def dia(magobj, gauge_orig=None): '''Part of rotational g-tensors. It is the direct second derivatives of the Lagrangian (corresponding to the zeroth order wavefunction). Unit hbar/mu_N is not included. This part may be different to the conventional dia-magnetic contributions of rotational g-tensors. ''' mol = magobj.mol im, mass_center = rhf_g.inertia_tensor(mol) if gauge_orig is None: # Eq. (35) of JCP, 105, 2804 e2 = uhf_mag.dia(magobj, gauge_orig) e2 -= uhf_mag.dia(magobj, mass_center) e2 = rhf_g._safe_solve(im, e2) return -4 * nist.PROTON_MASS_AU * e2 else: dm0a, dm0b = magobj._scf.make_rdm1() dm0 = dm0a + dm0b with mol.with_common_origin(gauge_orig): int_r = mol.intor('int1e_r', comp=3) cm = mass_center - gauge_orig e2 = numpy.einsum('xpq,qp,y->xy', int_r, dm0, cm) e2 = numpy.eye(3) * e2.trace() - e2 e2 *= .5 e2 = rhf_g._safe_solve(im, e2) return -2 * nist.PROTON_MASS_AU * e2
def kernel(self, mo1=None): cput0 = (time.clock(), time.time()) self.check_sanity() #self.dump_flags() dm0 = self._scf.make_rdm1() #print('dm0 from kernel', dm0.shape) #dm0 = dm0[0] - dm0[1] tt_dia = self.dia(dm0) tt_para = self.para(mo1, self._scf.mo_coeff, self._scf.mo_occ) im, mass_center = rhf_rotg.inertia_tensor(self.mol) im_inv = numpy.linalg.inv(im) #print('im', im) #print('im_inv', im_inv) To_MHz = 1804742.77343363 esr_para = -1.0 * numpy.einsum('ij,jk->ik', im_inv, tt_para) * To_MHz * 2 esr_dia = -1.0 * numpy.einsum('ij,jk->ik', im_inv, tt_dia) * To_MHz * 2 print('esr_dia', esr_dia) esr_tensor = esr_para + esr_dia #print('esr_para', esr_para) for debug #print('esr_dia', esr_dia) #print('esr_tot', esr_tot) esr_tot, v = self.align(esr_tensor) esr_dia = reduce(numpy.dot, (v.T, esr_dia, v)) esr_para = reduce(numpy.dot, (v.T, esr_para, v)) _write(self, esr_dia, 'esr-tensor diamagnetic terms (in MHz)') _write(self, esr_para, 'esr-tensor paramagnetic terms (in MHz)') _write(self, esr_tot, 'esr-tensor total (in MHz)') return esr_tot
def dia(magobj, gauge_orig=None): '''Part of rotational g-tensors. It is the direct second derivatives of the Lagrangian (corresponding to the zeroth order wavefunction). Unit hbar/mu_N is not included. This part may be different to the conventional dia-magnetic contributions of rotational g-tensors. ''' mol = magobj.mol im, mass_center = rhf_g.inertia_tensor(mol) if gauge_orig is None: # Eq. (35) of JCP, 105, 2804 e2 = uhf_mag.dia(magobj, gauge_orig) e2 -= uhf_mag.dia(magobj, mass_center) e2 = rhf_g._safe_solve(im, e2) return -4 * nist.PROTON_MASS_AU * e2 else: dm0a, dm0b = magobj._scf.make_rdm1() dm0 = dm0a + dm0b with mol.with_common_origin(gauge_orig): int_r = mol.intor('int1e_r', comp=3) cm = mass_center - gauge_orig e2 = numpy.einsum('xpq,qp,y->xy', int_r, dm0, cm) e2 = numpy.eye(3) * e2.trace() - e2 e2 *= .5 e2 = rhf_g._safe_solve(im, e2) return -2 * nist.PROTON_MASS_AU * e2
