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Merge pyscf upstream #3

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Merge pyscf upstream #3

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Commits on Mar 14, 2023

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Commits on Mar 15, 2023

  1. Release 2.2 (pyscf#1619)

    * Fix dimension error for 3c2e integrals
    
    * Update conda build jobs
    
    * Release 2.2.0
    sunqm authored Mar 15, 2023
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  2. Density fitting gradients and hessian for RSH functionals (pyscf#1630)

    * Fix gradients and hessian for density fitting DFT with RSH functionals
    
    * Add range_coulomb context for pbc.df modules
    sunqm authored Mar 15, 2023
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  3. Add SCS-MP2

    hongzhouye authored and sunqm committed Mar 15, 2023
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  5. Fix flake8 config file for flake8>6

    * Backslashes are not recognized and flake8 will fail under new versions
    wangenau authored and sunqm committed Mar 15, 2023
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  6. PBC DF K-build with a smaller overhead (pyscf#1550)

    * Add mo-based K-build
    
    * fix mdf bug & 0D bug
    
    * support mo-tagged dm
    
    ---------
    
    Co-authored-by: hongzhouye <>
    hongzhouye authored Mar 15, 2023
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Commits on Mar 16, 2023

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  2. pbc.df.CDERIArray compatibility improved (pyscf#1628)

    * Backward compatibility for class CDERIArray (fix issue pyscf#1451)
    
    * Fix CDERIArray for reading old data format
    
    * Check dimension
    sunqm authored Mar 16, 2023
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  3. Read cubefile xs, ys, zs correctly (pyscf#1532)

    * Read cubefile xs, ys, zs correctly
    
    * Read cubefile nx and use that to calculate xs (y and z as well)
    
    * Fix issue pyscf#1531
    
    * Read cubefile xs, ys, zs correctly
    
    * Read cubefile nx and use that to calculate xs (y and z as well)
    
    * Fix issue pyscf#1531
    
    * Add import Cell
    
    * import Cell in read function
    * swap order of nx and xs
    
    * add reading of box information
    
    * read function now reads box from cubefile
    
    * remove trailing whitespaces
    
    * Add tests
    
    * Solve conflicts
    
    * Update cubegen tests
    
    ---------
    
    Co-authored-by: Till Hanke <[email protected]>
    Co-authored-by: Qiming Sun <[email protected]>
    3 people authored Mar 16, 2023
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  4. ao2mo from scalar integral to complex GHF orbitals (pyscf#1411)

    * implements ao2mo from scalar ao integrals to complex ghf orbital or spinors
    
    * Add tests and bugfixes
    
    ---------
    
    Co-authored-by: Qiming Sun <[email protected]>
    xubwa and sunqm authored Mar 16, 2023
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  5. Fix SA-CASSCF tests

    sunqm committed Mar 16, 2023
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  6. DIIS instability due to numerical noises (fix issue pyscf#1524) (pysc…

    …f#1638)
    
    Improves DIIS numerical stability (issue pyscf#1524)
    sunqm authored Mar 16, 2023
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Commits on Mar 17, 2023

  1. Adds UCISD with density-fitting (pyscf#1450)

    * Adds support for UCISD with density fitting
    
    * Allows RCISD with df in ci.__init__
    
    * Remove trailing whitespaces
    
    * Removes unnecessary import
    maxnus authored Mar 17, 2023
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  2. Pretty printing in mcscf module (pyscf#1475)

    * MAINT: Format gradient norm in printout
    
    * MAINT: Modify format strings for pretty print number alingment
    
    * MAINT: Pretty printing for the mcscf module
    
    * MAINT: Eliminate spaces in AO labels
    bogdanoff authored Mar 17, 2023
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Commits on Mar 20, 2023

  1. Fix print format

    sunqm authored and fishjojo committed Mar 20, 2023
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  5. Fixes hybrid functional checks (pyscf#1646)

    * libxc.parse_xc memoization
    
    * Fix overwritten for lru cached results
    
    * Fix df-hessian for wb97 functional
    
    * Improves hybrid functional checks
    
    * undefined variable
    sunqm authored Mar 20, 2023
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  6. Updates github actions for release pipeline (pyscf#1639)

    * Updates github action configs
    
    * Update conda release scripts
    
    * Fix conda build recipe and release pipeline
    
    * Update conda recipe
    
    * Missing conda build config file
    sunqm authored Mar 20, 2023
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  7. lo/boys: Use same centers for r2 and r integrals, fix charge center e…

