#!/usr/bin/env python
# Copyright 2014-2023 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
# Author: Qiming Sun <osirpt.sun@gmail.com>
#
__all__ = ['ALIAS', 'GTH_ALIAS', 'PP_ALIAS',
'parse', 'parse_ecp', 'load', 'load_ecp', 'load_pseudo',
'optimize_contraction', 'to_general_contraction']
import os
import sys
import re
from os.path import join
import importlib
import pyscf
from pyscf.gto.basis import parse_nwchem, parse_nwchem_ecp
from pyscf.gto.basis import parse_cp2k, parse_cp2k_pp
from pyscf.lib.exceptions import BasisNotFoundError
from pyscf import __config__
ALIAS = {
'ano' : 'ano.dat' ,
'anorcc' : 'ano.dat' ,
'anoroosdz' : 'roos-dz.dat' ,
'anoroostz' : 'roos-tz.dat' ,
'roosdz' : 'roos-dz.dat' ,
'roostz' : 'roos-tz.dat' ,
'ccpvdz' : 'cc-pvdz.dat' ,
'ccpvtz' : 'cc-pvtz.dat' ,
'ccpvqz' : 'cc-pvqz.dat' ,
'ccpv5z' : 'cc-pv5z.dat' ,
'ccpvdpdz' : 'cc-pvdpdz.dat' ,
'augccpvdz' : 'aug-cc-pvdz.dat',
'augccpvtz' : 'aug-cc-pvtz.dat',
'augccpvqz' : 'aug-cc-pvqz.dat',
'augccpv5z' : 'aug-cc-pv5z.dat',
'augccpvdpdz': 'aug-cc-pvdpdz.dat',
'ccpvdzdk' : 'cc-pvdz-dk.dat' ,
'ccpvtzdk' : 'cc-pvtz-dk.dat' ,
'ccpvqzdk' : 'cc-pvqz-dk.dat' ,
'ccpv5zdk' : 'cc-pv5z-dk.dat' ,
'ccpvdzdkh' : 'cc-pvdz-dk.dat' ,
'ccpvtzdkh' : 'cc-pvtz-dk.dat' ,
'ccpvqzdkh' : 'cc-pvqz-dk.dat' ,
'ccpv5zdkh' : 'cc-pv5z-dk.dat' ,
'augccpvdzdk' : 'aug-cc-pvdz-dk.dat',
'augccpvtzdk' : 'aug-cc-pvtz-dk.dat',
'augccpvqzdk' : 'aug-cc-pvqz-dk.dat',
'augccpv5zdk' : 'aug-cc-pv5z-dk.dat',
'augccpvdzdkh': 'aug-cc-pvdz-dk.dat',
'augccpvtzdkh': 'aug-cc-pvtz-dk.dat',
'augccpvqzdkh': 'aug-cc-pvqz-dk.dat',
'augccpv5zdkh': 'aug-cc-pv5z-dk.dat',
'ccpvdzjkfit' : 'cc-pvdz-jkfit.dat' ,
'ccpvtzjkfit' : 'cc-pvtz-jkfit.dat' ,
'ccpvqzjkfit' : 'cc-pvqz-jkfit.dat' ,
'ccpv5zjkfit' : 'cc-pv5z-jkfit.dat' ,
'ccpvdzri' : 'cc-pvdz-ri.dat' ,
'ccpvtzri' : 'cc-pvtz-ri.dat' ,
'ccpvqzri' : 'cc-pvqz-ri.dat' ,
'ccpv5zri' : 'cc-pv5z-ri.dat' ,
'augccpvdzjkfit' : 'aug-cc-pvdz-jkfit.dat' ,
'augccpvdzpjkfit': 'aug-cc-pvdzp-jkfit.dat',
'augccpvtzjkfit' : 'aug-cc-pvtz-jkfit.dat' ,
'augccpvqzjkfit' : 'aug-cc-pvqz-jkfit.dat' ,
'augccpv5zjkfit' : 'aug-cc-pv5z-jkfit.dat' ,
'heavyaugccpvdzjkfit' : 'heavy-aug-cc-pvdz-jkfit.dat',
'heavyaugccpvtzjkfit' : 'heavy-aug-cc-pvtz-jkfit.dat',
'heavyaugccpvdzri' : 'heavy-aug-cc-pvdz-ri.dat',
'heavyaugccpvtzri' : 'heavy-aug-cc-pvtz-ri.dat',
'augccpvdzri' : 'aug-cc-pvdz-ri.dat' ,
'augccpvdzpri' : 'aug-cc-pvdzp-ri.dat' ,
'augccpvqzri' : 'aug-cc-pvqz-ri.dat' ,
'augccpvtzri' : 'aug-cc-pvtz-ri.dat' ,
'augccpv5zri' : 'aug-cc-pv5z-ri.dat' ,
'ccpvtzdk3' : 'cc-pVTZ-DK3.dat' ,
'ccpvqzdk3' : 'cc-pVQZ-DK3.dat' ,
'augccpvtzdk3': 'aug-cc-pVTZ-DK3.dat',
'augccpvqzdk3': 'aug-cc-pVQZ-DK3.dat',
'dyalldz' : 'dyall_dz' ,
'dyallqz' : 'dyall_qz' ,
'dyalltz' : 'dyall_tz' ,
'faegredz' : 'faegre_dz' ,
