape = dms.shape
nao = dm_shape[-1]
dms = dms.reshape(-1,nao,nao)
nset = dms.shape[0]
vj = [0] * nset
vk = [0] * nset
# DF-J and sgX set
mf.with_df = mf
mol = mf.mol
global int2c, ovlp, ao_loc, rao_loc
# use mf.opt to calc int2c once, cond, dm0, and rao, ao_loc, ovlp for sgX
if mf.opt is None:
mf.opt = mf.init_direct_scf()
cond = 0
# set auxbasis in input file, need self.auxbasis = None in __init__ of hf.py
# mf.auxbasis = 'weigend'
auxbasis = mf.auxbasis
auxbasis = comm.bcast(auxbasis)
mf.auxbasis = comm.bcast(mf.auxbasis)
auxmol = df.addons.make_auxmol(mol, auxbasis)
# (P|Q)
int2c = auxmol.intor('int2c2e', aosym='s1', comp=1)
if rank == 0: print('auxmol.basis',auxmol.basis,'number of aux basis',int2c.shape[0])
# for sgX
# ao_loc and rao_loc
intbn = mol._add_suffix('int3c2e')
intbn = gto.moleintor.ascint3(intbn)
ao_loc = gto.moleintor.make_loc(mol._bas, intbn)
#print('dsssa',mol.nbas, ao_loc.shape,ao_loc[0],ao_loc[-1],ao_loc[1],ao_loc[2],ao_loc[3],ao_loc[115])
rao_loc = numpy.zeros((nao),dtype=int)
for i in range(mol.nbas):
for j in range(ao_loc[i],ao_loc[i+1]):
rao_loc[j] = i
ovlp = mol.intor_symmetric('int1e_ovlp')
if rank == 0: print('thrd_nddm',thrd_nddm, 'sblk',sblk, 'intsp',intsp, 'gthrdu',gthrdu)
# coase and fine grids change
grdchg = 0
norm_ddm = 0
for k in range(nset):
norm_ddm += numpy.linalg.norm(dms[k])
if norm_ddm < thrd_nddm and cond == 2 :
cond = 1
if cond == 0:
wao_vx, ngridsx, coordsx, gridatm = get_gridss(mol,grdlvl_i, sblk)
if rank == 0: print('grids level at first is', grdlvl_i)
cond = 2
elif cond == 1:
wao_vx, ngridsx, coordsx, gridatm = get_gridss(mol,grdlvl_f, sblk)
if rank == 0: print('grids level change to', grdlvl_f)
dms = numpy.asarray(dmcur)
dms = dms.reshape(-1,nao,nao)
grdchg = 1
cond = 3
# DF-J
dmtril = []
for k in range(nset):
dmtril.append(lib.pack_tril(dms[k]+dms[k].T))
i = numpy.arange(nao)
dmtril[k][i*(i+1)//2+i] *= .5
rho = []
b0 = 0
for eri1 in loop(mf.with_df):
naux, nao_pair = eri1.shape
#if rank==0: print('slice-naux',naux,'rank',rank)
b1 = b0 + naux
assert(nao_pair == nao*(nao+1)//2)
for k in range(nset):
if b0 == 0: rho.append(numpy.empty(paux[rank]))
rho[k][b0:b1] = numpy.dot(eri1, dmtril[k])
b0 = b1
orho = []
rec = []
for k in range(nset):
orho.append(mpi.gather(rho[k]))
if rank == 0:
ivj0 = scipy.linalg.solve(int2c, orho[k])
else:
ivj0 = None
rec.append(numpy.empty(paux[rank]))
comm.Scatterv([ivj0,paux],rec[k],root=0)
b0 = 0
for eri1 in loop(mf.with_df):
naux, nao_pair = eri1.shape
b1 = b0 + naux
assert(nao_pair == nao*(nao+1)//2)
for k in range(nset):
vj[k] += numpy.dot(rec[k][b0:b1].T, eri1)
b0 = b1
for k in range(nset):
vj[k] = comm.reduce(vj[k])
# sgX
wao_v = wao_vx
coords = coordsx
for k in range(nset):
# Kuv = Sum(Xug Avt Dkt Xkg)
ngrids = coords.shape[0]
for ii in range(gridatm.shape[0]-1):
i0 = gridatm[ii]
i1 = gridatm[ii+1]
# screening u by value of grids
umaxg = numpy.amax(numpy.absolute(wao_v[i0:i1]), axis=0)
usi = numpy.argwhere(umaxg > gthrdu).reshape(-1)
# screening v by dm and ovlp then triangle matrix bn
uovl = ovlp[usi, :]
vmaxu = numpy.amax(numpy.absolute(uovl), axis=0)
osi = numpy.argwhere(vmaxu > gthrdvs).reshape(-1)
udms = dms[k][usi, :]
dmaxg = numpy.amax(numpy.absolute(udms), axis=0)
dsi = numpy.argwhere(dmaxg > gthrdvd).reshape(-1)
vsi = numpy.intersect1d(dsi, osi)
if len(vsi) != 0:
vsh = numpy.unique(rao_loc[vsi])
#vshbeg = vsh[0]
vshfin = vsh[-1]+1
# use gap between continurous v to save time
vsh1 = vsh
vsh1= numpy.delete(vsh1, 0)
vsh1 = numpy.append(vsh1, [vshfin])
