def test_index_tril_to_pair(self):
i_j = (numpy.random.random((2, 30)) * 100).astype(int)
i0 = numpy.max(i_j, axis=0)
j0 = numpy.min(i_j, axis=0)
ij = i0 * (i0 + 1) // 2 + j0
i1, j1 = lib.index_tril_to_pair(ij)
self.assertTrue(numpy.all(i0 == i1))
self.assertTrue(numpy.all(j0 == j1))
def test_index_tril_to_pair(self):
i_j = (numpy.random.random((2,30)) * 100).astype(int)
i0 = numpy.max(i_j, axis=0)
j0 = numpy.min(i_j, axis=0)
ij = i0 * (i0+1) // 2 + j0
i1, j1 = lib.index_tril_to_pair(ij)
self.assertTrue(numpy.all(i0 == i1))
self.assertTrue(numpy.all(j0 == j1))
def trans_e1_outcore(mol, mo, ncore, ncas, erifile,
max_memory=None, level=1, verbose=logger.WARN):
time0 = (time.clock(), time.time())
log = logger.new_logger(mol, verbose)
log.debug1('trans_e1_outcore level %d max_memory %d', level, max_memory)
nao, nmo = mo.shape
nao_pair = nao*(nao+1)//2
nocc = ncore + ncas
faapp_buf = lib.H5TmpFile()
if isinstance(erifile, h5py.Group):
feri = erifile
else:
feri = lib.H5TmpFile(erifile, 'w')
mo_c = numpy.asarray(mo, order='C')
mo = numpy.asarray(mo, order='F')
pashape = (0, nmo, ncore, nocc)
papa_buf = numpy.zeros((nao,ncas,nmo*ncas))
j_pc = numpy.zeros((nmo,ncore))
k_pc = numpy.zeros((nmo,ncore))
mem_words = int(max(2000,max_memory-papa_buf.nbytes/1e6)*1e6/8)
aobuflen = mem_words//(nao_pair+nocc*nmo) + 1
ao_loc = numpy.array(mol.ao_loc_nr(), dtype=numpy.int32)
shranges = outcore.guess_shell_ranges(mol, True, aobuflen, None, ao_loc)
intor = mol._add_suffix('int2e')
ao2mopt = _ao2mo.AO2MOpt(mol, intor,
'CVHFnr_schwarz_cond', 'CVHFsetnr_direct_scf')
nstep = len(shranges)
paapp = 0
maxbuflen = max([x[2] for x in shranges])
log.debug('mem_words %.8g MB, maxbuflen = %d', mem_words*8/1e6, maxbuflen)
bufs1 = numpy.empty((maxbuflen, nao_pair))
bufs2 = numpy.empty((maxbuflen, nmo*ncas))
if level == 1:
bufs3 = numpy.empty((maxbuflen, nao*ncore))
log.debug('mem cache %.8g MB',
(bufs1.nbytes+bufs2.nbytes+bufs3.nbytes)/1e6)
else:
log.debug('mem cache %.8g MB', (bufs1.nbytes+bufs2.nbytes)/1e6)
ti0 = log.timer('Initializing trans_e1_outcore', *time0)
# fmmm, ftrans, fdrv for level 1
fmmm = libmcscf.AO2MOmmm_ket_nr_s2
ftrans = libmcscf.AO2MOtranse1_nr_s4
fdrv = libmcscf.AO2MOnr_e2_drv
for istep,sh_range in enumerate(shranges):
log.debug('[%d/%d], AO [%d:%d], len(buf) = %d',
istep+1, nstep, *sh_range)
buf = bufs1[:sh_range[2]]
_ao2mo.nr_e1fill(intor, sh_range,
mol._atm, mol._bas, mol._env, 's4', 1, ao2mopt, buf)
if log.verbose >= logger.DEBUG1:
ti1 = log.timer('AO integrals buffer', *ti0)
bufpa = bufs2[:sh_range[2]]
_ao2mo.nr_e1(buf, mo, pashape, 's4', 's1', out=bufpa)
# jc_pp, kc_pp
if level == 1: # ppaa, papa and vhf, jcp, kcp
if log.verbose >= logger.DEBUG1:
ti1 = log.timer('buffer-pa', *ti1)
buf1 = bufs3[:sh_range[2]]
fdrv(ftrans, fmmm,
buf1.ctypes.data_as(ctypes.c_void_p),
buf.ctypes.data_as(ctypes.c_void_p),
mo.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(sh_range[2]), ctypes.c_int(nao),
(ctypes.c_int*4)(0, nao, 0, ncore),
ctypes.POINTER(ctypes.c_void_p)(), ctypes.c_int(0))
p0 = 0
for ij in range(sh_range[0], sh_range[1]):
i,j = lib.index_tril_to_pair(ij)
i0 = ao_loc[i]
j0 = ao_loc[j]
i1 = ao_loc[i+1]
j1 = ao_loc[j+1]
di = i1 - i0
dj = j1 - j0
if i == j:
dij = di * (di+1) // 2
buf = numpy.empty((di,di,nao*ncore))
idx = numpy.tril_indices(di)
buf[idx] = buf1[p0:p0+dij]