'iglo' : 'iglo3' ,
'iglo3' : 'iglo3' ,
'321++g' : join('pople-basis', '3-21++G.dat' ),
'321++g*' : join('pople-basis', '3-21++Gs.dat' ),
'321++gs' : join('pople-basis', '3-21++Gs.dat' ),
'321g' : join('pople-basis', '3-21G.dat' ),
'321g*' : join('pople-basis', '3-21Gs.dat' ),
'321gs' : join('pople-basis', '3-21Gs.dat' ),
'431g' : join('pople-basis', '4-31G.dat' ),
'631++g' : join('pople-basis', '6-31++G.dat' ),
'631++g*' : join('pople-basis', '6-31++Gs.dat' ),
'631++gs' : join('pople-basis', '6-31++Gs.dat' ),
'631++g**' : join('pople-basis', '6-31++Gss.dat' ),
'631++gss' : join('pople-basis', '6-31++Gss.dat' ),
'631+g' : join('pople-basis', '6-31+G.dat' ),
'631+g*' : join('pople-basis', '6-31+Gs.dat' ),
'631+gs' : join('pople-basis', '6-31+Gs.dat' ),
'631+g**' : join('pople-basis', '6-31+Gss.dat' ),
'631+gss' : join('pople-basis', '6-31+Gss.dat' ),
'6311++g' : join('pople-basis', '6-311++G.dat' ),
'6311++g*' : join('pople-basis', '6-311++Gs.dat' ),
'6311++gs' : join('pople-basis', '6-311++Gs.dat' ),
'6311++g**' : join('pople-basis', '6-311++Gss.dat'),
'6311++gss' : join('pople-basis', '6-311++Gss.dat'),
'6311+g' : join('pople-basis', '6-311+G.dat' ),
'6311+g*' : join('pople-basis', '6-311+Gs.dat' ),
'6311+gs' : join('pople-basis', '6-311+Gs.dat' ),
'6311+g**' : join('pople-basis', '6-311+Gss.dat' ),
'6311+gss' : join('pople-basis', '6-311+Gss.dat' ),
'6311g' : join('pople-basis', '6-311G.dat' ),
'6311g*' : join('pople-basis', '6-311Gs.dat' ),
'6311gs' : join('pople-basis', '6-311Gs.dat' ),
'6311g**' : join('pople-basis', '6-311Gss.dat' ),
'6311gss' : join('pople-basis', '6-311Gss.dat' ),
'631g' : join('pople-basis', '6-31G.dat' ),
'631g*' : join('pople-basis', '6-31Gs.dat' ),
'631gs' : join('pople-basis', '6-31Gs.dat' ),
'631g**' : join('pople-basis', '6-31Gss.dat' ),
'631gss' : join('pople-basis', '6-31Gss.dat' ),
'sto3g' : 'sto-3g.dat' ,
'sto6g' : 'sto-6g.dat' ,
'minao' : 'minao' ,
'dz' : 'dz.dat' ,
'dzpdunning' : 'dzp_dunning' ,
'dzvp' : 'dzvp.dat' ,
'dzvp2' : 'dzvp2.dat' ,
'dzp' : 'dzp.dat' ,
'tzp' : 'tzp.dat' ,
'qzp' : 'qzp.dat' ,
'adzp' : 'adzp.dat' ,
'atzp' : 'atzp.dat' ,
'aqzp' : 'aqzp.dat' ,
'dzpdk' : 'dzp-dkh.dat' ,
'tzpdk' : 'tzp-dkh.dat' ,
'qzpdk' : 'qzp-dkh.dat' ,
'dzpdkh' : 'dzp-dkh.dat' ,
'tzpdkh' : 'tzp-dkh.dat' ,
'qzpdkh' : 'qzp-dkh.dat' ,
'def2svp' : 'def2-svp.dat' ,
'def2svpd' : 'def2-svpd.dat' ,
'def2tzvpd' : 'def2-tzvpd.dat' ,
'def2tzvppd' : 'def2-tzvppd.dat',
'def2tzvpp' : 'def2-tzvpp.dat' ,
'def2tzvp' : 'def2-tzvp.dat' ,
'def2qzvpd' : 'def2-qzvpd.dat' ,
'def2qzvppd' : 'def2-qzvppd.dat',
'def2qzvpp' : 'def2-qzvpp.dat' ,
'def2qzvp' : 'def2-qzvp.dat' ,
'def2svpjfit' : 'def2-universal-jfit.dat',
'def2svpjkfit' : 'def2-universal-jkfit.dat',
'def2tzvpjfit' : 'def2-universal-jfit.dat',
