def aux_e2(mol,
auxmol,
intor='int3c2e',
aosym='s1',
comp=None,
out=None,
cintopt=None):
'''3-center AO integrals (ij|L), where L is the auxiliary basis.
Kwargs:
cintopt : Libcint-3.14 and newer version support to compute int3c2e
without the opt for the 3rd index. It can be precomputed to
reduce the overhead of cintopt initialization repeatedly.
cintopt = gto.moleintor.make_cintopt(mol._atm, mol._bas, mol._env, 'int3c2e')
'''
shls_slice = (0, mol.nbas, 0, mol.nbas, mol.nbas, mol.nbas + auxmol.nbas)
# Extract the call of the two lines below
# pmol = gto.mole.conc_mol(mol, auxmol)
# return pmol.intor(intor, comp, aosym=aosym, shls_slice=shls_slice, out=out)
intor = mol._add_suffix(intor)
hermi = 0
ao_loc = None
atm, bas, env = gto.mole.conc_env(mol._atm, mol._bas, mol._env,
auxmol._atm, auxmol._bas, auxmol._env)
return getints(intor, atm, bas, env, shls_slice, comp, hermi, aosym,
ao_loc, cintopt, out)
def get_int3c(shls_slice=None):
if shls_slice is None:
shls_slice = (0, nbas, 0, nbas, nbas, pmol.nbas)
else:
shls_slice = shls_slice[:4] + (nbas+shls_slice[4], nbas+shls_slice[5])
return getints(intor, pmol._atm, pmol._bas, pmol._env, shls_slice,
aosym=aosym, cintopt=opt)
def project_mo_r2r(mol1, mo1, mol2):
nbas1 = len(mol1._bas)
nbas2 = len(mol2._bas)
atm, bas, env = mole.conc_env(mol2._atm, mol2._bas, mol2._env,
mol1._atm, mol1._bas, mol1._env)
bras = kets = range(nbas2)
s22 = moleintor.getints('cint1e_ovlp', atm, bas, env,
bras, kets, comp=1, hermi=1)
t22 = moleintor.getints('cint1e_spsp', atm, bas, env,
bras, kets, comp=1, hermi=1)
bras = range(nbas2)
kets = range(nbas2, nbas1+nbas2)
s21 = moleintor.getints('cint1e_ovlp', atm, bas, env,
bras, kets, comp=1, hermi=0)
t21 = moleintor.getints('cint1e_spsp', atm, bas, env,
bras, kets, comp=1, hermi=0)
n2c = s21.shape[1]
pl = numpy.linalg.solve(s22, s21)
ps = numpy.linalg.solve(t22, t21)
return numpy.vstack((numpy.dot(pl, mo1[:n2c]),
numpy.dot(ps, mo1[n2c:])))
def aux_e2(mol, auxmol, intor='int3c2e', aosym='s1', comp=None, out=None,
cintopt=None):
'''3-center AO integrals (ij|L), where L is the auxiliary basis.
Kwargs:
cintopt : Libcint-3.14 and newer version support to compute int3c2e
without the opt for the 3rd index. It can be precomputed to
reduce the overhead of cintopt initialization repeatedly.
cintopt = gto.moleintor.make_cintopt(mol._atm, mol._bas, mol._env, intor)
'''
from pyscf.gto.moleintor import getints, make_cintopt
shls_slice = (0, mol.nbas, 0, mol.nbas, mol.nbas, mol.nbas+auxmol.nbas)
# Extract the call of the two lines below
# pmol = gto.mole.conc_mol(mol, auxmol)
# return pmol.intor(intor, comp, aosym=aosym, shls_slice=shls_slice, out=out)
intor = mol._add_suffix(intor)
hermi = 0
ao_loc = None
atm, bas, env = gto.mole.conc_env(mol._atm, mol._bas, mol._env,
auxmol._atm, auxmol._bas, auxmol._env)
return getints(intor, atm, bas, env, shls_slice, comp, hermi, aosym,
ao_loc, cintopt, out)
def get_E1(eda):
#atom_kinE = []
mol = eda.mol
#method = eda.method
#dm = eda.dm
nao = eda.nao
bas2atm = eda.bas2atm #get_bas2atm(atm2bas,nao,mol.natm)
if eda.showinter:
bas2frg = eda.bas2frg
atm2frg = eda.atm2frg
#print(bas2atm)
kinmat = mol.intor_symmetric('int1e_kin')
atom_kin = np.zeros(mol.natm)
if eda.showinter:
#kin1 = np.zeros(mol.natm)