    …valuation (pyscf#1635)
    
    * lo/boys: Use same centers for r2 and r integrals, fix charge center evaluation
    
    * Update localized orbitals tests
    
    * lo/boys: Remove factor 2 from <r>^2 in cost_function
    
    ---------
    
    Co-authored-by: Qiming Sun <[email protected]>
    wangenau and sunqm authored Mar 20, 2023
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  8. Moment resolved GF-CCSD (pyscf#1448)

    * Initial implementation of GF-CCSD
    
    * Bug fixes
    
    * Fix contractions, late contraction for ket
    
    * Nuke old functions
    
    * Clean comments, appease flake8
    
    * Adds GFCCSD to __init__.py
    
    * Change to amplitude passing
    
    * Fix to sign, niter argument and some logging
    
    * Adds tests for GFCCSD
    
    * Adds tests for density fitting
    
    * Adds simple GF-CCSD example
    
    * Adds more examples
    
    * Update examples and refs
    
    * Small comment in example 52
    
    * Renames ipccsd and eaccsd to ipgfccsd and eagfccsd
    
    * Moment input example now uses HF and AGF2 moments
    
    * Adds example of transformation to self-energy
    
    * Small changes to examples
    
    * Adds explicit ket routines
    
    * Fix function name
    
    * Changes name of solver to MomGFCCSD
    
    * Fix class name in some docstrings
    
    ---------
    
    Co-authored-by: George Booth <[email protected]>
    obackhouse and George Booth authored Mar 20, 2023
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Commits on Mar 21, 2023

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  3. Optimize qmmm interface (issue 1171)

    sunqm authored and fishjojo committed Mar 21, 2023
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  5. Update MEP example

    sunqm authored and fishjojo committed Mar 21, 2023
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  6. Add some comments in symm module

    sunqm authored and fishjojo committed Mar 21, 2023
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  7. Remove git submodule (fix issue pyscf#1392)

    sunqm authored and fishjojo committed Mar 21, 2023
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  10. Add example for issue pyscf#1205

    sunqm authored and fishjojo committed Mar 21, 2023
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  11. Update example for issue pyscf#961

    sunqm authored and fishjojo committed Mar 21, 2023
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Commits on Mar 22, 2023

  1. Fix multigrid vxc shape bug (pyscf#1647)

    * Fix multigrid vxc shape bug (pyscf#1356)
    
    * fix multigrid vxc shape
    
    ---------
    
    Co-authored-by: Xing Zhang <[email protected]>
    sunqm and fishjojo authored Mar 22, 2023
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Commits on Mar 23, 2023

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  2. Check the number of roots during davidson diagonalization (pyscf#1654)

    * Check the number of roots during davidson diagonalization (fix issue pyscf#1447)
    
    * Fix initial value of e in davidson1
    
    * Fix davidson solver
    
    * Fix davidson solver for diagonal matrix (issue pyscf#1362)
    
    * Update cisd default level_shift
    
    * Update tests for linalg_helper.py
    sunqm authored Mar 23, 2023
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  4. GDF custom cderi file for rsh functional (pyscf#1664)

    * More checks for groupname
    
    * Fix cderi dataset name conflicts (issue pyscf#768)
    
    * Add tests
    sunqm authored Mar 23, 2023
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  5. Clean up PBC TDDFT (pyscf#1658)

    * clean up pbc TDDFT classes (fix issue pyscf#1315)
    
    * Allow nto analysis in pbc tddft
    
    * Update example
    sunqm authored Mar 23, 2023
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Commits on Mar 27, 2023

  1. Cleanup logging messages for SACASSCF module (pyscf#1672)

    * Cleanup logging messages for SACASSCF module
    
    * Update tests
    sunqm authored Mar 27, 2023
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Commits on Mar 28, 2023

  1. Update examples (pyscf#1675)

    * Update examples
    
    * Update fci tests
    sunqm authored Mar 28, 2023
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  2. Frequency integration grid scaling factor as input to RPA calculations (

    pyscf#1670)
    
    * scaling factor of frequency integration grid as input parameter in RPA calculations
    
    * default values for nw and x0 in kernel
    EgorTrushin authored Mar 28, 2023
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Commits on Mar 29, 2023