def para(nsrobj, mo10=None, mo_coeff=None, mo_occ=None, shielding_nuc=None): '''Paramagnetic part of NSR shielding tensors. ''' if shielding_nuc is None: shielding_nuc = nsrobj.shielding_nuc # The first order Hamiltonian for rotation part is the same to the # first order Hamiltonian for magnetic field except a factor of 2. nsr_para = rhf_nmr.para(nsrobj, mo10, mo_coeff, mo_occ, shielding_nuc)[0] * 2 mol = nsrobj.mol im, mass_center = inertia_tensor(mol) nsr_para = _safe_solve(im, nsr_para) unit = _atom_gyro_list(mol)[shielding_nuc] * nist.ALPHA**2 return numpy.einsum('ixy,i->ixy', nsr_para, unit)
def dia(magobj, gauge_orig=None): '''Part of rotational g-tensors. It is the direct second derivatives of the Lagrangian (corresponding to the zeroth order wavefunction). Unit hbar/mu_N is not included. This part may be different to the conventional dia-magnetic contributions of rotational g-tensors. ''' if gauge_orig is None: mol = magobj.mol im, mass_center = rhf_g.inertia_tensor(mol) # Eq. (35) of JCP, 105, 2804 e2 = rks_mag.dia(magobj, gauge_orig) e2 -= rks_mag.dia(magobj, mass_center) e2 = rhf_g._safe_solve(im, e2) return -4 * nist.PROTON_MASS_AU * e2 else: return rhf_g.dia(magobj, gauge_orig)
def dia(magobj, gauge_orig=None): '''Part of rotational g-tensors. It is the direct second derivatives of the Lagrangian (corresponding to the zeroth order wavefunction). Unit hbar/mu_N is not included. This part may be different to the conventional dia-magnetic contributions of rotational g-tensors. ''' if gauge_orig is None: mol = magobj.mol im, mass_center = rhf_g.inertia_tensor(mol) # Eq. (35) of JCP, 105, 2804 e2 = uks_mag.dia(magobj, gauge_orig) e2 -= uks_mag.dia(magobj, mass_center) e2 = rhf_g._safe_solve(im, e2) return -4 * nist.PROTON_MASS_AU * e2 else: return uhf_g.dia(magobj, gauge_orig)
def para(magobj, gauge_orig=None, h1=None, s1=None, with_cphf=None): '''Part of rotational g-tensors from the first order wavefunctions. Unit hbar/mu_N is not included. This part may be different to the conventional para-magnetic contributions of rotational g-tensors. ''' mol = magobj.mol im, mass_center = rhf_g.inertia_tensor(mol) if gauge_orig is None: # The first order Hamiltonian for rotation part is the same to the # first order Hamiltonian for magnetic field except a factor of 2. It can # be computed using the magnetizability code. mag_para = uhf_mag.para(magobj, gauge_orig, h1, s1, with_cphf) * 2 else: mf = magobj._scf mo_energy = mf.mo_energy mo_coeff = mf.mo_coeff mo_occ = mf.mo_occ orboa = mo_coeff[0][:, mo_occ[0] > 0] orbob = mo_coeff[1][:, mo_occ[1] > 0] # for magnetic field with mol.with_common_origin(mass_center): h10 = .5 * mol.intor('int1e_cg_irxp', 3) h10a = lib.einsum('xpq,pi,qj->xij', h10, mo_coeff[0].conj(), orboa) h10b = lib.einsum('xpq,pi,qj->xij', h10, mo_coeff[1].conj(), orbob) # for rotation