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Getting started
User Guide
API reference
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Orbital transformation
pyscfad.ao2mo
pyscfad.ao2mo.general
pyscfad.ao2mo.addons
pyscfad.ao2mo.addons.load
pyscfad.ao2mo.addons.restore
pyscfad.ao2mo.incore
pyscfad.ao2mo.incore.full
pyscfad.ao2mo.incore.general
Coupled cluster methods
pyscfad.cc
pyscfad.cc.RCCSD
pyscfad.cc.ccsd
pyscfad.cc.ccsd.CCSD
pyscfad.cc.ccsd.amplitudes_to_vector
pyscfad.cc.ccsd.energy
pyscfad.cc.ccsd.kernel
pyscfad.cc.ccsd.update_amps
pyscfad.cc.ccsd.vector_to_amplitudes
pyscfad.cc.ccsd_rdm
pyscfad.cc.ccsd_t
pyscfad.cc.ccsd_t.kernel
pyscfad.cc.ccsd_t_slow
pyscfad.cc.ccsd_t_slow.P3
pyscfad.cc.ccsd_t_slow.P6
pyscfad.cc.ccsd_t_slow.energy
pyscfad.cc.ccsd_t_slow.get_d3
pyscfad.cc.ccsd_t_slow.get_ovvv
pyscfad.cc.ccsd_t_slow.get_v_6d
pyscfad.cc.ccsd_t_slow.get_w_6d
pyscfad.cc.ccsd_t_slow.iterative_kernel
pyscfad.cc.ccsd_t_slow.kernel
pyscfad.cc.ccsd_t_slow.r3_6d
pyscfad.cc.ccsd_t_slow.run_diis
pyscfad.cc.ccsd_t_slow.update_amps
pyscfad.cc.dfccsd
pyscfad.cc.dfccsd.RCCSD
pyscfad.cc.dfdcsd
pyscfad.cc.dfdcsd.RDCSD
pyscfad.cc.gccsd_t
pyscfad.cc.gccsd_t.kernel
pyscfad.cc.gccsd_t.spatial2spin
pyscfad.cc.rccsd
pyscfad.cc.rccsd.RCCSD
pyscfad.cc.rccsd.amplitude_equation
pyscfad.cc.rccsd.update_amps
pyscfad.cc.rintermediates
pyscfad.cc.rintermediates.Loo
pyscfad.cc.rintermediates.Lvv
pyscfad.cc.rintermediates.W1ovov
pyscfad.cc.rintermediates.W1ovvo
pyscfad.cc.rintermediates.W2ovov
pyscfad.cc.rintermediates.W2ovvo
pyscfad.cc.rintermediates.Woooo
pyscfad.cc.rintermediates.Wooov
pyscfad.cc.rintermediates.Wovoo
pyscfad.cc.rintermediates.Wovov
pyscfad.cc.rintermediates.Wovvo
pyscfad.cc.rintermediates.Wvovv
pyscfad.cc.rintermediates.Wvvvo
pyscfad.cc.rintermediates.Wvvvv
pyscfad.cc.rintermediates.cc_Foo
pyscfad.cc.rintermediates.cc_Fov
pyscfad.cc.rintermediates.cc_Fvv
pyscfad.cc.rintermediates.cc_Woooo
pyscfad.cc.rintermediates.cc_Wvoov
pyscfad.cc.rintermediates.cc_Wvovo
pyscfad.cc.rintermediates.cc_Wvvvv
Density fitting
pyscfad.df
pyscfad.df.addons
pyscfad.df.addons.load
pyscfad.df.addons.make_auxmol
pyscfad.df.addons.restore
pyscfad.df.df
pyscfad.df.df.DF
pyscfad.df.df_jk
pyscfad.df.df_jk.get_jk
pyscfad.df.df_jk.get_jk_gen
pyscfad.df.incore
pyscfad.df.incore.cholesky_eri
pyscfad.df.incore.int3c_cross_jvp
