def __init__(self, **kw):
""" Constructor a mean field class (store result of a mean-field calc, deliver density matrix etc) """
#print(__name__, 'before construct')
nao.__init__(self, **kw)
self.dtype = kw['dtype'] if 'dtype' in kw else np.float64
self.pseudo = hasattr(self, 'sp2ion')
self.gen_pb = kw['gen_pb'] if 'gen_pb' in kw else True
if 'mf' in kw:
self.init_mo_from_pyscf(**kw)
elif 'label' in kw: # init KS orbitals with SIESTA
self.init_mo_coeff_label(**kw)
self.k2xyzw = self.xml_dict["k2xyzw"]
self.xc_code = 'LDA,PZ' # just a guess...
elif 'fireball' in kw: # init KS orbitals with Fireball
self.init_mo_coeff_fireball(**kw)
self.xc_code = 'GGA,PBE' # just a guess...
elif 'gpaw' in kw:
self.init_mo_coeff_label(**kw)
self.k2xyzw = np.array([[0.0,0.0,0.0,1.0]])
self.xc_code = 'LDA,PZ' # just a guess, but in case of GPAW there is a field...
elif 'openmx' in kw:
self.xc_code = 'GGA,PBE' # just a guess...
pass
else:
raise RuntimeError('unknown constructor')
if self.verbosity>0: print(__name__, ' pseudo ', self.pseudo)
self.init_libnao()
if self.gen_pb:
self.pb = prod_basis(nao=self, **kw)
if self.verbosity>0: print(__name__, ' dtype ', self.dtype, ' norbs ', self.norbs)
def __init__(self, **kw):
""" Constructor a mean field class (store result of a mean-field calc, deliver density matrix etc) """
#print(__name__, 'before construct')
nao.__init__(self, **kw)
self.dtype = kw['dtype'] if 'dtype' in kw else np.float64
self.pseudo = hasattr(self, 'sp2ion')
self.gen_pb = kw['gen_pb'] if 'gen_pb' in kw else True
if 'mf' in kw:
self.init_mo_from_pyscf(**kw)
elif 'label' in kw: # init KS orbitals with SIESTA
self.init_mo_coeff_label(**kw)
self.k2xyzw = self.xml_dict["k2xyzw"]
self.xc_code = 'LDA,PZ' # just a guess...
elif 'fireball' in kw: # init KS orbitals with Fireball
self.init_mo_coeff_fireball(**kw)
self.xc_code = 'GGA,PBE' # just a guess...
elif 'gpaw' in kw:
self.init_mo_coeff_label(**kw)
self.k2xyzw = np.array([[0.0, 0.0, 0.0, 1.0]])
self.xc_code = 'LDA,PZ' # just a guess, but in case of GPAW there is a field...
elif 'openmx' in kw:
self.xc_code = 'GGA,PBE' # just a guess...
pass
else:
raise RuntimeError('unknown constructor')
if self.verbosity > 0: print(__name__, ' pseudo ', self.pseudo)
self.init_libnao()
if self.gen_pb:
self.pb = prod_basis(nao=self, **kw)
if self.verbosity > 0:
print(__name__, ' dtype ', self.dtype, ' norbs ', self.norbs)
def test_ls_contributing(self): """ To test the list of contributing centers """ sv = nao(gto=mol) pb = prod_basis() pb.sv = sv pb.sv.ao_log.sp2rcut[0] = 10.0 pb.prod_log = sv.ao_log pb.prod_log.sp2rcut[0] = 10.0 pb.ac_rcut = max(sv.ao_log.sp2rcut) pb.ac_npc_max = 10 lsc = pb.ls_contributing(0,1) self.assertEqual(len(lsc),10) lsref = [ 0, 1, 13, 7, 5, 43, 42, 39, 38, 10] for i,ref in enumerate(lsref) : self.assertEqual(lsc[i],ref)
def test_gw(self):
""" This is GW """
mol = gto.M( verbose = 0, atom = '''Ag 0.0 0.0 -0.3707; Ag 0.0 0.0 0.3707''', basis = 'cc-pvdz-pp',)
gto_mf = scf.RHF(mol)#.density_fit()
gto_mf.kernel()
print('gto_mf.mo_energy:', gto_mf.mo_energy)
s = nao(mf=gto_mf, gto=mol, verbosity=0)
oref = s.overlap_coo().toarray()
print('s.norbs:', s.norbs, oref.sum())
pb = prod_basis(nao=s, algorithm='fp')
pab2v = pb.get_ac_vertex_array()
mom0,mom1=pb.comp_moments()
orec = np.einsum('p,pab->ab', mom0, pab2v)
print( abs(orec-oref).sum()/oref.size, np.amax(abs(orec-oref)) )
def __init__(self, **kw):
"""
Constructor a mean field class
store result of a mean-field calc, deliver density matrix etc
"""
#print(__name__, 'before construct')
nao.__init__(self, **kw)
if 'mf' in kw:
self.init_mo_from_pyscf(**kw)
elif 'label' in kw: # init KS orbitals with SIESTA
self.k2xyzw = self.xml_dict["k2xyzw"]
self.xc_code = 'LDA,PZ' # just a guess...
