本文整理汇总了Python中pyscf.ao2mo.restore函数的典型用法代码示例。如果您正苦于以下问题:Python restore函数的具体用法?Python restore怎么用?Python restore使用的例子?那么恭喜您, 这里精选的函数代码示例或许可以为您提供帮助。
在下文中一共展示了restore函数的20个代码示例,这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞,您的评价将有助于我们的系统推荐出更棒的Python代码示例。
示例1: writeIntegralFile
def writeIntegralFile(shciobj, h1eff, eri_cas, ncas, nelec, ecore=0):
if isinstance(nelec, (int, numpy.integer)):
if shciobj.spin is None:
nelecb = nelec // 2
else:
nelecb = (nelec - shciobj.spin) // 2
neleca = nelec - nelecb
else :
neleca, nelecb = nelec
if shciobj.groupname is not None and shciobj.orbsym is not []:
# First removing the symmetry forbidden integrals. This has been done using
# the pyscf internal irrep-IDs (stored in shciobj.orbsym)
orbsym = numpy.asarray(shciobj.orbsym) % 10
pair_irrep = (orbsym.reshape(-1,1) ^ orbsym)[numpy.tril_indices(ncas)]
sym_forbid = pair_irrep.reshape(-1,1) != pair_irrep.ravel()
eri_cas = ao2mo.restore(4, eri_cas, ncas)
eri_cas[sym_forbid] = 0
eri_cas = ao2mo.restore(8, eri_cas, ncas)
# Convert the pyscf internal irrep-ID to molpro irrep-ID
orbsym = numpy.asarray(symmetry.convert_orbsym(shciobj.groupname, orbsym))
else:
orbsym = []
eri_cas = ao2mo.restore(8, eri_cas, ncas)
if not os.path.exists(shciobj.runtimedir):
os.makedirs(shciobj.runtimedir)
# The name of the FCIDUMP file, default is "FCIDUMP".
integralFile = os.path.join(shciobj.runtimedir, shciobj.integralfile)
tools.fcidump.from_integrals(integralFile, h1eff, eri_cas, ncas,
neleca+nelecb, ecore, ms=abs(neleca-nelecb),
orbsym=orbsym)
return integralFile
开发者ID:chrinide,项目名称:pyscf,代码行数:34,代码来源:shci.py
示例2: contract_2e
def contract_2e(eri, fcivec, nsite, nelec, nphonon):
neleca, nelecb = _unpack_nelec(nelec)
link_indexa = cistring.gen_linkstr_index(range(nsite), neleca)
link_indexb = cistring.gen_linkstr_index(range(nsite), nelecb)
cishape = make_shape(nsite, nelec, nphonon)
ci0 = fcivec.reshape(cishape)
t1a = numpy.zeros((nsite,nsite)+cishape)
t1b = numpy.zeros((nsite,nsite)+cishape)
for str0, tab in enumerate(link_indexa):
for a, i, str1, sign in tab:
t1a[a,i,str1] += sign * ci0[str0]
for str0, tab in enumerate(link_indexb):
for a, i, str1, sign in tab:
t1b[a,i,:,str1] += sign * ci0[:,str0]
g2e_aa = ao2mo.restore(1, eri[0], nsite)
g2e_ab = ao2mo.restore(1, eri[1], nsite)
g2e_bb = ao2mo.restore(1, eri[2], nsite)
t2a = numpy.dot(g2e_aa.reshape(nsite**2,-1), t1a.reshape(nsite**2,-1))
t2a+= numpy.dot(g2e_ab.reshape(nsite**2,-1), t1b.reshape(nsite**2,-1))
t2b = numpy.dot(g2e_ab.reshape(nsite**2,-1).T, t1a.reshape(nsite**2,-1))
t2b+= numpy.dot(g2e_bb.reshape(nsite**2,-1), t1b.reshape(nsite**2,-1))
t2a = t2a.reshape((nsite,nsite)+cishape)
t2b = t2b.reshape((nsite,nsite)+cishape)
fcinew = numpy.zeros(cishape)
for str0, tab in enumerate(link_indexa):
for a, i, str1, sign in tab:
fcinew[str1] += sign * t2a[a,i,str0]
for str0, tab in enumerate(link_indexb):
for a, i, str1, sign in tab:
fcinew[:,str1] += sign * t2b[a,i,:,str0]
return fcinew.reshape(fcivec.shape)
开发者ID:chrinide,项目名称:pyscf,代码行数:34,代码来源:direct_ep.py
示例3: writeIntegralFile
def writeIntegralFile(DMRGCI, h1eff, eri_cas, ncas, nelec, ecore=0):
if isinstance(nelec, (int, numpy.integer)):
neleca = nelec//2 + nelec%2
nelecb = nelec - neleca
else :