vshd = numpy.argwhere(vsh1-vsh > intsp)
vshd = numpy.append(vshd, vsh.shape[0]-1)
nvshd = vshd.shape[0]
#vbeg = ao_loc[vshbeg]
vfin = ao_loc[vshfin]
fakemol = gto.fakemol_for_charges(coords[i0:i1])
pmol = gto.mole.conc_mol(mol, fakemol)
bn = []
dmsk = []
bntp = [[0 for col in range(nvshd)] for row in range(nvshd)]
for i in range(nvshd):
if i==0:
ii0 = vsh[0]
ii1 = vsh[vshd[0]]+1
else:
ii0 = vsh[vshd[i-1]+1]
ii1 = vsh[vshd[i]]+1
dmsk.append(dms[k][:,ao_loc[ii0]:ao_loc[ii1]])
bnh = []
for j in range(0, i):
bnh.append(bntp[j][i].swapaxes(0,1))
for j in range(i, nvshd):
if j==0:
jj0 = vsh[0]
jj1 = vsh[vshd[0]]+1
else:
jj0 = vsh[vshd[j-1]+1]
jj1 = vsh[vshd[j]]+1
shls_slice = (ii0, ii1, jj0, jj1, mol.nbas, mol.nbas+fakemol.nbas)
bntp[i][j] = pmol.intor(intor='int3c2e', comp=1, aosym='s1', shls_slice=shls_slice)
bnh.append(bntp[i][j])
bnrow = numpy.concatenate(bnh, axis=1)
bn.append(bnrow)
bn = numpy.concatenate(bn, axis=0)
abn = numpy.absolute(bn)
#if cond==3: print(rank,'wet',numpy.amax(abn), numpy.median(abn))
dmsk = numpy.asarray(numpy.hstack(dmsk))
fg = numpy.dot(wao_v[i0:i1,usi],dmsk[usi])
gv = lib.einsum('vtg,gt->gv', bn, fg)
vk0 = numpy.zeros((nao,nao))
vksp = lib.einsum('gu,gv->uv', wao_v[i0:i1,usi], gv)
blen = 0
for i in range(nvshd):
if i==0:
ii0 = vsh[0]
ii1 = vsh[vshd[0]]+1
else:
ii0 = vsh[vshd[i-1]+1]
ii1 = vsh[vshd[i]]+1
baa = ao_loc[ii1]-ao_loc[ii0]
vk0[usi,ao_loc[ii0]:ao_loc[ii1]] = vksp[:,blen:(blen+baa)]
blen += baa
vk[k] += vk0
else:
vk0 = numpy.zeros((nao,nao))
vk[k] += vk0
sn = lib.einsum('gu,gv->uv', wao_v, wao_v)
vk[k] = comm.reduce(vk[k])
sn = comm.reduce(sn)
# SSn^-1 for grids to analitic
if rank == 0:
snsgk = scipy.linalg.solve(sn, vk[k])
vk[k] = numpy.matmul(ovlp, snsgk)
if rank == 0:
vj = lib.unpack_tril(numpy.asarray(vj), 1).reshape(dm_shape)
vk = numpy.asarray(vk).reshape(dm_shape)
#if cond==3: cond=4
return vj, vk, grdchg
def get_jk(mol_or_mf, dm, hermi=1):
'''MPI version of scf.hf.get_jk function'''
#vj = get_j(mol_or_mf, dm, hermi)
#vk = get_k(mol_or_mf, dm, hermi)
global eri1
with_j=True
with_k=True
if isinstance(mol_or_mf, gto.mole.Mole):
mf = hf.SCF(mol_or_mf).view(SCF)
else:
mf = mol_or_mf
# dm may be too big for mpi4py library to serialize. Broadcast dm here.
if any(comm.allgather(isinstance(dm, str) and dm == 'SKIPPED_ARG')):
dm = mpi.bcast_tagged_array_occdf(dm)
mf.unpack_(comm.bcast(mf.pack()))
if mf.opt is None:
mf.opt = mf.init_direct_scf()
mf.with_df = mf
mol = mf.mol
global int2c
# use sttr to calc int2c once
if not hasattr(dm, 'mo_coeff'):
# set auxbasis in input file, need self.auxbasis = None in __init__ of hf.py
# mf.auxbasis = 'weigend'
auxbasis = mf.auxbasis
auxbasis = comm.bcast(auxbasis)
mf.auxbasis = comm.bcast(mf.auxbasis)
auxmol = df.addons.make_auxmol(mol, auxbasis)
# (P|Q)
int2c = auxmol.intor('int2c2e', aosym='s1', comp=1)
naux0 = int2c.shape[0]
fmmm = _ao2mo.libao2mo.AO2MOmmm_bra_nr_s2
fdrv = _ao2mo.libao2mo.AO2MOnr_e2_drv
ftrans = _ao2mo.libao2mo.AO2MOtranse2_nr_s2
null = lib.c_null_ptr()
dms = numpy.asarray(dm)
dm_shape = dms.shape
nao = dm_shape[-1]
dms = dms.reshape(-1,nao,nao)
nset = dms.shape[0]
vj = [0] * nset
vk = [0] * nset
if hasattr(dm, 'mo_coeff'):
#TODO: test whether dm.mo_coeff matching dm
mo_coeff = numpy.asarray(dm.mo_coeff, order='F')
mo_occ = numpy.asarray(dm.mo_occ)
nmo = mo_occ.shape[-1]
mo_coeff = mo_coeff.reshape(-1,nao,nmo)
mo_occ = mo_occ.reshape(-1,nmo)
if mo_occ.shape[0] * 2 == nset: # handle ROHF DM
mo_coeff = numpy.vstack((mo_coeff, mo_coeff))
mo_occa = numpy.array(mo_occ> 0, dtype=numpy.double)