'def2tzvpjkfit' : 'def2-universal-jkfit.dat',
'def2tzvppjfit' : 'def2-universal-jfit.dat',
'def2tzvppjkfit' : 'def2-universal-jkfit.dat',
'def2qzvpjfit' : 'def2-universal-jfit.dat',
'def2qzvpjkfit' : 'def2-universal-jkfit.dat',
'def2qzvppjfit' : 'def2-universal-jfit.dat',
'def2qzvppjkfit' : 'def2-universal-jkfit.dat',
'def2universaljfit' : 'def2-universal-jfit.dat',
'def2universaljkfit' : 'def2-universal-jkfit.dat',
'def2svpri' : 'def2-svp-ri.dat' ,
'def2svpdri' : 'def2-svpd-ri.dat' ,
'def2tzvpri' : 'def2-tzvp-ri.dat' ,
'def2tzvpdri' : 'def2-tzvpd-ri.dat' ,
'def2tzvppri' : 'def2-tzvpp-ri.dat' ,
'def2tzvppdri' : 'def2-tzvppd-ri.dat' ,
'def2qzvpri' : 'def2-qzvp-ri.dat' ,
'def2qzvppri' : 'def2-qzvpp-ri.dat' ,
'def2qzvppdri' : 'def2-qzvppd-ri.dat' ,
'tzv' : 'tzv.dat' ,
'weigend' : 'def2-universal-jfit.dat',
'weigend+etb' : 'def2-universal-jfit.dat',
'weigendcfit' : 'def2-universal-jfit.dat',
'weigendjfit' : 'def2-universal-jfit.dat',
'weigendjkfit': 'def2-universal-jkfit.dat',
'demon' : 'demon_cfit.dat' ,
'demoncfit' : 'demon_cfit.dat' ,
'ahlrichs' : 'ahlrichs_cfit.dat',
'ahlrichscfit': 'ahlrichs_cfit.dat',
'ccpvtzfit' : 'cc-pvtz_fit.dat',
'ccpvdzfit' : 'cc-pvdz_fit.dat',
'ccpwcvtzmp2fit': 'cc-pwCVTZ_MP2FIT.dat',
'ccpvqzmp2fit': 'cc-pVQZ_MP2FIT.dat',
'ccpv5zmp2fit': 'cc-pV5Z_MP2FIT.dat',
'augccpwcvtzmp2fit': 'aug-cc-pwCVTZ_MP2FIT.dat',
'augccpvqzmp2fit': 'aug-cc-pVQZ_MP2FIT.dat',
'augccpv5zmp2fit': 'aug-cc-pV5Z_MP2FIT.dat',
'ccpcvdz' : ('cc-pvdz.dat', 'cc-pCVDZ.dat'),
'ccpcvtz' : ('cc-pvtz.dat', 'cc-pCVTZ.dat'),
'ccpcvqz' : ('cc-pvqz.dat', 'cc-pCVQZ.dat'),
'ccpcv5z' : 'cc-pCV5Z.dat',
'ccpcv6z' : 'cc-pCV6Z.dat',
'ccpwcvdz' : 'cc-pwCVDZ.dat',
'ccpwcvtz' : 'cc-pwCVTZ.dat',
'ccpwcvqz' : 'cc-pwCVQZ.dat',
'ccpwcv5z' : 'cc-pwCV5Z.dat',
'ccpwcvdzdk' : 'cc-pwCVDZ-DK.dat',
'ccpwcvtzdk' : 'cc-pwCVTZ-DK.dat',
'ccpwcvqzdk' : 'cc-pwCVQZ-DK.dat',
'ccpwcv5zdk' : 'cc-pwCV5Z-DK.dat',
'ccpwcvtzdk3': 'cc-pwCVTZ-DK3.dat',
'ccpwcvqzdk3': 'cc-pwCVQZ-DK3.dat',
'augccpwcvdz': 'aug-cc-pwcvdz.dat',
'augccpwcvtz': 'aug-cc-pwcvtz.dat',
'augccpwcvqz': 'aug-cc-pwcvqz.dat',
'augccpwcv5z': 'aug-cc-pwcv5z.dat',
'augccpwcvtzdk' : 'aug-cc-pwCVTZ-DK.dat',
'augccpwcvqzdk' : 'aug-cc-pwCVQZ-DK.dat',
'augccpwcv5zdk' : 'aug-cc-pwcv5z-dk.dat',
'augccpwcvtzdk3': 'aug-cc-pwCVTZ-DK3.dat',
'augccpwcvqzdk3': 'aug-cc-pwCVQZ-DK3.dat',
'dgaussa1cfit': 'DgaussA1_dft_cfit.dat',
'dgaussa1xfit': 'DgaussA1_dft_xfit.dat',
'dgaussa2cfit': 'DgaussA2_dft_cfit.dat',
'dgaussa2xfit': 'DgaussA2_dft_xfit.dat',
'ccpvdzpp' : 'cc-pvdz-pp.dat' ,
'ccpvtzpp' : 'cc-pvtz-pp.dat' ,
'ccpvqzpp' : 'cc-pvqz-pp.dat' ,
'ccpv5zpp' : 'cc-pv5z-pp.dat' ,
'crenbl' : 'crenbl.dat' ,
'crenbs' : 'crenbs.dat' ,
'lanl2dz' : 'lanl2dz.dat' ,
'lanl2tz' : 'lanl2tz.dat' ,
'lanl08' : 'lanl08.dat' ,
'sbkjc' : 'sbkjc.dat' ,