neleca, nelecb = nelec
# The name of the FCIDUMP file, default is "FCIDUMP".
integralFile = os.path.join(DMRGCI.runtimeDir, DMRGCI.integralFile)
if DMRGCI.groupname is not None and DMRGCI.orbsym is not []:
# First removing the symmetry forbidden integrals. This has been done using
# the pyscf internal irrep-IDs (stored in DMRGCI.orbsym)
orbsym = numpy.asarray(DMRGCI.orbsym) % 10
pair_irrep = (orbsym.reshape(-1,1) ^ orbsym)[numpy.tril_indices(ncas)]
sym_forbid = pair_irrep.reshape(-1,1) != pair_irrep.ravel()
eri_cas = ao2mo.restore(4, eri_cas, ncas)
eri_cas[sym_forbid] = 0
eri_cas = ao2mo.restore(8, eri_cas, ncas)
#orbsym = numpy.asarray(dmrg_sym.convert_orbsym(DMRGCI.groupname, DMRGCI.orbsym))
#eri_cas = pyscf.ao2mo.restore(8, eri_cas, ncas)
# Then convert the pyscf internal irrep-ID to molpro irrep-ID
orbsym = numpy.asarray(dmrg_sym.convert_orbsym(DMRGCI.groupname, orbsym))
else:
orbsym = []
eri_cas = ao2mo.restore(8, eri_cas, ncas)
if not os.path.exists(DMRGCI.scratchDirectory):
os.makedirs(DMRGCI.scratchDirectory)
if not os.path.exists(DMRGCI.runtimeDir):
os.makedirs(DMRGCI.runtimeDir)
tools.fcidump.from_integrals(integralFile, h1eff, eri_cas, ncas,
neleca+nelecb, ecore, ms=abs(neleca-nelecb),
orbsym=orbsym)
return integralFile
开发者ID:sunqm,项目名称:pyscf,代码行数:34,代码来源:dmrgci.py
示例4: test_nr_transe1incore
def test_nr_transe1incore(self):
eri_ao = _vhf.int2e_sph(mol._atm, mol._bas, mol._env)
eriref = ao2mo.restore(1, eri_ao, nao)
eriref = numpy.einsum("ijpl,pk->ijkl", eriref, mo)
eriref = numpy.einsum("ijkp,pl->ijkl", eriref, mo)
eriref = ao2mo.restore(4, eriref, nao)
eri_ao = ao2mo.restore(8, eri_ao, nao)
ftrans1 = f1pointer("AO2MOtranse1_incore_s8")
fmmm = f1pointer("AO2MOmmm_nr_s2_s2")
eri1 = numpy.empty((naopair, naopair))
libao2mo1.AO2MOnr_e1incore_drv(
ftrans1,
fmmm,
eri1.ctypes.data_as(ctypes.c_void_p),
eri_ao.ctypes.data_as(ctypes.c_void_p),
mo.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(0),
ctypes.c_int(naopair),
ctypes.c_int(nao),
ctypes.c_int(0),
ctypes.c_int(nao),
ctypes.c_int(0),
ctypes.c_int(nao),
)
self.assertTrue(numpy.allclose(eri1, eriref))
开发者ID:raybrad,项目名称:pyscf,代码行数:26,代码来源:test_ao2mo.py
示例5: test_mp2_contract_eri_dm
def test_mp2_contract_eri_dm(self):
nocc = mol.nelectron//2
nmo = mf.mo_energy.size
nvir = nmo - nocc
pt = mp.mp2.MP2(mf)
emp2, t2 = pt.kernel()
eri = ao2mo.restore(1, ao2mo.kernel(mf._eri, mf.mo_coeff), nmo)
hcore = mf.get_hcore()
rdm1 = pt.make_rdm1()
rdm2 = pt.make_rdm2()
h1 = reduce(numpy.dot, (mf.mo_coeff.T, hcore, mf.mo_coeff))
e1 = numpy.einsum('ij,ji', h1, rdm1)
e1+= numpy.einsum('ijkl,ijkl', eri, rdm2) * .5
e1+= mol.energy_nuc()
self.assertAlmostEqual(e1, pt.e_tot, 9)
pt.frozen = 2
pt.max_memory = 1
emp2, t2 = pt.kernel(with_t2=False)
eri = ao2mo.restore(1, ao2mo.kernel(mf._eri, mf.mo_coeff), nmo)
hcore = mf.get_hcore()
rdm1 = pt.make_rdm1()
rdm2 = pt.make_rdm2()
h1 = reduce(numpy.dot, (mf.mo_coeff.T, hcore, mf.mo_coeff))
e1 = numpy.einsum('ij,ji', h1, rdm1)
e1+= numpy.einsum('ijkl,ijkl', eri, rdm2) * .5
e1+= mol.energy_nuc()
self.assertAlmostEqual(e1, pt.e_tot, 9)
开发者ID:chrinide,项目名称:pyscf,代码行数:29,代码来源:test_mp2.py
示例6: __init__
def __init__(self, myci, mo_coeff, method='incore'):
mol = myci.mol
mf = myci._scf
nocc = myci.nocc
nmo = myci.nmo
nvir = nmo - nocc