elif 'wfsx_fname' in kw: # init KS orbitals with WFSX file from SIESTA output
self.xc_code = 'LDA,PZ' # just a guess...
elif 'fireball' in kw: # init KS orbitals with Fireball
self.init_mo_coeff_fireball(**kw)
self.xc_code = 'GGA,PBE' # just a guess...
elif 'gpaw' in kw:
self.init_mo_coeff_label(**kw)
self.k2xyzw = np.array([[0.0, 0.0, 0.0, 1.0]])
self.xc_code = 'LDA,PZ' # just a guess, but in case of GPAW there is a field...
elif 'openmx' in kw:
self.xc_code = 'GGA,PBE' # just a guess...
pass
else:
print(__name__, kw.keys())
raise RuntimeError('unknown constructor')
#_dft_common_init_(self)
if self.verbosity > 0:
print(__name__, '\t\t====> self.pseudo: ', self.pseudo)
print(__name__, '\t\t====> Number of orbitals: ', self.norbs)
self.init_libnao()
self.gen_pb = kw['gen_pb'] if 'gen_pb' in kw else True
if self.gen_pb:
self.pb = pb = prod_basis(nao=self, **kw)
self.v_dab = pb.get_dp_vertex_sparse(dtype=self.dtype).tocsr()
self.cc_da = cc = pb.get_da2cc_sparse(dtype=self.dtype).tocsr()
self.nprod = self.cc_da.shape[1]
if self.verbosity > 0:
print(
__name__,
'\t\t====> Number of dominant and atom-centered products {}'
.format(cc.shape))
def test_vrtx_cc_apairs(self):
""" This is to test a batch generation vertices for bilocal atomic pairs. """
from numpy import allclose
dname = os.path.dirname(os.path.abspath(__file__))
sv = mf(label='water', cd=dname)
pbb = sv.pb
pba = prod_basis(sv)
for a,b in zip(pba.bp2info,pbb.bp2info):
for a1,a2 in zip(a.atoms,b.atoms): self.assertEqual(a1,a2)
for a1,a2 in zip(a.cc2a, b.cc2a): self.assertEqual(a1,a2)
self.assertTrue(allclose(a.vrtx, b.vrtx))
self.assertTrue(allclose(a.cc, b.cc))
self.assertLess(abs(pbb.get_da2cc_sparse().tocsr()-pba.get_da2cc_sparse().tocsr()).sum(), 1e-9)
self.assertLess(abs(pbb.get_dp_vertex_sparse().tocsr()-pba.get_dp_vertex_sparse().tocsr()).sum(), 1e-10)
def test_gw(self):
""" This is GW """
mol = gto.M(
verbose=0,
atom='''Ag 0.0 0.0 -0.3707; Ag 0.0 0.0 0.3707''',
basis='cc-pvdz-pp',
)
gto_mf = scf.RHF(mol) #.density_fit()
gto_mf.kernel()
print('gto_mf.mo_energy:', gto_mf.mo_energy)
s = nao(mf=gto_mf, gto=mol, verbosity=0)
oref = s.overlap_coo().toarray()
print('s.norbs:', s.norbs, oref.sum())
pb = prod_basis(nao=s, algorithm='fp')
pab2v = pb.get_ac_vertex_array()
mom0, mom1 = pb.comp_moments()
orec = np.einsum('p,pab->ab', mom0, pab2v)
print(abs(orec - oref).sum() / oref.size, np.amax(abs(orec - oref)))
def test_vrtx_cc_apairs(self):
""" This is to test a batch generation vertices for bilocal atomic pairs. """
from numpy import allclose
dname = os.path.dirname(os.path.abspath(__file__))
sv = mf(label='water', cd=dname)
pbb = sv.pb
pba = prod_basis(sv)
for a, b in zip(pba.bp2info, pbb.bp2info):
for a1, a2 in zip(a.atoms, b.atoms):
self.assertEqual(a1, a2)
for a1, a2 in zip(a.cc2a, b.cc2a):
self.assertEqual(a1, a2)
self.assertTrue(allclose(a.vrtx, b.vrtx))
self.assertTrue(allclose(a.cc, b.cc))
self.assertLess(
abs(pbb.get_da2cc_sparse().tocsr() -
pba.get_da2cc_sparse().tocsr()).sum(), 1e-9)
self.assertLess(
abs(pbb.get_dp_vertex_sparse().tocsr() -
pba.get_dp_vertex_sparse().tocsr()).sum(), 1e-10)