# Stuttgart ECP http://www.tc.uni-koeln.de/PP/clickpse.en.html
'stuttgart' : 'stuttgart_dz.dat',
'stuttgartdz': 'stuttgart_dz.dat',
'stuttgartrlc': 'stuttgart_dz.dat',
'stuttgartrsc': 'stuttgart_rsc.dat',
'stuttgartrsc_mdf': 'cc-pvdz-pp.dat',
#'stuttgartrsc_mwb': 'stuttgart_rsc.dat',
'ccpwcvdzpp' : 'cc-pwCVDZ-PP.dat',
'ccpwcvtzpp' : 'cc-pwCVTZ-PP.dat',
'ccpwcvqzpp' : 'cc-pwCVQZ-PP.dat',
'ccpwcv5zpp' : 'cc-pwCV5Z-PP.dat',
'ccpvdzppnr' : 'cc-pVDZ-PP-NR.dat',
'ccpvtzppnr' : 'cc-pVTZ-PP-NR.dat',
'augccpvdzpp': ('cc-pvdz-pp.dat', 'aug-cc-pVDZ-PP.dat'),
'augccpvtzpp': ('cc-pvtz-pp.dat', 'aug-cc-pVTZ-PP.dat'),
'augccpvqzpp': ('cc-pvqz-pp.dat', 'aug-cc-pVQZ-PP.dat'),
'augccpv5zpp': ('cc-pv5z-pp.dat', 'aug-cc-pV5Z-PP.dat'),
'pc0' : 'pc-0.dat',
'pc1' : 'pc-1.dat',
'pc2' : 'pc-2.dat',
'pc3' : 'pc-3.dat',
'pc4' : 'pc-4.dat',
'augpc0' : 'aug-pc-0.dat',
'augpc1' : 'aug-pc-1.dat',
'augpc2' : 'aug-pc-2.dat',
'augpc3' : 'aug-pc-3.dat',
'augpc4' : 'aug-pc-4.dat',
'pcseg0' : 'pcseg-0.dat',
'pcseg1' : 'pcseg-1.dat',
'pcseg2' : 'pcseg-2.dat',
'pcseg3' : 'pcseg-3.dat',
'pcseg4' : 'pcseg-4.dat',
'augpcseg0' : 'aug-pcseg-0.dat',
'augpcseg1' : 'aug-pcseg-1.dat',
'augpcseg2' : 'aug-pcseg-2.dat',
'augpcseg3' : 'aug-pcseg-3.dat',
'augpcseg4' : 'aug-pcseg-4.dat',
'sarcdkh' : 'sarc-dkh2.dat',
# Burkatzki-Filippi-Dolg pseudo potential
'bfdvdz' : 'bfd_vdz.dat',
'bfdvtz' : 'bfd_vtz.dat',
'bfdvqz' : 'bfd_vqz.dat',
'bfdv5z' : 'bfd_v5z.dat',
'bfd' : 'bfd_pp.dat',
'bfdpp' : 'bfd_pp.dat',
#
'ccpcvdzf12optri': os.path.join('f12-basis', 'cc-pCVDZ-F12-OptRI.dat'),
'ccpcvtzf12optri': os.path.join('f12-basis', 'cc-pCVTZ-F12-OptRI.dat'),
'ccpcvqzf12optri': os.path.join('f12-basis', 'cc-pCVQZ-F12-OptRI.dat'),
'ccpvdzf12optri' : os.path.join('f12-basis', 'cc-pVDZ-F12-OptRI.dat' ),
'ccpvtzf12optri' : os.path.join('f12-basis', 'cc-pVTZ-F12-OptRI.dat' ),
'ccpvqzf12optri' : os.path.join('f12-basis', 'cc-pVQZ-F12-OptRI.dat' ),
'ccpv5zf12' : os.path.join('f12-basis', 'cc-pV5Z-F12.dat' ),
'ccpvdzf12rev2' : os.path.join('f12-basis', 'cc-pVDZ-F12rev2.dat' ),
'ccpvtzf12rev2' : os.path.join('f12-basis', 'cc-pVTZ-F12rev2.dat' ),
'ccpvqzf12rev2' : os.path.join('f12-basis', 'cc-pVQZ-F12rev2.dat' ),
'ccpv5zf12rev2' : os.path.join('f12-basis', 'cc-pV5Z-F12rev2.dat' ),
'ccpvdzf12nz' : os.path.join('f12-basis', 'cc-pVDZ-F12-nZ.dat' ),
'ccpvtzf12nz' : os.path.join('f12-basis', 'cc-pVTZ-F12-nZ.dat' ),
'ccpvqzf12nz' : os.path.join('f12-basis', 'cc-pVQZ-F12-nZ.dat' ),
'augccpvdzoptri' : os.path.join('f12-basis', 'aug-cc-pVDZ-OptRI.dat' ),
'augccpvtzoptri' : os.path.join('f12-basis', 'aug-cc-pVTZ-OptRI.dat' ),
'augccpvqzoptri' : os.path.join('f12-basis', 'aug-cc-pVQZ-OptRI.dat' ),
'augccpv5zoptri' : os.path.join('f12-basis', 'aug-cc-pV5Z-OptRI.dat' ),