if mo_coeff is None:
self.mo_coeff = mo_coeff = myci.mo_coeff
if (method == 'incore' and mf._eri is not None):
eri = ao2mo.kernel(mf._eri, mo_coeff, verbose=myci.verbose)
else:
eri = ao2mo.kernel(mol, mo_coeff, verbose=myci.verbose)
eri = ao2mo.restore(1, eri, nmo)
eri = eri.reshape(nmo,nmo,nmo,nmo)
self.oooo = eri[:nocc,:nocc,:nocc,:nocc]
self.vvoo = eri[nocc:,nocc:,:nocc,:nocc]
self.vooo = eri[nocc:,:nocc,:nocc,:nocc]
self.voov = eri[nocc:,:nocc,:nocc,nocc:]
self.vovv = lib.pack_tril(eri[nocc:,:nocc,nocc:,nocc:].reshape(-1,nvir,nvir))
self.vvvv = ao2mo.restore(4, eri[nocc:,nocc:,nocc:,nocc:].copy(), nvir)
dm = mf.make_rdm1()
vhf = mf.get_veff(mol, dm)
h1 = mf.get_hcore(mol)
self.fock = reduce(numpy.dot, (mo_coeff.T, h1 + vhf, mo_coeff))
开发者ID:eronca,项目名称:pyscf,代码行数:26,代码来源:cisd_slow.py
示例7: _gamma2_intermediates
def _gamma2_intermediates(cc, t1, t2, l1, l2):
d2 = ccsd_rdm._gamma2_intermediates(cc, t1, t2, l1, l2)
nocc, nvir = t1.shape
if cc.frozen is None or cc.frozen is 0:
dovov, dvvvv, doooo, doovv, dovvo, dvvov, dovvv, dooov = d2
dvvov = dovvv.transpose(2,3,0,1)
dvvvv = ao2mo.restore(1, d2[1], nvir)
return dovov, dvvvv, doooo, doovv, dovvo, dvvov, dovvv, dooov
nocc0 = numpy.count_nonzero(cc.mo_occ>0)
nvir0 = cc.mo_occ.size - nocc0
OA, VA, OF, VF = index_frozen_active(cc)
dovov = numpy.zeros((nocc0,nvir0,nocc0,nvir0))
dvvvv = numpy.zeros((nvir0,nvir0,nvir0,nvir0))
doooo = numpy.zeros((nocc0,nocc0,nocc0,nocc0))
doovv = numpy.zeros((nocc0,nocc0,nvir0,nvir0))
dovvo = numpy.zeros((nocc0,nvir0,nvir0,nocc0))
dovvv = numpy.zeros((nocc0,nvir0,nvir0,nvir0))
dooov = numpy.zeros((nocc0,nocc0,nocc0,nvir0))
dovov[OA[:,None,None,None],VA[:,None,None],OA[:,None],VA] = d2[0]
dvvvv[VA[:,None,None,None],VA[:,None,None],VA[:,None],VA] = ao2mo.restore(1, d2[1], nvir)
doooo[OA[:,None,None,None],OA[:,None,None],OA[:,None],OA] = d2[2]
doovv[OA[:,None,None,None],OA[:,None,None],VA[:,None],VA] = d2[3]
dovvo[OA[:,None,None,None],VA[:,None,None],VA[:,None],OA] = d2[4]
dovvv[OA[:,None,None,None],VA[:,None,None],VA[:,None],VA] = d2[6]
dooov[OA[:,None,None,None],OA[:,None,None],OA[:,None],VA] = d2[7]
dvvov = dovvv.transpose(2,3,0,1)
return dovov, dvvvv, doooo, doovv, dovvo, dvvov, dovvv, dooov
开发者ID:chrinide,项目名称:pyscf,代码行数:27,代码来源:ccsd_slow.py
示例8: mp2
def mp2(mol, h1e, eri, mo, nelec, with_1pdm, with_e2frag):
eri1 = ao2mo.restore(8, eri, mo.shape[1])
hf_energy, mo_energy, mo_coeff, mo_occ = simple_hf(h1e, eri1, mo, nelec)
mf = scf.RHF(mol)
mf.get_hcore = lambda mol: h1e
mf._eri = eri
mymp2 = mp.MP2(mf)
mymp2.nocc = nelec // 2
mymp2.nmo = len(mo_energy)
emp2, t2 = mymp2.kernel(mo_energy, mo_coeff)
if with_1pdm:
rdm1 = mymp2.make_rdm1(t2)
for i in range(nelec // 2):
rdm1[i, i] += 2
rdm1 = reduce(numpy.dot, (mo_coeff, rdm1, mo_coeff.T))
else:
rdm1 = None
if with_e2frag:
norb = mo_coeff.shape[0]
eri1 = part_eri_hermi(eri, norb, with_e2frag)
eri1 = ao2mo.incore.full(eri1, mo_coeff)
eri1 = ao2mo.restore(1, eri1, norb)
rdm2 = mymp2.make_rdm2(t2)
for i in range(nelec // 2):
for j in range(nelec // 2):
rdm2[i, i, j, j] += 4
rdm2[i, j, i, j] += -2
e2frag = 0.5 * numpy.dot(rdm2.reshape(-1), eri1.reshape(-1))
else:
e2frag = None
return hf_energy, emp2 + hf_energy, e2frag, rdm1
开发者ID:BB-Goldstein,项目名称:pydmet-1,代码行数:33,代码来源:impsolver.py
示例9: test_nroutcore_eri