mo_occb = numpy.array(mo_occ==2, dtype=numpy.double)
assert(mo_occa.sum() + mo_occb.sum() == mo_occ.sum())
mo_occ = numpy.vstack((mo_occa, mo_occb))
dmtril = []
orbo = []
orbo0 = []
kiv = []
for k in range(nset):
c = numpy.einsum('pi,i->pi', mo_coeff[k][:,mo_occ[k]>0],
numpy.sqrt(mo_occ[k][mo_occ[k]>0]))
orbo.append(numpy.asarray(c, order='F'))
orbo0.append(numpy.asarray(mo_coeff[k][:,mo_occ[k]>0], order='F'))
nocc = orbo[k].shape[1]
kiv.append(numpy.zeros((nocc,nao)))
rho = []
split = []
buf1 = []
# for eri1 in loop(mf.with_df):
if 1==1:
naux, nao_pair = eri1.shape
assert(nao_pair == nao*(nao+1)//2)
for k in range(nset):
nocc = orbo[k].shape[1]
if nocc > 0:
buf1.append(numpy.empty((naux*nocc,nao)))
fdrv(ftrans, fmmm,
buf1[k].ctypes.data_as(ctypes.c_void_p),
eri1.ctypes.data_as(ctypes.c_void_p),
orbo[k].ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(naux), ctypes.c_int(nao),
(ctypes.c_int*4)(0, nocc, 0, nao),
null, ctypes.c_int(0))
buf2r = lib.dot(buf1[k], orbo0[k]).reshape(naux,nocc,-1)
buf2r = lib.pack_tril(buf2r)
# gather buf2r
split.append(numpy.array_split(buf2r,mpi.pool.size,axis = 1))
# global iokr, rec for grad
global iokr, rec
iokr = []
rec = []
for k in range(nset):
for i in range(mpi.pool.size):
obuf2r0 = mpi.gather(split[k][i],root=i)
if rank == i:
obuf2r = obuf2r0
obuf2r0 = None
split[k] = None
# k
iok = scipy.linalg.solve(int2c, obuf2r)
for i in range(mpi.pool.size):
if i == 0:
j0 = 0
else:
j0 = pauxz[i-1]
j1 = pauxz[i]
iok0 = mpi.gather(iok[j0:j1].reshape(-1,order='F'),root=i)
if rank == i:
iokx = lib.unpack_tril(iok0.reshape((naux,-1),order='F'))
iok0 = None
iok = None
nocc = orbo[k].shape[1]
# j
rec.append(numpy.einsum('kii->ki', iokx.reshape(naux,nocc,-1)).dot
(numpy.sqrt(mo_occ[k][mo_occ[k]>0])))
iokr.append(iokx.reshape(naux*nocc,-1))
iokx = None
if 1==1:
naux, nao_pair = eri1.shape
assert(nao_pair == nao*(nao+1)//2)
for k in range(nset):
nocc = orbo[k].shape[1]
if nocc > 0:
kiv[k] += lib.dot(iokr[k].T, buf1[k])
if with_j:
vj[k] += numpy.dot(rec[k].T, eri1)
# vj[k] += numpy.tensordot(rec[k], eri1, axes=([0],[0]))
for k in range(nset):
kiv[k] = comm.reduce(kiv[k])
# project iv -> uv
if rank == 0:
kij = lib.einsum('ui,ju->ij', orbo0[k], kiv[k])
kr = scipy.linalg.solve(kij, kiv[k])
vk[k] = lib.dot(kiv[k].T,kr)
else:
vk[k] = None
vj[k] = comm.reduce(vj[k])
else:
dmtril = []
for k in range(nset):
if with_j:
dmtril.append(lib.pack_tril(dms[k]+dms[k].T))
i = numpy.arange(nao)
dmtril[k][i*(i+1)//2+i] *= .5
rho = []
for eri1 in loop(mf.with_df):
naux, nao_pair = eri1.shape
#print('slice-naux',naux,'rank',rank,auxmol.basis)
assert(nao_pair == nao*(nao+1)//2)
for k in range(nset):
if with_j:
rho.append(numpy.dot(eri1, dmtril[k]))
orho = []
rec = []
for k in range(nset):
orho.append(mpi.gather(rho[k]))
if rank == 0:
ivj0 = scipy.linalg.solve(int2c, orho[k])
else:
ivj0 = None
rec.append(numpy.empty(naux))
comm.Scatterv([ivj0,paux],rec[k],root=0)
if 1==1:
naux, nao_pair = eri1.shape
assert(nao_pair == nao*(nao+1)//2)
for k in range(nset):
if with_j:
vj[k] += numpy.dot(rec[k].T, eri1)
for k in range(nset):
vj[k] = comm.reduce(vj[k])
vk = numpy.zeros(dm_shape)
if rank == 0:
if with_j: vj = lib.unpack_tril(numpy.asarray(vj), 1).reshape(dm_shape)
if with_k: vk = numpy.asarray(vk).reshape(dm_shape)
return vj, vk
def get_jkgrd(mol_or_mf, dm, mo_coeff=None, mo_occ=None):
'''MPI version of scf.hf.get_jk function'''
if rank == 0: print('uuuu00', lib.current_memory()[0])
if isinstance(mol_or_mf, gto.mole.Mole):
mf = hf.SCF(mol_or_mf).view(SCF)
else:
mf = mol_or_mf
# dm may be too big for mpi4py library to serialize. Broadcast dm here.
if any(comm.allgather(isinstance(dm, str) and dm == 'SKIPPED_ARG')):
dm = mpi.bcast_tagged_array_occdf(dm)
mf.unpack_(comm.bcast(mf.pack()))
if mf.opt is None:
mf.opt = mf.init_direct_scf()
mf.with_df = mf
mol = mf.mol
auxbasis = mf.auxbasis
auxbasis = comm.bcast(auxbasis)
mf.auxbasis = comm.bcast(mf.auxbasis)
auxmol = df.addons.make_auxmol(mol, auxbasis)
nao = mol.nao_nr()
naux = auxmol.nao_nr()
if rank == 0:
print('number of AOs', nao)
print('number of auxiliary basis functions', naux)
# (d/dX i,j|P)
# int3c_e1 = df.incore.aux_e2(mol, auxmol, intor='int3c2e_ip1', aosym='s1', comp=3)
int3c_e1 = loop_aux(mf, intor='int3c2e_ip1', aosym='s1', comp=3)
# (i,j|d/dX P)
# int3c_e2 = df.incore.aux_e2(mol, auxmol, intor='int3c2e_ip2', aosym='s1', comp=3)
int3c_e2 = loop_aux(mf, intor='int3c2e_ip2', aosym='s1', comp=3)
# (d/dX P|Q)
int2c_e1 = auxmol.intor('int2c2e_ip1', aosym='s1', comp=3)
fmmm = _ao2mo.libao2mo.AO2MOmmm_bra_nr_s2
fdrv = _ao2mo.libao2mo.AO2MOnr_e2_drv
ftrans = _ao2mo.libao2mo.AO2MOtranse2_nr_s2
null = lib.c_null_ptr()
dms = numpy.asarray(dm)
dm_shape = dms.shape
nao = dm_shape[-1]
dms = dms.reshape(-1, nao, nao)
nset = dms.shape[0]
vj = [0] * nset
vk = [0] * nset
if 0 == 0:
nmo = mo_occ.shape[-1]
mo_coeff = mo_coeff.reshape(-1, nao, nmo)
mo_occ = mo_occ.reshape(-1, nmo)
if mo_occ.shape[0] * 2 == nset: # handle ROHF DM
mo_coeff = numpy.vstack((mo_coeff, mo_coeff))
mo_occa = numpy.array(mo_occ > 0, dtype=numpy.double)
mo_occb = numpy.array(mo_occ == 2, dtype=numpy.double)
assert (mo_occa.sum() + mo_occb.sum() == mo_occ.sum())
mo_occ = numpy.vstack((mo_occa, mo_occb))
dmtril = []
orbo = []
orbo0 = []
kiv = []
for k in range(nset):
c = numpy.einsum('pi,i->pi', mo_coeff[k][:, mo_occ[k] > 0],
numpy.sqrt(mo_occ[k][mo_occ[k] > 0]))
orbo.append(numpy.asarray(c, order='F'))
orbo0.append(
numpy.asarray(mo_coeff[k][:, mo_occ[k] > 0], order='F'))
nocc = orbo[k].shape[1]
kiv.append(numpy.zeros((nocc, nao)))
rho = []
split = []
buf1 = []
iokr = mpi_occ_df_incore.iokr
rec = mpi_occ_df_incore.rec
k = 0
dmtril = []
for k in range(nset):
dmtril.append(lib.pack_tril(dms[k] + dms[k].T))
i = numpy.arange(nao)
dmtril[k][i * (i + 1) // 2 + i] *= .5
tmp0 = int3c_e2.swapaxes(1, 3).reshape(-1, nao * nao)
tmp = numpy.dot(tmp0, dm.reshape(-1))
tmp0 = numpy.einsum('xp,p->xp', tmp.reshape(3, -1), rec[k])
ec1_3cp = mpi.gather(tmp0.reshape(-1, order='F')).reshape((3, -1),
order='F')
ec1_3cu_b = numpy.einsum('xuvp,p,uv->xu', int3c_e1, rec[k], dm)
ec1_3cu = comm.reduce(ec1_3cu_b)
if rank == 0:
j0 = 0
else:
j0 = pauxz[rank - 1]
j1 = pauxz[rank]
tmp0 = int2c_e1[:, :, j0:j1].dot(rec[k])
tmp = comm.allreduce(tmp0)
tmp0 = numpy.einsum('xp,p->xp', tmp[:, j0:j1], rec[k])
ec1_2c = mpi.gather(tmp0.reshape(-1, order='F')).reshape((3, -1),
order='F')
coeff3mo = numpy.sqrt(2.0e0) * (iokr[k].reshape(-1, nocc, nocc))
tmp = numpy.tensordot(coeff3mo, orbo[k], axes=([2], [1]))
coeffb = numpy.tensordot(tmp, orbo[k], axes=([1], [1]))
ex1_3cp_b = numpy.einsum('puv,xuvp->xp', coeffb, int3c_e2)
ex1_3cp = mpi.gather(ex1_3cp_b.reshape(-1, order='F')).reshape(
(3, -1), order='F')
ex1_3cu_b = numpy.einsum('puv,xuvp->xu', coeffb, int3c_e1)
ex1_3cu = comm.reduce(ex1_3cu_b)
tmp0 = mpi.allgather(coeff3mo)
tmp = numpy.tensordot(tmp0, coeff3mo, axes=([1, 2], [1, 2]))
ex1_2c_b = numpy.einsum('xpq,pq->xp', int2c_e1[:, :, j0:j1], tmp)
ex1_2c = comm.reduce(ex1_2c_b)
eaux1p = numpy.empty((3, naux))
eaux1u = numpy.empty((3, naux))
if rank == 0:
eaux1p = -0.5 * (2 * ec1_3cp - 2 * ec1_2c - 0.5 *
(2 * ex1_3cp - 2 * ex1_2c))
eaux1u = -0.5 * (4 * ec1_3cu - 0.5 * (4 * ex1_3cu))
return eaux1p, eaux1u
def get_jk(mol_or_mf, dm, hermi=1):
'''MPI version of scf.hf.get_jk function'''
#vj = get_j(mol_or_mf, dm, hermi)
#vk = get_k(mol_or_mf, dm, hermi)
if isinstance(mol_or_mf, gto.mole.Mole):
mf = hf.SCF(mol_or_mf).view(SCF)
else:
mf = mol_or_mf
# dm may be too big for mpi4py library to serialize. Broadcast dm here.
if any(comm.allgather(isinstance(dm, str) and dm == 'SKIPPED_ARG')):
dm = mpi.bcast_tagged_array_occdf(dm)
mf.unpack_(comm.bcast(mf.pack()))
# initial and final grids level
grdlvl_i = 0
grdlvl_f = 1
# norm_ddm threshold for grids change
thrd_nddm = 0.03
# set block size to adapt memory
sblk = 200
global cond, wao_vx, ngridsx, coordsx, gthrd, dm0
dms = numpy.asarray(dm)
dm_shape = dms.shape
nao = dm_shape[-1]
dms = dms.reshape(-1, nao, nao)
nset = dms.shape[0]
vj = [0] * nset
vk = [0] * nset
# DF-J set
mf.with_df = mf
mol = mf.mol
global int2c
# use mf.opt to calc int2c once, cond, dm0
if mf.opt is None:
mf.opt = mf.init_direct_scf()
cond = 0
dm0 = numpy.zeros((nset, nao, nao))
# set auxbasis in input file, need self.auxbasis = None in __init__ of hf.py
# mf.auxbasis = 'weigend'
auxbasis = mf.auxbasis
auxbasis = comm.bcast(auxbasis)
mf.auxbasis = comm.bcast(mf.auxbasis)
auxmol = df.addons.make_auxmol(mol, auxbasis)
# (P|Q)
int2c = auxmol.intor('int2c2e', aosym='s1', comp=1)
if rank == 0: print('auxmol.basis', auxmol.basis)
# coase and fine grids change
norm_ddm = 0
for k in range(nset):
norm_ddm += numpy.linalg.norm(dms[k] - dm0[k])
dm0 = dms
if norm_ddm < thrd_nddm and cond == 2:
cond = 1
if cond == 0:
wao_vx, ngridsx, coordsx, gthrd = get_gridss(mol, grdlvl_i)
if rank == 0: print('grids level at first is', grdlvl_i)
cond = 2
elif cond == 1:
wao_vx, ngridsx, coordsx, gthrd = get_gridss(mol, grdlvl_f)
if rank == 0: print('grids level change to', grdlvl_f)
cond = 3
# DF-J
dmtril = []
for k in range(nset):
dmtril.append(lib.pack_tril(dms[k] + dms[k].T))
i = numpy.arange(nao)
dmtril[k][i * (i + 1) // 2 + i] *= .5
rho = []
b0 = 0
for eri1 in loop(mf.with_df):
naux, nao_pair = eri1.shape
# if rank==0: print('slice-naux',naux,'rank',rank)
b1 = b0 + naux
assert (nao_pair == nao * (nao + 1) // 2)
for k in range(nset):
if b0 == 0: rho.append(numpy.empty(paux[rank]))
rho[k][b0:b1] = numpy.dot(eri1, dmtril[k])
b0 = b1
orho = []
rec = []
for k in range(nset):
orho.append(mpi.gather(rho[k]))
if rank == 0:
ivj0 = scipy.linalg.solve(int2c, orho[k])
else:
ivj0 = None
rec.append(numpy.empty(paux[rank]))
comm.Scatterv([ivj0, paux], rec[k], root=0)
b0 = 0
for eri1 in loop(mf.with_df):
naux, nao_pair = eri1.shape
b1 = b0 + naux
assert (nao_pair == nao * (nao + 1) // 2)
for k in range(nset):
vj[k] += numpy.dot(rec[k][b0:b1].T, eri1)
b0 = b1
for k in range(nset):
vj[k] = comm.reduce(vj[k])
# sgX
for k in range(nset):
# screening from Fg
fg = numpy.dot(wao_vx, dms[k])
sngds = []
ss = 0
for i in range(ngridsx):
if numpy.amax(numpy.absolute(fg[i, :])) < gthrd:
sngds.append(i)
ss += 1
if ss < ngridsx:
wao_v = numpy.delete(wao_vx, sngds, 0)
fg = numpy.delete(fg, sngds, 0)
coords = numpy.delete(coordsx, sngds, 0)
else:
wao_v = wao_vx
coords = coordsx
# Kuv = Sum(Xug Avt Dkt Xkg)
ngrids = coords.shape[0]
blksize = min(ngrids, sblk)
for i0, i1 in lib.prange(0, ngrids, blksize):
bn = batch_nuc(mol, coords[i0:i1])
gbn = bn.swapaxes(0, 2)
gv = lib.einsum('gvt,gt->gv', gbn, fg[i0:i1])
vk[k] += lib.einsum('gu,gv->uv', wao_v[i0:i1], gv)
sn = lib.einsum('gu,gv->uv', wao_v, wao_v)
vk[k] = comm.reduce(vk[k])
sn = comm.reduce(sn)
# SSn^-1 for grids to analitic
if rank == 0:
snsgk = scipy.linalg.solve(sn, vk[k])
ovlp = mol.intor_symmetric('int1e_ovlp')
vk[k] = numpy.matmul(ovlp, snsgk)
if rank == 0:
vj = lib.unpack_tril(numpy.asarray(vj), 1).reshape(dm_shape)
vk = numpy.asarray(vk).reshape(dm_shape)
return vj, vk
def get_jk(mol_or_mf, dm, hermi=1):
'''MPI version of scf.hf.get_jk function'''
#vj = get_j(mol_or_mf, dm, hermi)
#vk = get_k(mol_or_mf, dm, hermi)
if isinstance(mol_or_mf, gto.mole.Mole):
mf = hf.SCF(mol_or_mf).view(SCF)
else:
mf = mol_or_mf
# dm may be too big for mpi4py library to serialize. Broadcast dm here.
if any(comm.allgather(isinstance(dm, str) and dm == 'SKIPPED_ARG')):
dm = mpi.bcast_tagged_array_occdf(dm)
mf.unpack_(comm.bcast(mf.pack()))
# initial and final grids level
grdlvl_i = 1
grdlvl_f = 1
# norm_ddm threshold for grids change
thrd_nddm = 0.03
# set block size to adapt memory
sblk = 200
global cond, wao_vx, ngridsx, coordsx, gthrd, dm0
dms = numpy.asarray(dm)
dm_shape = dms.shape
nao = dm_shape[-1]
dms = dms.reshape(-1, nao, nao)
nset = dms.shape[0]
vj = [0] * nset
vk = [0] * nset
mol = mf.mol
if mf.opt is None:
mf.opt = mf.init_direct_scf()
cond = 0
dm0 = numpy.zeros((nset, nao, nao))
# coase and fine grids change
norm_ddm = 0
for k in range(nset):
norm_ddm += numpy.linalg.norm(dms[k] - dm0[k])
dm0 = dms
if norm_ddm < thrd_nddm and cond == 2:
cond = 1
if cond == 0:
wao_vx, ngridsx, coordsx, gthrd = get_gridss(mol, grdlvl_i)
if rank == 0: print('grids level at first is', grdlvl_i)
cond = 2
elif cond == 1:
wao_vx, ngridsx, coordsx, gthrd = get_gridss(mol, grdlvl_f)
if rank == 0: print('grids level change to', grdlvl_f)
cond = 3
for k in range(nset):
# screening from Fg
fg = numpy.dot(wao_vx, dms[k])
sngds = []
ss = 0
for i in range(ngridsx):
if numpy.amax(numpy.absolute(fg[i, :])) < gthrd:
sngds.append(i)
ss += 1
if ss < ngridsx:
wao_v = numpy.delete(wao_vx, sngds, 0)
fg = numpy.delete(fg, sngds, 0)
coords = numpy.delete(coordsx, sngds, 0)
else:
wao_v = wao_vx
coords = coordsx
# Kuv = Sum(Xug Avt Dkt Xkg)
ngrids = coords.shape[0]
blksize = min(ngrids, sblk)
for i0, i1 in lib.prange(0, ngrids, blksize):
bn = batch_nuc(mol, coords[i0:i1])
gbn = bn.swapaxes(0, 2)
jg = numpy.dot(gbn.reshape(-1, nao * nao), dms[k].reshape(-1))
xj = lib.einsum('gv,g->gv', wao_v[i0:i1], jg)
vj[k] += lib.einsum('gu,gv->uv', wao_v[i0:i1], xj)
gv = lib.einsum('gvt,gt->gv', gbn, fg[i0:i1])
vk[k] += lib.einsum('gu,gv->uv', wao_v[i0:i1], gv)
sn = lib.einsum('gu,gv->uv', wao_v, wao_v)
# comm.Barrier()
vj[k] = comm.reduce(vj[k])
vk[k] = comm.reduce(vk[k])
sn = comm.reduce(sn)
# SSn^-1 for grids to analitic
if rank == 0:
# sn = lib.einsum('gu,gv->uv', wao_v, wao_v)
snsgk = scipy.linalg.solve(sn, vk[k])
ovlp = mol.intor_symmetric('int1e_ovlp')
vk[k] = numpy.matmul(ovlp, snsgk)
snsgj = scipy.linalg.solve(sn, vj[k])
vj[k] = numpy.matmul(ovlp, snsgj)
if rank == 0:
vj = numpy.asarray(vj).reshape(dm_shape)
vk = numpy.asarray(vk).reshape(dm_shape)
return vj, vk
def get_jk(mol_or_mf, dm, hermi, dmcur):
#, *args, **kwargs
'''MPI version of scf.hf.get_jk function'''
#vj = get_j(mol_or_mf, dm, hermi)
#vk = get_k(mol_or_mf, dm, hermi)
if isinstance(mol_or_mf, gto.mole.Mole):
mf = hf.SCF(mol_or_mf).view(SCF)
else:
mf = mol_or_mf
# dm may be too big for mpi4py library to serialize. Broadcast dm here.
if any(comm.allgather(isinstance(dm, str) and dm == 'SKIPPED_ARG')):
#dm = mpi.bcast_tagged_array_occdf(dm)
dm = mpi.bcast_tagged_array(dm)
mf.unpack_(comm.bcast(mf.pack()))
# initial and final grids level
grdlvl_i = 0
grdlvl_f = 1
# norm_ddm threshold for grids change
thrd_nddm = 0.01
# set block size to adapt memory
sblk = 100
# interspace betweeen v shell
intsp = 1
# threshold for u and v
gthrdu = 1e-7
gthrdvs = 1e-4
gthrdvd = 1e-4
global cond, wao_vx, ngridsx, coordsx, weightsx
dms = numpy.asarray(dm)
dm_shape = dms.shape
nao = dm_shape[-1]
dms = dms.reshape(-1,nao,nao)
nset = dms.shape[0]
vj = [0] * nset
vk = [0] * nset
# DF-J and sgX set
mf.with_df = mf
mol = mf.mol
global int2c, ovlp, ao_loc, rao_loc, ov_scr
# need set mf.initsgx = None in scf.SCF __init_
if mf.initsgx is None:
mf.initsgx = 0
cond = 0
# set auxbasis in input file, need self.auxbasis = None in __init__ of hf.py
# mf.auxbasis = 'weigend'
auxbasis = mf.auxbasis
auxbasis = comm.bcast(auxbasis)
mf.auxbasis = comm.bcast(mf.auxbasis)
auxmol = df.addons.make_auxmol(mol, auxbasis)
# (P|Q)
int2c = auxmol.intor('int2c2e', aosym='s1', comp=1)
if rank == 0: print('auxmol.basis',auxmol.basis,'number of aux basis',int2c.shape[0])
# for sgX
# ao_loc and rao_loc
intbn = mol._add_suffix('int3c2e')
intbn = gto.moleintor.ascint3(intbn)
ao_loc = gto.moleintor.make_loc(mol._bas, intbn)
rao_loc = numpy.zeros((nao),dtype=int)
ovlp = mol.intor_symmetric('int1e_ovlp')
for i in range(mol.nbas):
for jj in range(ao_loc[i],ao_loc[i+1]):
rao_loc[jj] = i
# ovlp screening
ov_scr = numpy.zeros((mol.nbas,mol.nbas),dtype=int)
for i in range(mol.nbas):
for j in range(mol.nbas):
if mol.bas_atom(i) == mol.bas_atom(j):
ov_scr[i,j] = 1
else:
movlp = numpy.amax(numpy.absolute(ovlp[ao_loc[i]:ao_loc[i+1],ao_loc[j]:ao_loc[j+1]]))
if movlp > gthrdvs:
ov_scr[i,j] = 1
if rank == 0: print('thrd_nddm',thrd_nddm, 'sblk',sblk, 'intsp',intsp, 'gthrdu',gthrdu)
if rank == 0: print('gthrdvs',gthrdvs, 'gthrdvd',gthrdvd)
# coase and fine grids change
grdchg = 0
norm_ddm = 0
for k in range(nset):
norm_ddm += numpy.linalg.norm(dms[k])
if norm_ddm < thrd_nddm and cond == 2 :
cond = 1
if cond == 0:
wao_vx, ngridsx, coordsx, weightsx = get_gridss(mol,grdlvl_i, sblk)
if rank == 0: print('grids level at first is', grdlvl_i)
cond = 2
elif cond == 1:
wao_vx, ngridsx, coordsx, weightsx = get_gridss(mol,grdlvl_f, sblk)
if rank == 0: print('grids level change to', grdlvl_f)
dms = numpy.asarray(dmcur)
dms = dms.reshape(-1,nao,nao)
grdchg = 1
cond = 3
if rank==0: Jtime=time.time()
# DF-J
dmtril = []
for k in range(nset):
dmtril.append(lib.pack_tril(dms[k]+dms[k].T))
i = numpy.arange(nao)
dmtril[k][i*(i+1)//2+i] *= .5
rho = []
b0 = 0
for eri1 in loop(mf.with_df):
naux, nao_pair = eri1.shape
#if rank==0: print('slice-naux',naux,'rank',rank)
b1 = b0 + naux
assert(nao_pair == nao*(nao+1)//2)
for k in range(nset):
if b0 == 0: rho.append(numpy.empty(paux[rank]))
rho[k][b0:b1] = numpy.dot(eri1, dmtril[k])
b0 = b1
orho = []
rec = []
for k in range(nset):
orho.append(mpi.gather(rho[k]))
if rank == 0:
ivj0 = scipy.linalg.solve(int2c, orho[k])
else:
ivj0 = None
rec.append(numpy.empty(paux[rank]))
comm.Scatterv([ivj0,paux],rec[k],root=0)
b0 = 0
for eri1 in loop(mf.with_df):
naux, nao_pair = eri1.shape
b1 = b0 + naux
assert(nao_pair == nao*(nao+1)//2)
for k in range(nset):
vj[k] += numpy.dot(rec[k][b0:b1].T, eri1)
b0 = b1
for k in range(nset):
vj[k] = comm.reduce(vj[k])
if rank==0: print "Took this long for J: ", time.time()-Jtime
if rank==0: Jtime=time.time()
# sgX
wao_v = wao_vx
coords = coordsx
weights = weightsx
for k in range(nset):
'''# Plus density screening
ov_scr = numpy.zeros((mol.nbas,mol.nbas),dtype=int)
for i in range(mol.nbas):
for j in range(mol.nbas):
movlp = numpy.amax(numpy.absolute(dms[k][ao_loc[i]:ao_loc[i+1],ao_loc[j]:ao_loc[j+1]]))
if movlp > gthrdvd:
ov_scr[i,j] = 1'''