# All-electron basis designed for periodic calculations, available in Crystal
'pobtzvp' : 'pob-tzvp.dat',
'pobtzvpp' : 'pob-tzvpp.dat',
'crystalccpvdz' : 'crystal-cc-pvdz.dat',
# ccECP
'ccecp' : join('ccecp-basis', 'ccECP', 'ccECP.dat' ),
'ccecpccpvdz' : join('ccecp-basis', 'ccECP', 'ccECP_cc-pVDZ.dat'),
'ccecpccpvtz' : join('ccecp-basis', 'ccECP', 'ccECP_cc-pVTZ.dat'),
'ccecpccpvqz' : join('ccecp-basis', 'ccECP', 'ccECP_cc-pVQZ.dat'),
'ccecpccpv5z' : join('ccecp-basis', 'ccECP', 'ccECP_cc-pV5Z.dat'),
'ccecpccpv6z' : join('ccecp-basis', 'ccECP', 'ccECP_cc-pV6Z.dat'),
'ccecpaugccpvdz': join('ccecp-basis', 'ccECP', 'ccECP_aug-cc-pVDZ.dat'),
'ccecpaugccpvtz': join('ccecp-basis', 'ccECP', 'ccECP_aug-cc-pVTZ.dat'),
'ccecpaugccpvqz': join('ccecp-basis', 'ccECP', 'ccECP_aug-cc-pVQZ.dat'),
'ccecpaugccpv5z': join('ccecp-basis', 'ccECP', 'ccECP_aug-cc-pV5Z.dat'),
'ccecpaugccpv6z': join('ccecp-basis', 'ccECP', 'ccECP_aug-cc-pV6Z.dat'),
# ccECP_He_core
'ccecphe' : join('ccecp-basis', 'ccECP_He_core', 'ccECP.dat' ),
'ccecpheccpvdz' : join('ccecp-basis', 'ccECP_He_core', 'ccECP_cc-pVDZ.dat'),
'ccecpheccpvtz' : join('ccecp-basis', 'ccECP_He_core', 'ccECP_cc-pVTZ.dat'),
'ccecpheccpvqz' : join('ccecp-basis', 'ccECP_He_core', 'ccECP_cc-pVQZ.dat'),
'ccecpheccpv5z' : join('ccecp-basis', 'ccECP_He_core', 'ccECP_cc-pV5Z.dat'),
'ccecpheccpv6z' : join('ccecp-basis', 'ccECP_He_core', 'ccECP_cc-pV6Z.dat'),
'ccecpheaugccpvdz': join('ccecp-basis', 'ccECP_He_core', 'ccECP_aug-cc-pVDZ.dat'),
'ccecpheaugccpvtz': join('ccecp-basis', 'ccECP_He_core', 'ccECP_aug-cc-pVTZ.dat'),
'ccecpheaugccpvqz': join('ccecp-basis', 'ccECP_He_core', 'ccECP_aug-cc-pVQZ.dat'),
'ccecpheaugccpv5z': join('ccecp-basis', 'ccECP_He_core', 'ccECP_aug-cc-pV5Z.dat'),
'ccecpheaugccpv6z': join('ccecp-basis', 'ccECP_He_core', 'ccECP_aug-cc-pV6Z.dat'),
# ccECP_reg
'ccecpreg' : join('ccecp-basis', 'ccECP_reg', 'ccECP.dat' ),
'ccecpregccpvdz' : join('ccecp-basis', 'ccECP_reg', 'ccECP_cc-pVDZ.dat'),
'ccecpregccpvtz' : join('ccecp-basis', 'ccECP_reg', 'ccECP_cc-pVTZ.dat'),
'ccecpregccpvqz' : join('ccecp-basis', 'ccECP_reg', 'ccECP_cc-pVQZ.dat'),
'ccecpregccpv5z' : join('ccecp-basis', 'ccECP_reg', 'ccECP_cc-pV5Z.dat'),
'ccecpregaugccpvdz': join('ccecp-basis', 'ccECP_reg', 'ccECP_aug-cc-pVDZ.dat'),
'ccecpregaugccpvtz': join('ccecp-basis', 'ccECP_reg', 'ccECP_aug-cc-pVTZ.dat'),
'ccecpregaugccpvqz': join('ccecp-basis', 'ccECP_reg', 'ccECP_aug-cc-pVQZ.dat'),
'ccecpregaugccpv5z': join('ccecp-basis', 'ccECP_reg', 'ccECP_aug-cc-pV5Z.dat'),
#spin-orbit ECPs
'ecpds10mdfso' : os.path.join('soecp', 'ECPDS10MDFSO.dat'),
'ecpds28mdfso' : os.path.join('soecp', 'ECPDS28MDFSO.dat'),
'ecpds28mwbso' : os.path.join('soecp', 'ECPDS28MWBSO.dat'),
'ecpds46mdfso' : os.path.join('soecp', 'ECPDS46MDFSO.dat'),
'ecpds60mdfso' : os.path.join('soecp', 'ECPDS60MDFSO.dat'),