def test_nroutcore_eri(self):
ftmp = tempfile.NamedTemporaryFile(dir=lib.param.TMPDIR)
erifile = ftmp.name
eri_ao = ao2mo.restore(1, mol.intor('int2e', aosym='s2kl'), nao)
eriref = numpy.einsum('pjkl,pi->ijkl', eri_ao, mo)
eriref = numpy.einsum('ipkl,pj->ijkl', eriref, mo)
eriref = numpy.einsum('ijpl,pk->ijkl', eriref, mo)
eriref = numpy.einsum('ijkp,pl->ijkl', eriref, mo)
mos = (mo[:,:4], mo[:,:3], mo[:,:3], mo[:,:2])
ao2mo.outcore.general(mol, mos, erifile, dataname='eri_mo',
intor='int2e', aosym=1)
with ao2mo.load(erifile) as eri1:
eri1 = numpy.asarray(eri1).reshape(4,3,3,2)
self.assertTrue(numpy.allclose(eri1, eriref[:4,:3,:3,:2]))
ao2mo.outcore.full(mol, mo, erifile, dataname='eri_mo',
intor='int2e_sph', aosym='s2ij', comp=1)
with ao2mo.load(erifile, 'eri_mo') as eri:
eri1 = ao2mo.restore(1, numpy.array(eri), nao)
eri1 = eri1.reshape(nao,nao,nao,nao)
self.assertTrue(numpy.allclose(eri1, eriref))
mos = (mo[:,:3], mo[:,:3], mo[:,:3], mo[:,:2])
ao2mo.outcore.general(mol, mos, erifile, dataname='eri_mo',
intor='int2e_sph', aosym='s4', comp=1,
compact=False)
with ao2mo.load(erifile, 'eri_mo') as eri1:
eri1 = numpy.asarray(eri1).reshape(3,3,3,2)
self.assertTrue(numpy.allclose(eri1, eriref[:3,:3,:3,:2]))
ao2mo.outcore.full(mol, mo[:,:0], erifile,
intor='int2e', aosym='1', comp=1)
with ao2mo.load(erifile, 'eri_mo') as eri:
self.assertTrue(eri.size == 0)
开发者ID:chrinide,项目名称:pyscf,代码行数:35,代码来源:test_outcore.py
示例10: part_eri_hermi
def part_eri_hermi(eri, norb, nimp):
eri1 = ao2mo.restore(4, eri, norb)
for i in range(eri1.shape[0]):
tmp = lib.unpack_tril(eri1[i])
tmp[nimp:] = 0
eri1[i] = lib.pack_tril(tmp + tmp.T)
eri1 = lib.transpose_sum(eri1, inplace=True)
return ao2mo.restore(8, eri1, norb) * 0.25
开发者ID:BB-Goldstein,项目名称:pydmet-1,代码行数:8,代码来源:impsolver.py
示例11: contract_2e
def contract_2e(eri, civec_strs, norb, nelec, link_index=None):
ci_coeff, nelec, ci_strs = _unpack(civec_strs, nelec)
if link_index is None:
link_index = _all_linkstr_index(ci_strs, norb, nelec)
cd_indexa, dd_indexa, cd_indexb, dd_indexb = link_index
na, nlinka = cd_indexa.shape[:2]
nb, nlinkb = cd_indexb.shape[:2]
eri = ao2mo.restore(1, eri, norb)
eri1 = eri.transpose(0,2,1,3) - eri.transpose(0,2,3,1)
idx,idy = numpy.tril_indices(norb, -1)
idx = idx * norb + idy
eri1 = lib.take_2d(eri1.reshape(norb**2,-1), idx, idx) * 2
fcivec = ci_coeff.reshape(na,nb)
# (bb|bb)
if nelec[1] > 1:
mb, mlinkb = dd_indexb.shape[:2]
fcivecT = lib.transpose(fcivec)
ci1T = numpy.zeros((nb,na))
libfci.SCIcontract_2e_aaaa(eri1.ctypes.data_as(ctypes.c_void_p),
fcivecT.ctypes.data_as(ctypes.c_void_p),
ci1T.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(norb),
ctypes.c_int(nb), ctypes.c_int(na),
ctypes.c_int(mb), ctypes.c_int(mlinkb),
dd_indexb.ctypes.data_as(ctypes.c_void_p))
ci1 = lib.transpose(ci1T, out=fcivecT)
else:
ci1 = numpy.zeros_like(fcivec)
# (aa|aa)
if nelec[0] > 1:
ma, mlinka = dd_indexa.shape[:2]
libfci.SCIcontract_2e_aaaa(eri1.ctypes.data_as(ctypes.c_void_p),
fcivec.ctypes.data_as(ctypes.c_void_p),
ci1.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(norb),
ctypes.c_int(na), ctypes.c_int(nb),
ctypes.c_int(ma), ctypes.c_int(mlinka),
dd_indexa.ctypes.data_as(ctypes.c_void_p))
h_ps = numpy.einsum('pqqs->ps', eri)
eri1 = eri * 2
for k in range(norb):