buf[idx[1],idx[0]] = buf1[p0:p0+dij]
buf = buf.reshape(di,di,nao,ncore)
mo1 = mo_c[i0:i1]
tmp = numpy.einsum('uvpc,pc->uvc', buf, mo[:,:ncore])
tmp = lib.dot(mo1.T, tmp.reshape(di,-1))
j_pc += numpy.einsum('vp,pvc->pc', mo1, tmp.reshape(nmo,di,ncore))
tmp = numpy.einsum('uvpc,uc->vcp', buf, mo1[:,:ncore])
tmp = lib.dot(tmp.reshape(-1,nmo), mo).reshape(di,ncore,nmo)
k_pc += numpy.einsum('vp,vcp->pc', mo1, tmp)
else:
dij = di * dj
buf = buf1[p0:p0+dij].reshape(di,dj,nao,ncore)
mo1 = mo_c[i0:i1]
mo2 = mo_c[j0:j1]
tmp = numpy.einsum('uvpc,pc->uvc', buf, mo[:,:ncore])
tmp = lib.dot(mo1.T, tmp.reshape(di,-1))
j_pc += numpy.einsum('vp,pvc->pc',
mo2, tmp.reshape(nmo,dj,ncore)) * 2
tmp = numpy.einsum('uvpc,uc->vcp', buf, mo1[:,:ncore])
tmp = lib.dot(tmp.reshape(-1,nmo), mo).reshape(dj,ncore,nmo)
k_pc += numpy.einsum('vp,vcp->pc', mo2, tmp)
tmp = numpy.einsum('uvpc,vc->ucp', buf, mo2[:,:ncore])
tmp = lib.dot(tmp.reshape(-1,nmo), mo).reshape(di,ncore,nmo)
k_pc += numpy.einsum('up,ucp->pc', mo1, tmp)
p0 += dij
if log.verbose >= logger.DEBUG1:
ti1 = log.timer('j_cp and k_cp', *ti1)
if log.verbose >= logger.DEBUG1:
ti1 = log.timer('half transformation of the buffer', *ti1)
# ppaa, papa
faapp_buf[str(istep)] = \
bufpa.reshape(sh_range[2],nmo,ncas)[:,ncore:nocc].reshape(-1,ncas**2).T
p0 = 0
for ij in range(sh_range[0], sh_range[1]):
i,j = lib.index_tril_to_pair(ij)
i0 = ao_loc[i]
j0 = ao_loc[j]
i1 = ao_loc[i+1]
j1 = ao_loc[j+1]
di = i1 - i0
dj = j1 - j0
if i == j:
dij = di * (di+1) // 2
buf1 = numpy.empty((di,di,nmo*ncas))
idx = numpy.tril_indices(di)
buf1[idx] = bufpa[p0:p0+dij]
buf1[idx[1],idx[0]] = bufpa[p0:p0+dij]
else:
dij = di * dj
buf1 = bufpa[p0:p0+dij].reshape(di,dj,-1)
mo1 = mo[j0:j1,ncore:nocc].copy()
for i in range(di):
lib.dot(mo1.T, buf1[i], 1, papa_buf[i0+i], 1)
mo1 = mo[i0:i1,ncore:nocc].copy()
buf1 = lib.dot(mo1.T, buf1.reshape(di,-1))
papa_buf[j0:j1] += buf1.reshape(ncas,dj,-1).transpose(1,0,2)
p0 += dij
if log.verbose >= logger.DEBUG1:
ti1 = log.timer('ppaa and papa buffer', *ti1)
ti0 = log.timer('gen AO/transform MO [%d/%d]'%(istep+1,nstep), *ti0)
buf = buf1 = bufpa = None
bufs1 = bufs2 = bufs3 = None
time1 = log.timer('mc_ao2mo pass 1', *time0)
log.debug1('Half transformation done. Current memory %d',
lib.current_memory()[0])
nblk = int(max(8, min(nmo, (max_memory*1e6/8-papa_buf.size)/(ncas**2*nmo))))
log.debug1('nblk for papa = %d', nblk)
dset = feri.create_dataset('papa', (nmo,ncas,nmo,ncas), 'f8')
for i0, i1 in prange(0, nmo, nblk):
tmp = lib.dot(mo[:,i0:i1].T, papa_buf.reshape(nao,-1))
dset[i0:i1] = tmp.reshape(i1-i0,ncas,nmo,ncas)
papa_buf = tmp = None
time1 = log.timer('papa pass 2', *time1)
tmp = numpy.empty((ncas**2,nao_pair))
p0 = 0
for istep, sh_range in enumerate(shranges):
tmp[:,p0:p0+sh_range[2]] = faapp_buf[str(istep)]
p0 += sh_range[2]
nblk = int(max(8, min(nmo, (max_memory*1e6/8-tmp.size)/(ncas**2*nmo)-1)))
log.debug1('nblk for ppaa = %d', nblk)
dset = feri.create_dataset('ppaa', (nmo,nmo,ncas,ncas), 'f8')
for i0, i1 in prange(0, nmo, nblk):
tmp1 = _ao2mo.nr_e2(tmp, mo, (i0,i1,0,nmo), 's4', 's1', ao_loc=ao_loc)
tmp1 = tmp1.reshape(ncas,ncas,i1-i0,nmo)
for j in range(i1-i0):
dset[i0+j] = tmp1[:,:,j].transpose(2,0,1)
tmp = tmp1 = None
time1 = log.timer('ppaa pass 2', *time1)
time0 = log.timer('mc_ao2mo', *time0)
return j_pc, k_pc