#kin2 = np.zeros((mol.natm, mol.natm))
kin1 = np.zeros(eda.nfrag + 2)
kin2 = np.zeros((eda.nfrag + 2, eda.nfrag + 2))
naorange = range(nao)
#if eda.exclude_cap:
# naorange -= eda.capbas_p
for i in naorange:
for j in naorange:
#print(dm,kin)
kin = eda.dm[i, j] * kinmat[i, j]
a = bas2atm[i]
b = bas2atm[j]
atom_kin[a] = atom_kin[a] + kin
atom_kin[b] = atom_kin[b] + kin
if eda.showinter:
aa = bas2frg[i]
bb = bas2frg[j]
if aa == bb:
kin1[aa - 1] += kin
else:
kin2[aa - 1, bb - 1] += kin
kin2[bb - 1, aa - 1] += kin
atom_kin = atom_kin / 2
#with open(eda.output+'-eda.log','a') as f:
logger.log(eda.stdout, "atom_kinE=", atom_kin)
if eda.showinter:
logger.log(eda.stdout_inter, "kin1", kin1)
logger.log(eda.stdout_inter, "kin2", kin2)
fakeatm = []
for n in range(mol.natm):
#if eda.exclude_cap and (n+1 in eda.capatoms):
# continue
back = copy.copy(mol._atm)
for i in range(mol.natm):
if (i != n):
back[i, 0] = 0
fakeatm.append(back)
#fakeatm = np.array(fakeatm)
#print(mol._atm)
#print(fakeatm)
int1enuc = []
for i in range(mol.natm):
#if eda.exclude_cap and (n+1 in eda.capatoms):
# #int1en =
# continue
if mol.cart:
int1en = moleintor.getints("int1e_nuc_cart", fakeatm[i], mol._bas,
mol._env)
else:
int1en = moleintor.getints("int1e_nuc_sph", fakeatm[i], mol._bas,
mol._env)
int1enuc.append(int1en)
#e1 = 0.0
#atom_h1E = np.zeros(atom_number)
if eda.showinter:
#print(atm2frg,mol.natm)
#print(int1enuc[0][:3,:3])
atom_1enuc, e1_1, e1_2, e1_3 = h1e_inter(eda.dm, bas2atm, bas2frg,
atm2frg, int1enuc, mol.natm,
nao, eda.nfrag + 2)
atom_1enuc = np.asarray(atom_1enuc)[0:mol.natm]
logger.log(eda.stdout, "e1n_1", e1_1)
e1_1 = np.asarray(e1_1) + kin1
#print(e1_2)
#print(kin1,kin2)
e1_2 = np.triu(np.asarray(e1_2) + kin2)
#intersum = e1_1.sum() + e1_2.sum() + e1_3
#e1_3 = np.asarray(e1_3)
#print(e1_3)
e1_3 = eda_inter.simp3(e1_3, eda.nfrag, eda.frag2layer)
else:
atom_1enuc = np.asarray(h1e(eda.dm, bas2atm, int1enuc, mol.natm,
nao))[0:mol.natm]
#with open(eda.output+'-eda.log','a') as f:
logger.log(eda.stdout, "atom_1enuc=", atom_1enuc)
atm_e1 = atom_kin + atom_1enuc
logger.log(eda.stdout, "atom_e1=", atm_e1)
if eda.showinter:
logger.log(eda.stdout_inter, "e1_1", e1_1)
logger.log(eda.stdout_inter, "e1_2", e1_2)
logger.ilog(eda.stdout_inter, "e1_3 ", e1_3)
#with open(eda.output+'-eda.log','a') as f:
#anal = True
if eda.anal and eda.showinter:
tot_akin = atom_kin.sum()
tot_kin = np.einsum('ij,ji', eda.dm, mol.intor_symmetric('int1e_kin'))
tot_fkin = kin1.sum() + np.triu(kin2).sum()
tot_a1enuc = atom_1enuc.sum()
tot_1enuc = np.einsum(
'ij,ji', eda.dm,
moleintor.getints("int1e_nuc_sph", mol._atm, mol._bas, mol._env))
tot_fe1 = e1_1.sum() + e1_2.sum() + sum(e1_3.energies())
'''basis_range = range(53)
dm1 = eda.dm[np.ix_(basis_range, basis_range)]
inte1n1 = np.zeros((nao,nao))
for i in range(7):
inte1n1 += int1enuc[i]
inte1n1 = inte1n1[np.ix_(basis_range, basis_range)]
e1n1 = np.einsum('ij,ji', dm1, inte1n1)
logger.mlog(eda.stdout, "old_e1_1", e1n1)'''
logger.mlog(eda.stdout, "a_e1 ", tot_akin + tot_a1enuc)
#logger.mlog(eda.stdout,"a_e1k ", tot_akin)
#logger.mlog(eda.stdout,"a_e1n ", tot_a1enuc)
logger.mlog(eda.stdout, "f_e1 ", tot_fe1)
logger.mlog(eda.stdout, "t_e1", tot_kin + tot_1enuc)
if eda.showinter: atm_e1 = atm_e1, e1_1, e1_2, e1_3
return atm_e1