eri1[:,:,k,k] += h_ps/nelec[0]
eri1[k,k,:,:] += h_ps/nelec[1]
eri1 = ao2mo.restore(4, eri1, norb)
# (bb|aa)
libfci.SCIcontract_2e_bbaa(eri1.ctypes.data_as(ctypes.c_void_p),
fcivec.ctypes.data_as(ctypes.c_void_p),
ci1.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(norb),
ctypes.c_int(na), ctypes.c_int(nb),
ctypes.c_int(nlinka), ctypes.c_int(nlinkb),
cd_indexa.ctypes.data_as(ctypes.c_void_p),
cd_indexb.ctypes.data_as(ctypes.c_void_p))
return _as_SCIvector(ci1.reshape(ci_coeff.shape), ci_strs)
开发者ID:eronca,项目名称:pyscf,代码行数:57,代码来源:select_ci.py
示例12: test_ccsd
def test_ccsd(self):
mol = gto.M()
mf = scf.RHF(mol)
mcc = cc.CCSD(mf)
numpy.random.seed(12)
mcc.nocc = nocc = 5
mcc.nmo = nmo = 12
nvir = nmo - nocc
eri0 = numpy.random.random((nmo,nmo,nmo,nmo))
eri0 = ao2mo.restore(1, ao2mo.restore(8, eri0, nmo), nmo)
fock0 = numpy.random.random((nmo,nmo))
fock0 = fock0 + fock0.T + numpy.diag(range(nmo))*2
t1 = numpy.random.random((nocc,nvir))
t2 = numpy.random.random((nocc,nocc,nvir,nvir))
t2 = t2 + t2.transpose(1,0,3,2)
l1 = numpy.random.random((nocc,nvir))
l2 = numpy.random.random((nocc,nocc,nvir,nvir))
l2 = l2 + l2.transpose(1,0,3,2)
eris = cc.ccsd._ChemistsERIs()
eris.oooo = eri0[:nocc,:nocc,:nocc,:nocc].copy()
eris.ovoo = eri0[:nocc,nocc:,:nocc,:nocc].copy()
eris.oovv = eri0[:nocc,:nocc,nocc:,nocc:].copy()
eris.ovvo = eri0[:nocc,nocc:,nocc:,:nocc].copy()
idx = numpy.tril_indices(nvir)
eris.ovvv = eri0[:nocc,nocc:,nocc:,nocc:][:,:,idx[0],idx[1]].copy()
eris.vvvv = ao2mo.restore(4,eri0[nocc:,nocc:,nocc:,nocc:],nvir)
eris.fock = fock0
eris.mo_energy = fock0.diagonal()
saved = ccsd_lambda.make_intermediates(mcc, t1, t2, eris)
l1new, l2new = ccsd_lambda.update_lambda(mcc, t1, t2, l1, l2, eris, saved)
self.assertAlmostEqual(abs(l1new).sum(), 38172.7896467303, 8)
self.assertAlmostEqual(numpy.dot(l1new.flatten(), numpy.arange(35)), 739312.005491083, 8)
self.assertAlmostEqual(numpy.dot(l1new.flatten(), numpy.sin(numpy.arange(35))), 7019.50937051188, 8)
self.assertAlmostEqual(numpy.dot(numpy.sin(l1new.flatten()), numpy.arange(35)), 69.6652346635955, 8)
self.assertAlmostEqual(abs(l2new).sum(), 72035.4931071527, 8)
self.assertAlmostEqual(abs(l2new-l2new.transpose(1,0,3,2)).sum(), 0, 9)
self.assertAlmostEqual(numpy.dot(l2new.flatten(), numpy.arange(35**2)), 48427109.5409886, 7)
self.assertAlmostEqual(numpy.dot(l2new.flatten(), numpy.sin(numpy.arange(35**2))), 137.758016736487, 8)
self.assertAlmostEqual(numpy.dot(numpy.sin(l2new.flatten()), numpy.arange(35**2)), 507.656936701192, 8)
mcc.max_memory = 0
saved = ccsd_lambda.make_intermediates(mcc, t1, t2, eris)
l1new, l2new = ccsd_lambda.update_lambda(mcc, t1, t2, l1, l2, eris, saved)
self.assertAlmostEqual(abs(l1new).sum(), 38172.7896467303, 8)
self.assertAlmostEqual(numpy.dot(l1new.flatten(), numpy.arange(35)), 739312.005491083, 8)
self.assertAlmostEqual(numpy.dot(l1new.flatten(), numpy.sin(numpy.arange(35))), 7019.50937051188, 8)
self.assertAlmostEqual(numpy.dot(numpy.sin(l1new.flatten()), numpy.arange(35)), 69.6652346635955, 8)
self.assertAlmostEqual(abs(l2new).sum(), 72035.4931071527, 8)
self.assertAlmostEqual(abs(l2new-l2new.transpose(1,0,3,2)).sum(), 0, 9)
self.assertAlmostEqual(numpy.dot(l2new.flatten(), numpy.arange(35**2)), 48427109.5409886, 7)