DFT methods
pyscfad.dft
pyscfad.dft.libxc
pyscfad.dft.libxc.eval_xc
pyscfad.dft.numint
pyscfad.dft.numint.NumInt
pyscfad.dft.numint.eval_mat
pyscfad.dft.numint.eval_rho
pyscfad.dft.numint.nr_nlc_vxc
pyscfad.dft.numint.nr_rks
pyscfad.dft.numint.nr_uks
pyscfad.dft.rks
pyscfad.dft.rks.KohnShamDFT
pyscfad.dft.rks.RKS
pyscfad.dft.rks.VXC
pyscfad.dft.rks.energy_elec
pyscfad.dft.rks.get_veff
pyscfad.dft.rks.prune_small_rho_grids_
pyscfad.dft.uks
pyscfad.dft.uks.UKS
pyscfad.dft.uks.energy_elec
pyscfad.dft.uks.get_veff
Full CI
pyscfad.fci
pyscfad.fci.solve_fci
pyscfad.fci.fci_slow
pyscfad.fci.fci_slow.absorb_h1e
pyscfad.fci.fci_slow.contract_2e
pyscfad.fci.fci_slow.fci_ovlp
pyscfad.fci.fci_slow.get_occ_loc
pyscfad.fci.fci_slow.kernel
pyscfad.fci.fci_slow.make_hdiag
Geometry optimization
pyscfad.geomopt
pyscfad.geomopt.optimize
pyscfad.geomopt.optimize_mpi
pyscfad.geomopt.geometric_solver
pyscfad.geomopt.geometric_solver.PySCFADEngine
pyscfad.geomopt.geometric_solver.kernel
Molecular information
pyscfad.gto
pyscfad.gto.eval_gto
pyscfad.gto.eval_gto.eval_gto
pyscfad.gto.mole
pyscfad.gto.mole.Mole
pyscfad.gto.mole.inter_distance
pyscfad.gto.mole.nao_nr_range
pyscfad.gto.mole_lite
pyscfad.gto.mole_lite.MoleLite
pyscfad.gto.mole_lite.gaussian_int
pyscfad.gto.mole_lite.gto_norm
pyscfad.gto.mole_lite.make_atm_env
pyscfad.gto.mole_lite.make_bas_env
pyscfad.gto.mole_lite.make_env
pyscfad.gto.moleintor
pyscfad.gto.moleintor.intor
pyscfad.gto.moleintor.intor_cross
pyscfad.gto.moleintor_lite
pyscfad.gto.moleintor_lite.getints_jvp
GW methods
pyscfad.gw
pyscfad.gw.rpa
pyscfad.gw.rpa.RPA
pyscfad.gw.rpa.get_rho_response
pyscfad.gw.rpa.get_rpa_ecorr
pyscfad.gw.rpa.kernel
Machine learning
pyscfad.ml
pyscfad.ml.gto
pyscfad.ml.gto.basis_array
pyscfad.ml.gto.mole_pad
pyscfad.ml.scf
pyscfad.ml.scf.hf
pyscfad.ml.scf.hf_pad
pyscfad.ml.xtb
pyscfad.ml.xtb.param
pyscfad.ml.xtb.xtb_pad
MP2 methods
pyscfad.mp
pyscfad.mp.dfmp2
pyscfad.mp.dfmp2.MP2
pyscfad.mp.dfmp2.kernel
pyscfad.mp.mp2
pyscfad.mp.mp2.MP2
pyscfad.mp.mp2.RMP2
pyscfad.mp.mp2.make_rdm1
Methods for Solids
pyscfad.pbc
pyscfad.pbc.df
pyscfad.pbc.df.df_jk
pyscfad.pbc.df.fft
pyscfad.pbc.df.fft_jk
pyscfad.pbc.dft
pyscfad.pbc.dft.KRKS
pyscfad.pbc.dft.RKS
pyscfad.pbc.dft.gen_grid
pyscfad.pbc.dft.krks
pyscfad.pbc.dft.numint
pyscfad.pbc.dft.rks
pyscfad.pbc.gto