'ecpds60mwbso' : os.path.join('soecp', 'ECPDS60MWBSO.dat'),
'ecpds78mdfso' : os.path.join('soecp', 'ECPDS78MDFSO.dat'),
'ecpds92mdfbso' : os.path.join('soecp', 'ECPDS92MDFBSO.dat'),
'ecpds92mdfbqso' : os.path.join('soecp', 'ECPDS92MDFBQSO.dat'),
# dyall's sets
'dyall2zp' : 'dyall-basis.dyall_2zp',
'dyall3zp' : 'dyall-basis.dyall_3zp',
'dyall4zp' : 'dyall-basis.dyall_4zp',
'dyallaae2z' : 'dyall-basis.dyall_aae2z',
'dyallaae3z' : 'dyall-basis.dyall_aae3z',
'dyallaae4z' : 'dyall-basis.dyall_aae4z',
'dyallacv2z' : 'dyall-basis.dyall_acv2z',
'dyallacv3z' : 'dyall-basis.dyall_acv3z',
'dyallacv4z' : 'dyall-basis.dyall_acv4z',
'dyallae2z' : 'dyall-basis.dyall_ae2z',
'dyallae3z' : 'dyall-basis.dyall_ae3z',
'dyallae4z' : 'dyall-basis.dyall_ae4z',
'dyallav2z' : 'dyall-basis.dyall_av2z',
'dyallav3z' : 'dyall-basis.dyall_av3z',
'dyallav4z' : 'dyall-basis.dyall_av4z',
'dyallcv2z' : 'dyall-basis.dyall_cv2z',
'dyallcv3z' : 'dyall-basis.dyall_cv3z',
'dyallcv4z' : 'dyall-basis.dyall_cv4z',
'dyallv2z' : 'dyall-basis.dyall_v2z',
'dyallv3z' : 'dyall-basis.dyall_v3z',
'dyallv4z' : 'dyall-basis.dyall_v4z',
}
GTH_ALIAS = {
'gthaugdzvp' : 'gth-aug-dzvp.dat',
'gthaugqzv2p' : 'gth-aug-qzv2p.dat',
'gthaugqzv3p' : 'gth-aug-qzv3p.dat',
'gthaugtzv2p' : 'gth-aug-tzv2p.dat',
'gthaugtzvp' : 'gth-aug-tzvp.dat',
'gthdzv' : 'gth-dzv.dat',
'gthdzvp' : 'gth-dzvp.dat',
'gthqzv2p' : 'gth-qzv2p.dat',
'gthqzv3p' : 'gth-qzv3p.dat',
'gthszv' : 'gth-szv.dat',
'gthtzv2p' : 'gth-tzv2p.dat',
'gthtzvp' : 'gth-tzvp.dat',
'gthccdzvp' : 'gth-cc-dzvp.dat',
'gthcctzvp' : 'gth-cc-tzvp.dat',
'gthccqzvp' : 'gth-cc-qzvp.dat',
'gthszvmolopt' : 'gth-szv-molopt.dat',
'gthdzvpmolopt' : 'gth-dzvp-molopt.dat',
'gthtzvpmolopt' : 'gth-tzvp-molopt.dat',
'gthtzv2pmolopt' : 'gth-tzv2p-molopt.dat',
'gthszvmoloptsr' : 'gth-szv-molopt-sr.dat',
'gthdzvpmoloptsr' : 'gth-dzvp-molopt-sr.dat',
}
PP_ALIAS = {
'gthblyp' : 'gth-blyp.dat' ,
'gthbp' : 'gth-bp.dat' ,
'gthhcth120' : 'gth-hcth120.dat',
'gthhcth407' : 'gth-hcth407.dat',
'gtholyp' : 'gth-olyp.dat' ,
'gthlda' : 'gth-pade.dat' ,
'gthpade' : 'gth-pade.dat' ,
'gthpbe' : 'gth-pbe.dat' ,
'gthpbesol' : 'gth-pbesol.dat' ,
'gthhf' : 'gth-hf.dat' ,
'gthhfrev' : 'gth-hf-rev.dat' ,
}
SAP_ALIAS = {
'sapgraspsmall' : 'sap_grasp_small.dat',
'sapgrasplarge' : 'sap_grasp_large.dat',
}
def _is_pople_basis(basis):
return (basis.startswith('631') or
basis.startswith('321') or
basis.startswith('431'))
_BASIS_DIR = os.path.dirname(__file__)
_GTH_BASIS_DIR = os.path.abspath(f'{pyscf.__file__}/../pbc/gto/basis')
_GTH_PP_DIR = os.path.abspath(f'{_GTH_BASIS_DIR}/../pseudo')
def _parse_pople_basis(basis, symb):
if '(' in basis:
mbas = basis[:basis.find('(')]
extension = basis[basis.find('(')+1:basis.find(')')]
else:
mbas = basis
extension = ''