self.assertAlmostEqual(numpy.dot(l2new.flatten(), numpy.sin(numpy.arange(35**2))), 137.758016736487, 8)
self.assertAlmostEqual(numpy.dot(numpy.sin(l2new.flatten()), numpy.arange(35**2)), 507.656936701192, 8)
开发者ID:chrinide,项目名称:pyscf,代码行数:56,代码来源:test_ccsd_lambda.py
示例13: gen_hop_uhf_external
def gen_hop_uhf_external(mf):
mol = mf.mol
mo_a, mo_b = mf.mo_coeff
mo_ea, mo_eb = mf.mo_energy
mo_occa, mo_occb = mf.mo_occ
nmo = mo_a.shape[1]
nocca = numpy.count_nonzero(mo_occa)
noccb = numpy.count_nonzero(mo_occb)
nvira = nmo - nocca
nvirb = nmo - noccb
eri_aa = ao2mo.restore(1, ao2mo.full(mol, mo_a), nmo)
eri_ab = ao2mo.restore(1, ao2mo.general(mol, [mo_a,mo_a,mo_b,mo_b]), nmo)
eri_bb = ao2mo.restore(1, ao2mo.full(mol, mo_b), nmo)
# alpha -> alpha
haa =-numpy.einsum('abji->iajb', eri_aa[nocca:,nocca:,:nocca,:nocca])
haa+= numpy.einsum('ajbi->iajb', eri_aa[nocca:,:nocca,nocca:,:nocca])
for a in range(nvira):
for i in range(nocca):
haa[i,a,i,a] += mo_ea[nocca+a] - mo_ea[i]
# beta -> beta
hbb =-numpy.einsum('abji->iajb', eri_bb[noccb:,noccb:,:noccb,:noccb])
hbb+= numpy.einsum('ajbi->iajb', eri_bb[noccb:,:noccb,noccb:,:noccb])
for a in range(nvirb):
for i in range(noccb):
hbb[i,a,i,a] += mo_eb[noccb+a] - mo_eb[i]
nova = nocca * nvira
novb = noccb * nvirb
h1 = numpy.zeros((nova+novb,nova+novb))
h1[:nova,:nova] = haa.transpose(1,0,3,2).reshape(nova,nova)
h1[nova:,nova:] = hbb.transpose(1,0,3,2).reshape(novb,novb)
def hop1(x):
return h1.dot(x)
h11 =-numpy.einsum('abji->iajb', eri_ab[nocca:,nocca:,:noccb,:noccb])
for a in range(nvira):
for i in range(noccb):
h11[i,a,i,a] += mo_ea[nocca+a] - mo_eb[i]
h22 =-numpy.einsum('jiab->iajb', eri_ab[:nocca,:nocca,noccb:,noccb:])
for a in range(nvirb):
for i in range(nocca):
h22[i,a,i,a] += mo_eb[noccb+a] - mo_ea[i]
h12 =-numpy.einsum('ajbi->iajb', eri_ab[nocca:,:nocca,noccb:,:noccb])
h21 =-numpy.einsum('biaj->iajb', eri_ab[nocca:,:nocca,noccb:,:noccb])
n1 = noccb * nvira
n2 = nocca * nvirb
h2 = numpy.empty((n1+n2,n1+n2))
h2[:n1,:n1] = h11.transpose(1,0,3,2).reshape(n1,n1)
h2[n1:,n1:] = h22.transpose(1,0,3,2).reshape(n2,n2)
h2[:n1,n1:] = h12.transpose(1,0,3,2).reshape(n1,n2)
h2[n1:,:n1] = h21.transpose(1,0,3,2).reshape(n2,n1)
def hop2(x):
return h2.dot(x)
return hop1, hop2
开发者ID:chrinide,项目名称:pyscf,代码行数:56,代码来源:test_stability.py
示例14: test_kernel
def test_kernel(self):
h1 = h1e + h1e.T
eri = .5* ao2mo.restore(1, ao2mo.restore(8, h2e, norb), norb)
h = fci.direct_spin1.pspace(h1, eri, norb, nelec, np=5000)[1]
eref, c0 = numpy.linalg.eigh(h)
sol = fci.direct_nosym.FCI()
e, c1 = sol.kernel(h1, eri, norb, nelec, max_space=40)
self.assertAlmostEqual(eref[0], e, 9)
self.assertAlmostEqual(abs(c0[:,0].dot(c1.ravel())), 1, 9)
开发者ID:chrinide,项目名称:pyscf,代码行数:10,代码来源:test_direct_nosym.py
示例15: _get_VVVV
def _get_VVVV(eris):
if eris.VVVV is None and getattr(eris, 'VVL', None) is not None: # DF eris
VVL = np.asarray(eris.VVL)
nvir = int(np.sqrt(eris.VVL.shape[0]*2))
return ao2mo.restore(1, lib.dot(VVL, VVL.T), nvir)
elif len(eris.VVVV.shape) == 2:
nvir = int(np.sqrt(eris.VVVV.shape[0]*2))
return ao2mo.restore(1, np.asarray(eris.VVVV), nvir)
else:
return eris.VVVV
开发者ID:chrinide,项目名称:pyscf,代码行数:10,代码来源:uintermediates.py
示例16: absorb_h1e
def absorb_h1e(h1e, eri, norb, nelec, fac=1):
'''Modify 2e Hamiltonian to include 1e Hamiltonian contribution.