pyscfad.pbc.gto.cell
pyscfad.pbc.gto.cell_lite
pyscfad.pbc.gto.eval_gto
pyscfad.pbc.gto.pseudo
pyscfad.pbc.lib
pyscfad.pbc.lib.kpts_helper
pyscfad.pbc.scf
pyscfad.pbc.scf.KRHF
pyscfad.pbc.scf.RHF
pyscfad.pbc.scf.hf
pyscfad.pbc.scf.khf
pyscfad.pbc.scf.khf_lite
pyscfad.pbc.tools
pyscfad.pbc.tools.pbc
Property methods
pyscfad.prop
pyscfad.prop.polarizability
pyscfad.prop.polarizability.rhf
pyscfad.prop.thermo
pyscfad.prop.thermo.vib
Hartree-Fock methods
pyscfad.scf
pyscfad.scf.RHF
pyscfad.scf.ROHF
pyscfad.scf.UHF
pyscfad.scf.addons
pyscfad.scf.addons.canonical_orth_
pyscfad.scf.addons.get_occ_smearing
pyscfad.scf.anderson
pyscfad.scf.anderson.Anderson
pyscfad.scf.anderson.AndersonState
pyscfad.scf.anderson.anderson_step
pyscfad.scf.anderson.minimize_residual
pyscfad.scf.anderson.update_history
pyscfad.scf.chkfile
pyscfad.scf.chkfile.dump_scf
pyscfad.scf.cphf
pyscfad.scf.cphf.solve
pyscfad.scf.cphf.solve_nos1
pyscfad.scf.diis
pyscfad.scf.diis.CDIIS
pyscfad.scf.diis.DIIS
pyscfad.scf.diis.SCFDIIS
pyscfad.scf.diis.SCF_DIIS
pyscfad.scf.diis.get_err_vec
pyscfad.scf.diis.get_err_vec_orig
pyscfad.scf.diis.get_err_vec_orth
pyscfad.scf.hf
pyscfad.scf.hf.RHF
pyscfad.scf.hf.SCF
pyscfad.scf.hf.dip_moment
pyscfad.scf.hf.dot_eri_dm
pyscfad.scf.hf.energy_elec
pyscfad.scf.hf.energy_tot
pyscfad.scf.hf.get_fock
pyscfad.scf.hf.kernel
pyscfad.scf.hf.level_shift
pyscfad.scf.hf.make_rdm1
pyscfad.scf.hf_lite
pyscfad.scf.hf_lite.SCF
pyscfad.scf.hf_lite.SCFLite
pyscfad.scf.hf_lite.get_grad
pyscfad.scf.hf_lite.get_homo_lumo_energy
pyscfad.scf.hf_lite.get_occ
pyscfad.scf.hf_lite.kernel
pyscfad.scf.hf_lite.update_dm
pyscfad.scf.rohf
pyscfad.scf.rohf.ROHF
pyscfad.scf.rohf.get_fock
pyscfad.scf.rohf.get_occ
pyscfad.scf.rohf.get_roothaan_fock
pyscfad.scf.rohf.make_rdm1
pyscfad.scf.sp2
pyscfad.scf.sp2.dot2
pyscfad.scf.sp2.gershgorin_real_bounds
pyscfad.scf.sp2.scf
pyscfad.scf.sp2.sp2
pyscfad.scf.sp2.update_dm
pyscfad.scf.sp2.update_sp2_dm
pyscfad.scf.uhf
pyscfad.scf.uhf.UHF
TDSCF methods
pyscfad.tdscf
pyscfad.tdscf.rhf
pyscfad.tdscf.rhf.CIS
pyscfad.tdscf.rhf.TDA
pyscfad.tdscf.rhf.TDBase
pyscfad.tdscf.rhf.cis_ovlp
pyscfad.tdscf.rhf.gen_tda_hop
pyscfad.tdscf.rhf.gen_tda_operation
pyscfad.tdscf.rhf.get_ab
Tools
pyscfad.tools
pyscfad.tools.linear_solver
pyscfad.tools.linear_solver.GMRESDisp
pyscfad.tools.linear_solver.gen_gmres