# polarized functions are defined based on pople basis name prefix like
# 6-31G, 6-311G etc.
basename = mbas[0] + '-' + mbas[1:].upper()
basename = basename.replace('+', '').replace('*', '')
pathtmp = join('pople-basis', basename + '-polarization-%s.dat')
def convert(s):
if len(s) == 0:
return []
elif s[0].isalpha():
return [pathtmp % s[0]] + convert(s[1:])
else:
return [pathtmp % s[:2]] + convert(s[2:])
if symb in ('H', 'He'):
if ',' in extension:
return tuple([ALIAS[mbas]] + convert(extension.split(',')[1]))
else:
return ALIAS[mbas]
else:
return tuple([ALIAS[mbas]] + convert(extension.split(',')[0]))
OPTIMIZE_CONTRACTION = getattr(__config__, 'gto_basis_parse_optimize', False)
[docs]
def parse(string, symb=None, optimize=OPTIMIZE_CONTRACTION):
'''Parse the basis (ECP, PP) text in NWChem or CP2K format, returns internal format
Args:
string : Blank linke and the lines of "BASIS SET" and "END" will be ignored
Examples:
>>> mol = gto.Mole()
>>> mol.basis = gto.basis.parse("""
... He S
... 13.6267000 0.1752300
... 1.9993500 0.8934830
... 0.3829930 0.0000000
... He S
... 13.6267000 0.0000000
... 1.9993500 0.0000000
... 0.3829930 1.0000000
... """, optimize=True)
>>> cell = pbc.gto.Cell()
>>> cell.basis = {'C': gto.basis.parse("""
... C DZVP-GTH
... 2
... 2 0 1 4 2 2
... 4.3362376436 0.1490797872 0.0000000000 -0.0878123619 0.0000000000
... 1.2881838513 -0.0292640031 0.0000000000 -0.2775560300 0.0000000000
... 0.4037767149 -0.6882040510 0.0000000000 -0.4712295093 0.0000000000
... 0.1187877657 -0.3964426906 1.0000000000 -0.4058039291 1.0000000000
... 3 2 2 1 1
... 0.5500000000 1.0000000000
... #
... """)}
'''
if 'ECP' in string:
return parse_nwchem_ecp.parse(string, symb)
elif 'GTH' in string:
if 'PSEUDOPOTENTIAL' in string:
return parse_cp2k_pp.parse(string, symb)
else:
return parse_cp2k.parse(string, symb, optimize)
else:
return parse_nwchem.parse(string, symb, optimize)
parse.__doc__ = parse_nwchem.parse.__doc__
[docs]
def parse_ecp(string, symb=None):
# TODO: catch KeyError and provide suggestion for the possible keys
return parse_nwchem_ecp.parse(string, symb)
parse_ecp.__doc__ = parse_nwchem_ecp.parse.__doc__
def _convert_contraction(contr_string):
'''Parse contraction scheme string into a list
Args:
contr_string : str
Desired contraction scheme in conventional 'XsYpZd...' form,
where X, Y, Z are the total numbers of corresponding functions.
'''
import re
l_fun={'s': 0, 'p': 1, 'd': 2, 'f': 3, 'g': 4, 'h': 5, 'i': 6}
l_fun.update({chr(num): num-100 for num in range(ord('k'), ord('p'))})
num_contr = [int(digit) for digit in re.findall(r'\d+', contr_string)]
basis_labels = re.findall(r'[d-z]+', contr_string)
assert len(num_contr)==len(basis_labels)
basis_l = [l_fun[basis] for basis in basis_labels]
assert basis_l == sorted(basis_l), 'Contraction scheme ' + contr_string +\
' has to be ordered by l'
assert len(basis_l) == len(set(basis_l)), 'Some of l in ' + contr_string +\
' appears more than once'
# Prepare zero list to ensure the total length is equal to the highest l+1
contraction_list = [0] * (1+max(basis_l))
for (l, n_contr) in zip(basis_l, num_contr):
contraction_list[l] = n_contr
return contraction_list
def _truncate(basis, contr_scheme, symb, split_name):
# keep only first n_keep contractions for each l
contr_b = []
for l, n_keep in enumerate(contr_scheme):
n_saved = 0
if n_keep > 0:
for segm in basis:
segm_l = segm[0]
if segm_l == l:
segm_len = len(segm[1][1:])
n_save = min(segm_len, n_keep - n_saved)
if n_save > 0:
save_segm = [line[:n_save+1] for line in
segm[:][1:]]
contr_b.append([l] + save_segm)
n_saved += n_save
assert n_saved == n_keep, ("@{} implies {} l={} function(s), but" +
"only {} in {}:{}").format(split_name[1],
contr_scheme[l],
l, n_saved, symb,
split_name[0])
return contr_b
optimize_contraction = parse_nwchem.optimize_contraction
to_general_contraction = parse_nwchem.to_general_contraction
[docs]
def load(filename_or_basisname, symb, optimize=OPTIMIZE_CONTRACTION):
'''Convert the basis of the given symbol to internal format
Args:
filename_or_basisname : str
Case insensitive basis set name. Special characters will be removed.
or a string of "path/to/file" which stores the basis functions
symb : str
Atomic symbol, Special characters will be removed.