'''
if not isinstance(nelec, (int, numpy.number)):
nelec = sum(nelec)
h2e = ao2mo.restore(1, eri.copy(), norb)
f1e = h1e - numpy.einsum('jiik->jk', h2e) * .5
f1e = f1e * (1./(nelec+1e-100))
for k in range(norb):
h2e[k,k,:,:] += f1e
h2e[:,:,k,k] += f1e
return ao2mo.restore(4, h2e, norb) * fac
开发者ID:chrinide,项目名称:pyscf,代码行数:12,代码来源:direct_spin1.py
示例17: contract_2e
def contract_2e(eri, civec_strs, norb, nelec, link_index=None, orbsym=None):
ci_coeff, nelec, ci_strs = selected_ci._unpack(civec_strs, nelec)
if link_index is None:
link_index = selected_ci._all_linkstr_index(ci_strs, norb, nelec)
cd_indexa, dd_indexa, cd_indexb, dd_indexb = link_index
na, nlinka = nb, nlinkb = cd_indexa.shape[:2]
eri = ao2mo.restore(1, eri, norb)
eri1 = eri.transpose(0,2,1,3) - eri.transpose(0,2,3,1)
idx,idy = numpy.tril_indices(norb, -1)
idx = idx * norb + idy
eri1 = lib.take_2d(eri1.reshape(norb**2,-1), idx, idx) * 2
lib.transpose_sum(eri1, inplace=True)
eri1 *= .5
eri1, dd_indexa, dimirrep = selected_ci_symm.reorder4irrep(eri1, norb, dd_indexa, orbsym, -1)
fcivec = ci_coeff.reshape(na,nb)
ci1 = numpy.zeros_like(fcivec)
# (aa|aa)
if nelec[0] > 1:
ma, mlinka = mb, mlinkb = dd_indexa.shape[:2]
libfci.SCIcontract_2e_aaaa_symm(eri1.ctypes.data_as(ctypes.c_void_p),
fcivec.ctypes.data_as(ctypes.c_void_p),
ci1.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(norb),
ctypes.c_int(na), ctypes.c_int(nb),
ctypes.c_int(ma), ctypes.c_int(mlinka),
dd_indexa.ctypes.data_as(ctypes.c_void_p),
dimirrep.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(len(dimirrep)))
h_ps = numpy.einsum('pqqs->ps', eri) * (.5/nelec[0])
eri1 = eri.copy()
for k in range(norb):
eri1[:,:,k,k] += h_ps
eri1[k,k,:,:] += h_ps
eri1 = ao2mo.restore(4, eri1, norb)
lib.transpose_sum(eri1, inplace=True)
eri1 *= .5
eri1, cd_indexa, dimirrep = selected_ci_symm.reorder4irrep(eri1, norb, cd_indexa, orbsym)
# (bb|aa)
libfci.SCIcontract_2e_bbaa_symm(eri1.ctypes.data_as(ctypes.c_void_p),
fcivec.ctypes.data_as(ctypes.c_void_p),
ci1.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(norb),
ctypes.c_int(na), ctypes.c_int(nb),
ctypes.c_int(nlinka), ctypes.c_int(nlinkb),
cd_indexa.ctypes.data_as(ctypes.c_void_p),
cd_indexa.ctypes.data_as(ctypes.c_void_p),
dimirrep.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(len(dimirrep)))
lib.transpose_sum(ci1, inplace=True)
return selected_ci._as_SCIvector(ci1.reshape(ci_coeff.shape), ci_strs)
开发者ID:chrinide,项目名称:pyscf,代码行数:53,代码来源:selected_ci_spin0_symm.py
示例18: test_large_ci
def test_large_ci(self):
norb = 6
nelec = (3,3)
numpy.random.seed(10)
h1e = numpy.random.random((norb,norb))
h1e = h1e + h1e.T
g2e = numpy.random.random((norb,norb,norb,norb))
eri = .5* ao2mo.restore(1, ao2mo.restore(8, g2e, norb), norb)
sol = fci.direct_spin1.FCI(mol)
e, c1 = sol.kernel(h1e, eri, norb, nelec)
self.assertAlmostEqual(e, -4.742664117996546, 9)