# xfg screening
ngrids = coords.shape[0]
blksize = min(ngrids, sblk)
gscr = []
for i0, i1 in lib.prange(0, ngrids, blksize):
# screening u by value of grids
umaxg = numpy.amax(numpy.absolute(wao_v[i0:i1]), axis=0)
usi = numpy.argwhere(umaxg > gthrdu).reshape(-1)
if len(usi) != 0:
# screening v by ovlp then triangle matrix bn
uovl = ovlp[usi, :]
vmaxu = numpy.amax(numpy.absolute(uovl), axis=0)
osi = numpy.argwhere(vmaxu > gthrdvs).reshape(-1)
udms = dms[k][usi, :]
# screening v by dm and ovlp then triangle matrix bn
dmaxg = numpy.amax(numpy.absolute(udms), axis=0)
dsi = numpy.argwhere(dmaxg > gthrdvd).reshape(-1)
vsi = numpy.intersect1d(dsi, osi)
if len(vsi) != 0:
vsh = numpy.unique(rao_loc[vsi])
vshi = []
for i in range(vsh.shape[0]):
ista = ao_loc[vsh[i]]
iend = ao_loc[vsh[i]+1]
vshi.append(numpy.arange(ista, iend))
vshi = numpy.asarray(numpy.hstack(vshi))
dmsi = dms[k][usi]
fg = weights[i0:i1,None] * numpy.dot(wao_v[i0:i1,usi],dmsi[:,vshi])
gmaxfg = numpy.amax(numpy.absolute(fg), axis=1)
gmaxwao_v = numpy.amax(numpy.absolute(wao_v[i0:i1,usi]), axis=1)
gmaxtt = gmaxfg * gmaxwao_v
gscr0 = numpy.argwhere(gmaxtt > gthrdu).reshape(-1)
if gscr0.shape[0] > 0:
gscr.append(gscr0 + i0)
hgscr = numpy.hstack(gscr).reshape(-1)
coords = mpi.gather(coords[hgscr])
wao_v = mpi.gather(wao_v[hgscr])
weights = mpi.gather(weights[hgscr])
if rank == 0:
print('screened grids', coords.shape[0])
coords = numpy.array_split(coords, mpi.pool.size)
wao_v = numpy.array_split(wao_v, mpi.pool.size)
weights = numpy.array_split(weights, mpi.pool.size)
coords = mpi.scatter(coords)
wao_v = mpi.scatter(wao_v)
weights = mpi.scatter(weights)
# Kuv = Sum(Xug Avt Dkt Xkg)
ngrids = coords.shape[0]
for i0, i1 in lib.prange(0, ngrids, blksize):
# screening u by value of grids
umaxg = numpy.amax(numpy.absolute(wao_v[i0:i1]), axis=0)
usi = numpy.argwhere(umaxg > gthrdu).reshape(-1)
if len(usi) != 0:
# screening v by ovlp then triangle matrix bn
uovl = ovlp[usi, :]
vmaxu = numpy.amax(numpy.absolute(uovl), axis=0)
osi = numpy.argwhere(vmaxu > gthrdvs).reshape(-1)
udms = dms[k][usi, :]
# screening v by dm and ovlp then triangle matrix bn
dmaxg = numpy.amax(numpy.absolute(udms), axis=0)
dsi = numpy.argwhere(dmaxg > gthrdvd).reshape(-1)
vsi = numpy.intersect1d(dsi, osi)
if len(vsi) != 0:
vsh = numpy.unique(rao_loc[vsi])
nvsh = vsh.shape[0]
vov0 = ov_scr[vsh]
vov = vov0[:,vsh]
vshi = []
xvsh = vsh
ivx = [0]
vx = 0
for i in range(vsh.shape[0]):
ista = ao_loc[vsh[i]]
iend = ao_loc[vsh[i]+1]
vshi.append(numpy.arange(ista, iend))
vx += iend - ista
ivx.append(vx)
vshi = numpy.asarray(numpy.hstack(vshi))
nvshi = vshi.shape[0]
#print('ee',nvshi)
ivx = numpy.asarray(ivx)
vshbeg = vsh[0]
vshfin = vsh[-1]+1
dmsi = dms[k][usi]
fg = weights[i0:i1,None] * numpy.dot(wao_v[i0:i1,usi],dmsi[:,vshi])
fakemol = gto.fakemol_for_charges(coords[i0:i1])
#pmol = gto.mole.conc_mol(mol, fakemol)
intor = mol._add_suffix('int3c2e')
atm, bas, env = gto.mole.conc_env(mol._atm, mol._bas, mol._env,
fakemol._atm, fakemol._bas, fakemol._env)
shls_slice = (vshbeg, vshfin, vshbeg, vshfin, mol.nbas, mol.nbas+fakemol.nbas)
comp=1
#aosym='s1'
aosym='s2ij'
if aosym == 's2ij':
gv = getints3c_scr(intor, atm, bas, env, shls_slice, comp,
xvsh, nvshi, ivx, vov, fg, aosym)
else:
gv = getints3c_scr(intor, atm, bas, env, shls_slice, comp,
xvsh, nvshi, ivx, vov, fg, aosym)
vk0 = numpy.zeros((nao,nao))
vksp = lib.einsum('gu,gv->uv', wao_v[i0:i1,usi], gv)
vk1 = vk0[usi]
vk1[:,vshi] = vksp
vk0[usi] = vk1
vk[k] += vk0
wao_vw = weights[:,None] * wao_v
sn = lib.einsum('gu,gv->uv', wao_v, wao_vw)
vk[k] = comm.reduce(vk[k])
sn = comm.reduce(sn)
# SSn^-1 for grids to analitic
if rank == 0:
snsgk = scipy.linalg.solve(sn, vk[k])
vk[k] = numpy.matmul(ovlp, snsgk)
if hermi == 1:
vk[k] = (vk[k] + vk[k].T)*.5
if rank == 0:
print "Took this long for K: ", time.time()-Jtime
vj = lib.unpack_tril(numpy.asarray(vj), 1).reshape(dm_shape)
vk = numpy.asarray(vk).reshape(dm_shape)
return vj, vk, grdchg