part with mol.with_common_origin(gauge_orig): h01 = -mol.intor('int1e_cg_irxp', 3) h01a = lib.einsum('xpq,pi,qj->xij', h01, mo_coeff[0].conj(), orboa) h01b = lib.einsum('xpq,pi,qj->xij', h01, mo_coeff[1].conj(), orbob) s10a = numpy.zeros_like(h10a) s10b = numpy.zeros_like(h10b) mo10 = uhf_nmr._solve_mo1_uncoupled(mo_energy, mo_occ, (h10a, h10b), (s10a, s10b))[0] mag_para = numpy.einsum('xji,yji->xy', mo10[0].conj(), h01a) mag_para += numpy.einsum('xji,yji->xy', mo10[1].conj(), h01b) mag_para = mag_para + mag_para.conj() mag_para = rhf_g._safe_solve(im, mag_para) # unit = hbar/mu_N, mu_N is nuclear magneton unit = -2 * nist.PROTON_MASS_AU return mag_para * unit
def para(magobj, gauge_orig=None, h1=None, s1=None, with_cphf=None): '''Part of rotational g-tensors from the first order wavefunctions. Unit hbar/mu_N is not included. This part may be different to the conventional para-magnetic contributions of rotational g-tensors. ''' mol = magobj.mol im, mass_center = rhf_g.inertia_tensor(mol) if gauge_orig is None: # The first order Hamiltonian for rotation part is the same to the # first order Hamiltonian for magnetic field except a factor of 2. It can # be computed using the magnetizability code. mag_para = uhf_mag.para(magobj, gauge_orig, h1, s1, with_cphf) * 2 else: mf = magobj._scf mo_energy = mf.mo_energy mo_coeff = mf.mo_coeff mo_occ = mf.mo_occ orboa = mo_coeff[0][:,mo_occ[0]>0] orbob = mo_coeff[1][:,mo_occ[1]>0] # for magnetic field with mol.with_common_origin(mass_center): h10 = .5 * mol.intor('int1e_cg_irxp', 3) h10a = lib.einsum('xpq,pi,qj->xij', h10, mo_coeff[0].conj(), orboa) h10b = lib.einsum('xpq,pi,qj->xij', h10, mo_coeff[1].conj(), orbob) # for rotation part with mol.with_common_origin(gauge_orig): h01 = -mol.intor('int1e_cg_irxp', 3) h01a = lib.einsum('xpq,pi,qj->xij', h01, mo_coeff[0].conj(), orboa) h01b = lib.einsum('xpq,pi,qj->xij', h01, mo_coeff[1].conj(), orbob) s10a = numpy.zeros_like(h10a) s10b = numpy.zeros_like(h10b) mo10 = uhf_nmr._solve_mo1_uncoupled(mo_energy, mo_occ, (h10a,h10b), (s10a,s10b))[0] mag_para = numpy.einsum('xji,yji->xy', mo10[0].conj(), h01a) mag_para+= numpy.einsum('xji,yji->xy', mo10[1].conj(), h01b) mag_para = mag_para + mag_para.conj() mag_para = rhf_g._safe_solve(im, mag_para) # unit = hbar/mu_N, mu_N is nuclear magneton unit = -2 * nist.PROTON_MASS_AU return mag_para * unit
def nuc(mol, shielding_nuc): '''Nuclear contributions''' im, mass_center = inertia_tensor(mol) charges = mol.atom_charges() coords = mol.atom_coords() nsr_nuc = [] for n, atm_id in enumerate(shielding_nuc): rkl = coords - coords[atm_id] d = numpy.linalg.norm(rkl, axis=1) d[atm_id] = 1e100 e11 = numpy.einsum('z,zx,zy->xy', charges / d**3, rkl, rkl) e11 = numpy.eye(3) * e11.trace() - e11 nsr_nuc.append(e11) nsr_nuc = _safe_solve(im, numpy.asarray(nsr_nuc)) unit = _atom_gyro_list(mol)[shielding_nuc] * nist.ALPHA**2 return numpy.einsum('ixy,i->ixy', nsr_nuc, unit)