  1. Add low-level interface to Basis Set Exchange (pyscf#1166)

    * Add low-level interface to Basis Set Exchange
    
    * Include examples on how to print out version data and basis set references
    
    * Use basis-set-exchange as the last option for basis parser
    
    * Fix df.make_auxbasis
    
    * Fix lint error
    
    ---------
    
    Co-authored-by: Qiming Sun <[email protected]>
    susilehtola and sunqm authored Mar 29, 2023
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Commits on Mar 30, 2023

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Commits on Apr 1, 2023

  1. fix chemcore bug when ecp exists

    hebrewsnabla authored and sunqm committed Apr 1, 2023
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  2. Release 2.2.1

    sunqm committed Apr 1, 2023
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Commits on Apr 3, 2023

  1. Add examples and other cleanups (pyscf#1693)

    * Example of custom pbc-gdf and other cleanups
    
    * Update example dft/24-define_xc_functional: add fxc functional
    sunqm authored Apr 3, 2023
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Commits on Apr 11, 2023

  1. Refactor NLC parser and integral code (pyscf#1681)

    * Update nlc parser for molecular dft
    
    * Refactor nlc for gradients
    
    * Fix bug in nlc_coeff parser and change nlc_coeff API
    
    * check NLC in PBC DFT
    sunqm authored Apr 11, 2023
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Commits on Apr 14, 2023

  1. Fix github action (pyscf#1702)

    * codecov was removed from pypi
    
    * Re-enable codecov action
    sunqm authored Apr 14, 2023
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  2. Update geomeTRIC library interface (pyscf#1700)

    * Update interface of geomeTRIC library to support initial hessian
    
    * Fix bug in MP2 gradients scanner
    sunqm authored Apr 14, 2023
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Commits on Apr 19, 2023

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  2. GHF density fitting (pyscf#1708)

    * Fix density-fitting GHF
    
    * Update tests
    sunqm authored Apr 19, 2023
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Commits on Apr 29, 2023

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  3. Create FUNDING.yml

    Creates github sponsors button
    sunqm committed Apr 29, 2023
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Commits on Apr 30, 2023

  1. Refactors FCI cylindrical symmetry implementation (pyscf#1623)

    * Optimize direct_spin1_symm and direct_spin1_cyl_sym
    
    * Optimize fcivec size for spin1_symm solvers
    
    * Update relevant mcscf modules
    
    * Add example for fci-cyl-sym solver
    
    * Optimize direct_spin1_cyl_sym
    
    * fix
    
    * Add tests for FCI-ep
    
    * Disable fix_spin for FCI of UHF orbitals
    
    * FCI initial guess may introduce problematic states
    
    * Add timer for fci (issue pyscf#1562)
    
    * Restore fci.direct_spin1 initial guess treatment
    sunqm authored Apr 30, 2023
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Commits on May 9, 2023

  1. BUGFIX: SACASSCF grad fcasscf right track nelecas (pyscf#1721)

    * SACASSCF grad fcasscf right nelecas
    
    one of the fcisolver refactors exposed that the fcasscf object
    wasn't keeping track of nelecas properly
    
    * Add some docstring because why not
    
    ---------
    
    Co-authored-by: Matthew R Hermes <[email protected]>
    MatthewRHermes and MatthewRHermes authored May 9, 2023
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  2. Pass atom_symbol in all calls to ecp.core_configuration (pyscf#1723)

    * MAINT: Pass atom_symbol in all calls to ecp.core_configuration
    
    * BUG: Pass pure atom_symbol to ecp.core_configuration
    
    * MAINT: Adapt minao and atom initial guess to f-in-core ECPs
    
    * MAINT: Add newline for the atom initial guess to visually separate the actual calculation
    
    * MAINT: Add test for f-in-core ECP
    
    * Update test_ecp.py
    
    ---------
    
    Co-authored-by: Qiming Sun <[email protected]>
    bogdanoff and sunqm authored May 9, 2023
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Commits on May 22, 2023

  1. Fix bug in xc parser for hybrid LDA functional (pyscf#1738)

    * Handle HYB_LDA_XC in xc_parser
    
    * Cleanup dft.gen_grid
    sunqm authored May 22, 2023
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  2. Fix bug in pbcdft eval_rho2

    sunqm committed May 22, 2023
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Commits on Jun 4, 2023

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Commits on Jun 6, 2023

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