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June 8, 2024 21:50
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* Updates due to NumPy 2.0 API changes * Fix __array_wrap__ * Fix a bug caused by an inplace operation in linalg_helper._qr * Fix inplace operation bug in pbc.cc.kintermediates_uhf * Retore a few np.array(copy=True) statement
* Fix platform issue in bdist_wheel * In case fail to import bdist_wheel
* Fix integer overflow for large ano basis (fix #2201) * More int type issues
* add atmlst to examples; fix examples/hessian/01-scf_hessian.py * fix atmlst for hessian * fix lint issue * fix scipy.sparse.linalg.cg issue * fix scipy.sparse.linalg.cg issue * fix scipy.sparse.linalg.cg issue * fix scipy.sparse.linalg.cg issue
* allow modifying tol and nroots * add example for tight tol * pass kwargs to mf.stability * fix typo
* fix bug in convert_to_kscf * fix bug in convert_to_kscf * fix kuhf case in convert_to_kscf
* Update mp2.py * Update ump2.py
… for HF-SCF calculations (#2301) * Added VSAP initial guess implementation for Hartree-Fock SCF calculations (described by S. Lehtola here: https://doi.org/10.1021/acs.jctc.8b01089) Modified fakemol_for_charges to be usable for SAP 3C2E integrals. Supplied sap_grasp coefficients computed by S. Lehtola. * Added 'large' and 'small' sap coefficient functionality * Fixed some bugs in recognition of DFT and HF objects and their SAP guesses. Made other cleanups and fixes proposed by S. Lehtola. * Changed logger.error to logger.warn * Renamed HF SAP guess functions from 'vsap' to 'sap' to avoid confusion with DFT counterparts using a different method with same name. * Fixed a bug I had created by accident. Created new fakemol_for_cgtf_charge function to be used in forming SAP guess and to avoid breaking other functionality which use the fakemol_for_charges function. * Removed redundant attribute check * vsap -> sap * charge sumcheck tolerance set to 1e-6 * Apply suggestions from code review Co-authored-by: Susi Lehtola <[email protected]> * Changed sap initial guess to accept basis set in internal format (python dict) or as a string (will look for basis file locally and from basis set exhcange if bse api is installed) * Added SAP guess to restricted open-shell Hartree-Fock (ROHF) * Added SAP guess to non-relativistic generalized Hartree-Fock (GHF) * Tidy up SAP function in GHF, make sap_grasp_large to default SAP basis * Add example for SAP inital guess. * Added SAP guess to Dirac-Hartree-Fock (DHF) * small cleanups * SAP now accepts internally formatted python dictionary as basis. SCF object has new attribute sap_basis * Apply suggestions from code review Co-authored-by: Susi Lehtola <[email protected]> * Clarified example using explicit dictionary format basis for SAP * Apply suggestions from code review Co-authored-by: Susi Lehtola <[email protected]> * Comment for vsap added back * Fixed issue * Fixed style issues * Fix style issue with extraneous 'f' prefix * fix ROHF SAP guess call tree, add SAP unittest for rhf and rohf * Fixed accidental incorrect test * Add SAP guess to UHF * Add SAP unittest for uhf * Add SAP unittest for GHF * Add SAP unittest for DHF * flake8 warning --------- Co-authored-by: Susi Lehtola <[email protected]> Co-authored-by: Qiming Sun <[email protected]>
* Use weakref for automatic deletion of tmpfiles * github actions tests check number of leftover temporary files * temporary file check pytest exit status * Avoid h5f.flush() on closed file --------- Co-authored-by: Qiming Sun <[email protected]>
* fix mix solver * fix flake
* use casscf.ci if set * also fix the free kernel * update test * remove global mols * update test to align with casci * Improve error types in FCI modules --------- Co-authored-by: Qiming Sun <[email protected]>
* Small fix for mol sanity check * Fix for special atom_symbol * import error fixed * Small fix in 'default' basis
…2959) * Allow QMMM gradient for MM point charges, not just Gaussian charges * Add tests * Disable Gaussian charge for QMMM, since the nuclear term doesn't actually support it, and it's not tested * Update qm/mm gradients tests --------- Co-authored-by: Qiming Sun <[email protected]>
… k-point calculations (#2946) * Fixes mismatch exchange between cell-kmesh and supercell * Update tests * Update MDF.weighted_coulG * Update tests * Adjust tests
* move state_average_mix to CASBase * update example
* Refactor molecular DFT+U code * Add RKS+U gradients * Add UKS+U gradients * Analytical gradients for KRKS+U and KUKS+U * Fix weights bug in symmetry adapted KDFT+U * syntax error * Fix linear_response Hubbard U for UKS * Fix KUKS+U linear response U method * Disable geometry optimizer for PBC methods * Fix DFT+U gradient tests * sanity checks
* Fix PBC ksym-mean-field initialization when calling the shortcut method cell.KKS * Adjust kwargs * Fix to_gpu function * Fix to_gpu compatibility issue * update to_gpu * Clean up .kpts attributes * Update docstring of get_nuc and get_pp * Fix backward compatibility * lint * lint * lint * Fix fftdf ao2mo_7d * Add warnings
* re-enable gaussian MM charges * add periodic QMMM using multipoles * minor * minor * pep8 * pep8 * pep8 * minor --------- Co-authored-by: MoleOrbitalHybridAnalyst <[email protected]>
* parallel broadcasted elementwise multiplication * Update np_broadcast.c __restrict -> __restrict__ --------- Co-authored-by: Qiming Sun <[email protected]>
* Fix nuclear gradients for MM particles with guassian charge model * Handle deprecated warning msgs from numpy
* Improve DFT Grids configuration methods * Improve docstring
* Fix bug for KUKS vxc with hybrids * Fix dimension error for KUKS when xc='hf' --------- Co-authored-by: Qiming Sun <[email protected]>
* Debug rks_stress * AO derivatives * Fix get_veff * RKS stress tensor works * Add KRKS stress tensor * ao transpose * Circular reference caused by space_group_symmetry in cell * Fix unit bug in cell.set_geom_ * Add UKS and KUKS stress tensors * Store scaled kpts (fractional coordinates) in the .kpts attributes in PBC classes * Improve get_kconserv; Add more tests for get_kconserv * Various compatibility fixes for pbc-gdf and symmetry adapted k-points * Fix khf_ksymm.KHF.reset method * Fix pbc.df reset method for k-symmetry adapted calculations * Adjust tests * Adjust tests
* Update ASE interface to support lattice relaxation * Update DFT+U docstring
* Bugfixes in SMD Hessian (fix #2988)
* Update docstrings for solvent and multigrid modules * Update docstrings for df, dft and other modules
* Using relative tolerance to check space group symmetry (fix #2996) * check_mesh_symmetry updates
* Release 2.11 * Update Contributors list
Update README for the 3rd PySCF Conference
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