def dia(nsrobj, gauge_orig=None, shielding_nuc=None, dm0=None): '''Diamagnetic part of NSR tensors. ''' if shielding_nuc is None: shielding_nuc = nsrobj.shielding_nuc if dm0 is None: dm0 = nsrobj._scf.make_rdm1() mol = nsrobj.mol im, mass_center = inertia_tensor(mol) if gauge_orig is None: ao_coords = rhf_mag._get_ao_coords(mol) # Eq. (34) of JCP, 105, 2804 nsr_dia = rhf_nmr.dia(nsrobj, gauge_orig, shielding_nuc, dm0) for n, atm_id in enumerate(shielding_nuc): coord = mol.atom_coord(atm_id) with mol.with_common_origin(coord): with mol.with_rinv_origin(coord): # a11part = (B dot) -1/2 frac{\vec{r}_N}{r_N^3} r_N (dot mu) h11 = mol.intor('int1e_cg_a11part', comp=9) e11 = numpy.einsum('xpq,qp->x', h11, dm0).reshape(3, 3) nsr_dia[n] -= e11 - numpy.eye(3) * e11.trace() nsr_dia[n] *= 2 else: nsr_dia = [] for n, atm_id in enumerate(shielding_nuc): coord = mol.atom_coord(atm_id) with mol.with_rinv_origin(coord): with mol.with_common_origin(gauge_orig): # a11part = (B dot) -1/2 frac{\vec{r}_N}{r_N^3} (r-R_c) (dot mu) h11 = mol.intor('int1e_cg_a11part', comp=9) e11 = numpy.einsum('xpq,qp->x', h11, dm0).reshape(3, 3) with mol.with_common_origin(coord): # a11part = (B dot) -1/2 frac{\vec{r}_N}{r_N^3} r_N (dot mu) h11 = mol.intor('int1e_cg_a11part', comp=9) # e11 ~ (B dot) -1/2 frac{\vec{r}_N}{r_N^3} (R_N-R_c) (dot mu) e11 -= numpy.einsum('xpq,qp->x', h11, dm0).reshape(3, 3) e11 = e11 - numpy.eye(3) * e11.trace() nsr_dia.append(e11) nsr_dia = _safe_solve(im, numpy.asarray(nsr_dia)) unit = _atom_gyro_list(mol)[shielding_nuc] * nist.ALPHA**2 return numpy.einsum('ixy,i->ixy', nsr_dia, unit)
def dia(gobj, dm0, gauge_orig=None): '''Note the side effects of set_common_origin''' if isinstance(dm0, numpy.ndarray) and dm0.ndim == 2: # RHF DM return numpy.zeros((3, 3)) mol = gobj.mol effspin = mol.spin * .5 muB = .5 # Bohr magneton dma, dmb = dm0 totdm = dma + dmb spindm = dma - dmb alpha2 = nist.ALPHA**2 #Many choices of qed_fac, see JPC, 101, 3388 #qed_fac = (nist.G_ELECTRON - 1) #qed_fac = nist.G_ELECTRON / 2 qed_fac = 1 assert (not mol.has_ecp()) if gauge_orig is not None: mol.set_common_origin(gauge_orig) e11 = numpy.zeros((3, 3)) im, mass_center = rhf_rotg.inertia_tensor(mol) for ia in range(mol.natm): Z = koseki_charge(mol.atom_charge(ia)) R = mol.atom_coord(ia) - mass_center with mol.with_rinv_origin(R): h11 = mol.intor('int1e_drinv', comp=3) * Z # * mol.atom_charge(ia) t1 = numpy.einsum('xij,ij->x', h11, spindm) e11 += numpy.dot(R, t1) * numpy.eye(3) - numpy.kron(R, t1).reshape( 3, 3) #GIAO part of dia-magnetic constribution #print('kron', numpy.kron(R, t1).reshape(3,3)) #h22 = mol.intor('int1e_a01gp', comp=9) #e11 -= Z * numpy.einsum('xij,ij->x', h22, spindm).reshape(3,3) gdia = e11 * alpha2 / effspin / 4. return gdia