pyscfad.tools.linear_solver.gen_gmres_with_default_kwargs
pyscfad.tools.linear_solver.precond_by_hdiag
pyscfad.tools.timer
pyscfad.tools.timer.Timer
pyscfad.tools.util
pyscfad.tools.util.rotate_mo1
pyscfad.tools.util.rotate_mo1_ov
Utility functions
pyscfad.util
pyscfad.util.is_tracer
pyscfad.util.pytree_node
pyscfad.util.to_pyscf
XTB models
pyscfad.xtb
pyscfad.xtb.basis
pyscfad.xtb.basis.get_basis_filename
pyscfad.xtb.data
pyscfad.xtb.data.elements
pyscfad.xtb.data.radii
pyscfad.xtb.kxtb
pyscfad.xtb.kxtb.GFN1KXTB
pyscfad.xtb.kxtb.KXTB
pyscfad.xtb.kxtb.EHT_PI_GFN1
pyscfad.xtb.kxtb.energy_nuc_GFN1
pyscfad.xtb.kxtb.gamma_GFN1
pyscfad.xtb.kxtb.mulliken_charge
pyscfad.xtb.param
pyscfad.xtb.param.Element
pyscfad.xtb.param.GFN1MolParam
pyscfad.xtb.param.GFN1Param
pyscfad.xtb.param.cn_d3
pyscfad.xtb.param.load_param
pyscfad.xtb.qbroyden
pyscfad.xtb.qbroyden.normalize_tot_charge
pyscfad.xtb.qbroyden.scf
pyscfad.xtb.util
pyscfad.xtb.util.aoslice_by_shell
pyscfad.xtb.util.atom_to_ao_indices
pyscfad.xtb.util.atom_to_ao_indices_2d
pyscfad.xtb.util.atom_to_bas_indices
pyscfad.xtb.util.atom_to_bas_indices_2d
pyscfad.xtb.util.bas_to_ao_indices
pyscfad.xtb.util.bas_to_ao_indices_2d
pyscfad.xtb.util.ke_cutoff_ewald
pyscfad.xtb.util.load_global_element_pair_params
pyscfad.xtb.util.load_global_params
pyscfad.xtb.util.load_global_shell_pair_params
pyscfad.xtb.util.load_global_shell_pair_params_gfn1
pyscfad.xtb.util.load_unique_element_params
pyscfad.xtb.util.load_unique_element_shell_params
pyscfad.xtb.util.mask_atom_pairs
pyscfad.xtb.util.mask_valence_shell_gfn1
pyscfad.xtb.util.r_and_inv_r
pyscfad.xtb.util.rcut_enuc_GFN1
pyscfad.xtb.util.rcut_erfc_over_r
pyscfad.xtb.util.unique_bas_to_bas_indices
pyscfad.xtb.util.unique_element_to_atom_indices
pyscfad.xtb.util.unique_l_to_bas_indices
pyscfad.xtb.xtb
pyscfad.xtb.xtb.GFN1XTB
pyscfad.xtb.xtb.XTB
pyscfad.xtb.xtb.EHT_Hdiag_GFN1
pyscfad.xtb.xtb.EHT_PI_GFN1
pyscfad.xtb.xtb.EHT_X_GFN1
pyscfad.xtb.xtb.EHT_Y_GFN1
pyscfad.xtb.xtb.gamma_GFN1
pyscfad.xtb.xtb.mulliken_charge
pyscfad.xtb.xtb.sum_shell_charges
pyscfad.xtb.xtb.tot_valence_electrons
API reference
XTB models
pyscfad.xtb
pyscfad.xtb.util
pyscfad.xtb.util.mask_atom_pairs
pyscfad.xtb.util.mask_atom_pairs
#
pyscfad.xtb.util.
mask_atom_pairs
(
mol
,
exclude_diag
=
True
)
[source]
#
On this page
mask_atom_pairs()
Edit on GitHub