val = sol.large_ci(c1, norb, nelec)
self.assertAlmostEqual(val[0][0], c1[0,0], 9)
开发者ID:chrinide,项目名称:pyscf,代码行数:14,代码来源:test_spin1.py
示例19: test_restore4
def test_restore4(self):
self.assertTrue(numpy.allclose(a4, ao2mo.restore(4, a1, n)))
self.assertTrue(numpy.allclose(a4, ao2mo.restore('4', a4, n)))
self.assertTrue(numpy.allclose(a4, ao2mo.restore('s4', a8, n)))
self.assertTrue(numpy.allclose(a4, ao2mo.restore('s4', a2ij, n)))
self.assertTrue(numpy.allclose(a4, ao2mo.restore('s4', a2kl, n)))
self.assertTrue(numpy.allclose(b4, ao2mo.restore(4, b1, n)))
self.assertTrue(numpy.allclose(b4, ao2mo.restore('4', b4, n)))
self.assertTrue(numpy.allclose(b4, ao2mo.restore('4', b2ij, n)))
self.assertTrue(numpy.allclose(b4, ao2mo.restore('4', b2kl, n)))
开发者ID:chrinide,项目名称:pyscf,代码行数:11,代码来源:test_addons.py
示例20: test_uccsd_rdm2_mo2ao
def test_uccsd_rdm2_mo2ao(self):
mol = gto.Mole()
mol.verbose = 0
mol.atom = [
[8 , (0. , 0. , 0.)],
[1 , (0. , -0.757 , 0.587)],
[1 , (0. , 0.757 , 0.587)]]
mol.spin = 2
mol.basis = '631g'
mol.build(0, 0)
mf = scf.UHF(mol)
mf.conv_tol_grad = 1e-8
mf.kernel()
mycc = cc.UCCSD(mf)
mycc.diis_start_cycle = 1
mycc.conv_tol = 1e-10
eris = mycc.ao2mo()
ecc, t1, t2 = mycc.kernel(eris=eris)
l1, l2 = mycc.solve_lambda(eris=eris)
fdm2 = lib.H5TmpFile()
d2 = cc.uccsd_rdm._gamma2_outcore(mycc, t1, t2, l1, l2, fdm2, True)
nao = mycc.mo_coeff[0].shape[0]
ref = cc.uccsd_rdm._make_rdm2(mycc, None, d2, with_dm1=False)
aa = lib.einsum('ijkl,pi,qj,rk,sl->pqrs', ref[0], mycc.mo_coeff[0],
mycc.mo_coeff[0], mycc.mo_coeff[0], mycc.mo_coeff[0])
ab = lib.einsum('ijkl,pi,qj,rk,sl->pqrs', ref[1], mycc.mo_coeff[0],
mycc.mo_coeff[0], mycc.mo_coeff[1], mycc.mo_coeff[1])
bb = lib.einsum('ijkl,pi,qj,rk,sl->pqrs', ref[2], mycc.mo_coeff[1],
mycc.mo_coeff[1], mycc.mo_coeff[1], mycc.mo_coeff[1])
aa = aa + aa.transpose(0,1,3,2)
aa = aa + aa.transpose(1,0,2,3)
aa = ao2mo.restore(4, aa, nao) * .5
bb = bb + bb.transpose(0,1,3,2)
bb = bb + bb.transpose(1,0,2,3)
bb = ao2mo.restore(4, bb, nao) * .5
ab = ab + ab.transpose(0,1,3,2)
ab = ab + ab.transpose(1,0,2,3)
ab = ao2mo.restore(4, ab, nao) * .5
ref = (aa+ab, bb+ab.T)
rdm2 = uccsd_grad._rdm2_mo2ao(mycc, d2, mycc.mo_coeff)
self.assertAlmostEqual(abs(ref[0]-rdm2[0]).max(), 0, 10)
self.assertAlmostEqual(abs(ref[1]-rdm2[1]).max(), 0, 10)
uccsd_grad._rdm2_mo2ao(mycc, d2, mycc.mo_coeff, fdm2)
self.assertAlmostEqual(abs(ref[0]-fdm2['dm2aa+ab'].value).max(), 0, 10)
self.assertAlmostEqual(abs(ref[1]-fdm2['dm2bb+ab'].value).max(), 0, 10)
self.assertAlmostEqual(lib.finger(rdm2[0]), -1.6247203743431637, 7)
self.assertAlmostEqual(lib.finger(rdm2[1]), -0.44062825991527471, 7)
开发者ID:chrinide,项目名称:pyscf,代码行数:48,代码来源:test_ccsd.py
注:本文中的pyscf.ao2mo.restore函数示例由纯净天空整理自Github/MSDocs等源码及文档管理平台,相关代码片段筛选自各路编程大神贡献的开源项目,源码版权归原作者所有,传播和使用请参考对应项目的License;未经允许,请勿转载。 |
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