Examples:
Load STO 3G basis of carbon to oxygen atom
>>> mol = gto.Mole()
>>> mol.basis = {'O': load('sto-3g', 'C')}
'''
symb = ''.join([i for i in symb if i.isalpha()])
if '@' in filename_or_basisname:
split_name = filename_or_basisname.split('@')
assert len(split_name) == 2
filename_or_basisname = split_name[0]
contr_scheme = _convert_contraction(split_name[1].lower())
else:
contr_scheme = 'Full'
if os.path.isfile(filename_or_basisname):
try:
b = _load_external(parse_nwchem, filename_or_basisname, symb,
optimize=optimize)
except BasisNotFoundError:
b = _load_external(parse_cp2k, filename_or_basisname, symb,
optimize=optimize)
if contr_scheme != 'Full':
b = _truncate(b, contr_scheme, symb, split_name)
return b
name = _format_basis_name(filename_or_basisname)
fload = parse_nwchem.load
basis_dir = _BASIS_DIR
if name in ALIAS:
basmod = ALIAS[name]
elif name in GTH_ALIAS:
basmod = GTH_ALIAS[name]
fload = parse_cp2k.load
basis_dir = _GTH_BASIS_DIR
elif _is_pople_basis(name):
basmod = _parse_pople_basis(name, symb)
elif name in SAP_ALIAS:
basmod = SAP_ALIAS[name]
else:
try:
return parse_nwchem.parse(filename_or_basisname, symb,
optimize=optimize)
except BasisNotFoundError:
pass
except Exception:
raise BasisNotFoundError(filename_or_basisname)
try:
return parse_nwchem.parse(filename_or_basisname, optimize=optimize)
except BasisNotFoundError:
pass
except Exception:
raise BasisNotFoundError(f'Invalid basis {filename_or_basisname}')
try:
return parse_cp2k.parse(filename_or_basisname, optimize=optimize)
except BasisNotFoundError:
pass
except Exception:
raise BasisNotFoundError(f'Invalid basis {filename_or_basisname}')
# Last, a trial to access Basis Set Exchange database
from pyscf.gto.basis import bse
if bse.basis_set_exchange is None:
import warnings
warnings.warn(
'Basis may be available in basis-set-exchange. '
'It is recommended to install basis-set-exchange: '
'pip install basis-set-exchange')
else:
try:
bse_obj = bse.basis_set_exchange.api.get_basis(
filename_or_basisname, elements=symb)
except KeyError:
raise BasisNotFoundError(filename_or_basisname)
else:
return bse._orbital_basis(bse_obj)[0]
raise BasisNotFoundError(f'Unknown basis format or basis name for {filename_or_basisname}')
if 'dat' in basmod:
b = fload(join(basis_dir, basmod), symb, optimize)
elif isinstance(basmod, (tuple, list)) and isinstance(basmod[0], str):
b = []
for f in basmod:
b += fload(join(basis_dir, f), symb, optimize)
else:
mod = importlib.import_module('.'+basmod, __package__)
b = mod.__getattribute__(symb)
if contr_scheme != 'Full':
b = _truncate(b, contr_scheme, symb, split_name)
return b
[docs]
def load_ecp(filename_or_basisname, symb):
'''Parses ECP database file
'''
symb = ''.join([i for i in symb if i.isalpha()])
if os.path.isfile(filename_or_basisname):
return _load_external(parse_nwchem_ecp, filename_or_basisname, symb)
name = _format_basis_name(filename_or_basisname)
if name in ALIAS:
basmod = ALIAS[name]
return parse_nwchem_ecp.load(join(_BASIS_DIR, basmod), symb)
try:
return parse_nwchem_ecp.parse(filename_or_basisname, symb)
except BasisNotFoundError:
pass
except Exception:
raise BasisNotFoundError(filename_or_basisname)
try:
return parse_nwchem_ecp.parse(filename_or_basisname)
except BasisNotFoundError:
pass
except Exception:
raise BasisNotFoundError(f'Invalid ECP {filename_or_basisname}')
# Last, a trial to access Basis Set Exchange database
from pyscf.gto.basis import bse
if bse.basis_set_exchange is not None:
try:
bse_obj = bse.basis_set_exchange.api.get_basis(
filename_or_basisname, elements=symb)
except KeyError:
raise BasisNotFoundError(filename_or_basisname)
else:
return bse._ecp_basis(bse_obj)[0]
raise BasisNotFoundError('Unknown ECP format or ECP name')
[docs]
def load_pseudo(filename_or_basisname, symb):
'''Parses PP database file
'''
symb = ''.join([i for i in symb if i.isalpha()])
if os.path.isfile(filename_or_basisname):
return _load_external(parse_cp2k_pp, filename_or_basisname, symb)
name, suffix = _format_pseudo_name(filename_or_basisname)
if name in PP_ALIAS:
basmod = PP_ALIAS[name]
return parse_cp2k_pp.load(join(_GTH_PP_DIR, basmod), symb, suffix)
try:
return parse_cp2k_pp.parse(filename_or_basisname)
except BasisNotFoundError:
raise
except Exception:
raise BasisNotFoundError(f'Invalid PP {filename_or_basisname}')
def _load_external(module, filename_or_basisname, symb, **kwargs):
'''Try to read basis from given file'''
try:
return module.load(filename_or_basisname, symb, **kwargs)
except BasisNotFoundError:
with open(filename_or_basisname, 'r') as fin:
return module.parse(fin.read(), **kwargs)
def _format_basis_name(basisname):
return basisname.lower().replace('-', '').replace('_', '').replace(' ', '')
SUFFIX_PATTERN = re.compile(r'q\d+$')
def _format_pseudo_name(pseudo_name):
name_suffix = _format_basis_name(pseudo_name)
match = re.search(SUFFIX_PATTERN, name_suffix)
if match:
name = name_suffix[:match.start()]
suffix = name_suffix[match.start():]
else:
name, suffix = name_suffix, None
return name, suffix
