pyscf 2.6.0__py3-none-macosx_11_0_arm64.whl → 2.6.1__py3-none-macosx_11_0_arm64.whl

pyscf/pbc/df/rsdf.py

@@ -47,6 +47,7 @@ import numpy as np
 
 from pyscf import lib
 from pyscf.lib import logger, zdotCN
+from pyscf.lib import parameters as param
 from pyscf.pbc.df.df import GDF
 from pyscf.pbc.df import aft, aft_jk
 from pyscf.pbc.df import ft_ao
@@ -421,9 +422,11 @@ class _RSGDFBuilder(rsdf_builder._RSGDFBuilder):
     def outcore_auxe2(self, cderi_file, intor='int3c2e', aosym='s2', comp=None,
                       kptij_lst=None, j_only=False, dataname='j3c-junk',
                       shls_slice=None):
-        swapfile = tempfile.NamedTemporaryFile(dir=os.path.dirname(cderi_file))
-        fswap = lib.H5TmpFile(swapfile.name)
-        swapfile = None
+        # Deadlock on NFS if you open an already-opened tmpfile in H5PY
+        # swapfile = tempfile.NamedTemporaryFile(dir=os.path.dirname(cderi_file))
+        fswap = lib.H5TmpFile(dir=os.path.dirname(cderi_file), prefix='.outcore_auxe2_swap')
+        # avoid trash files
+        os.unlink(fswap.filename)
 
         cell = self.cell
         if self.use_bvk and self.kpts_band is None:
@@ -573,7 +576,7 @@ class _RSGDFBuilder(rsdf_builder._RSGDFBuilder):
         # Add (1) short-range G=0 (i.e., charge) part and (2) long-range part
         tspans = np.zeros((3,2))    # lr, j2c_inv, j2c_cntr
         tspannames = ["ftaop+pw", "j2c_inv", "j2c_cntr"]
-        feri = h5py.File(cderi_file, 'w')
+        feri = lib.H5FileWrap(cderi_file, 'w')
 
         # TODO: Store rs_density_fit cderi tensor in v1 format for the moment.
         # It should be changed to 'v2' format in the future.

pyscf/pbc/df/rsdf_builder.py

@@ -384,10 +384,9 @@ class _RSGDFBuilder(Int3cBuilder):
         # separated temporary file can avoid this issue.  The DF intermediates may
         # be terribly huge. The temporary file should be placed in the same disk
         # as cderi_file.
-        swapfile = tempfile.NamedTemporaryFile(dir=os.path.dirname(cderi_file))
-        fswap = lib.H5TmpFile(swapfile.name)
+        fswap = lib.H5TmpFile(dir=os.path.dirname(cderi_file), prefix='.outcore_auxe2_swap')
         # Unlink swapfile to avoid trash files
-        swapfile = None
+        os.unlink(fswap.filename)
 
         log = logger.new_logger(self)
         cell = self.cell
@@ -926,7 +925,7 @@ class _RSGDFBuilder(Int3cBuilder):
                                    'j3c', shls_slice, kk_idx=kk_idx)
         cpu1 = log.timer('pass1: real space int3c2e', *cpu0)
 
-        feri = h5py.File(cderi_file, 'w')
+        feri = lib.H5FileWrap(cderi_file, 'w')
         feri['kpts'] = kpts
         feri['aosym'] = aosym
 

pyscf/pbc/df/rsdf_helper.py

@@ -1052,9 +1052,9 @@ def _aux_e2_nospltbas(cell, auxcell_or_auxbasis, omega, erifile,
     if isinstance(erifile, h5py.Group):
         feri = erifile
     elif h5py.is_hdf5(erifile):
-        feri = h5py.File(erifile, 'a')
+        feri = lib.H5FileWrap(erifile, 'a')
     else:
-        feri = h5py.File(erifile, 'w')
+        feri = lib.H5FileWrap(erifile, 'w')
     if dataname in feri:
         del (feri[dataname])
     if dataname+'-kptij' in feri:

pyscf/pbc/dft/__init__.py

@@ -37,9 +37,6 @@ from pyscf.pbc.lib import kpts as libkpts
 GKS = gks.GKS
 UKS = uks.UKS
 ROKS = roks.ROKS
-gto.Cell.GKS = property(GKS)
-gto.Cell.UKS = property(UKS)
-gto.Cell.ROKS = property(ROKS)
 
 def KRKS(cell, *args, **kwargs):
     for arg in args:
@@ -49,7 +46,6 @@ def KRKS(cell, *args, **kwargs):
         if isinstance(kwargs['kpts'], libkpts.KPoints):
             return krks_ksymm.KRKS(cell, *args, **kwargs)
     return krks.KRKS(cell, *args, **kwargs)
-gto.Cell.KRKS = property(KRKS)
 
 def KUKS(cell, *args, **kwargs):
     for arg in args:
@@ -59,12 +55,9 @@ def KUKS(cell, *args, **kwargs):
         if isinstance(kwargs['kpts'], libkpts.KPoints):
             return kuks_ksymm.KUKS(cell, *args, **kwargs)
     return kuks.KUKS(cell, *args, **kwargs)
-gto.Cell.KUKS = property(KUKS)
 
 KROKS = kroks.KROKS
 KGKS = kgks.KGKS
-gto.Cell.KROKS = property(KROKS)
-gto.Cell.KGKS =  property(KGKS)
 
 def KRKSpU(cell, *args, **kwargs):
     for arg in args:
@@ -74,7 +67,6 @@ def KRKSpU(cell, *args, **kwargs):
         if isinstance(kwargs['kpts'], libkpts.KPoints):
             return krkspu_ksymm.KRKSpU(cell, *args, **kwargs)
     return krkspu.KRKSpU(cell, *args, **kwargs)
-gto.Cell.KRKSpU = property(KRKSpU)
 
 def KUKSpU(cell, *args, **kwargs):
     for arg in args:
@@ -84,7 +76,6 @@ def KUKSpU(cell, *args, **kwargs):
         if isinstance(kwargs['kpts'], libkpts.KPoints):
             return kukspu_ksymm.KUKSpU(cell, *args, **kwargs)
     return kukspu.KUKSpU(cell, *args, **kwargs)
-gto.Cell.KUKSpU = property(KUKSpU)
 
 def RKS(cell, *args, **kwargs):
     if cell.spin == 0:
@@ -92,7 +83,6 @@ def RKS(cell, *args, **kwargs):
     else:
         return roks.ROKS(cell, *args, **kwargs)
 RKS.__doc__ = rks.RKS.__doc__
-gto.Cell.RKS = property(RKS)
 
 def KS(cell, *args, **kwargs):
     if cell.spin == 0:
@@ -102,7 +92,6 @@ def KS(cell, *args, **kwargs):
 KS.__doc__ = '''
 A wrap function to create DFT object (RKS or UKS) for PBC systems.\n
 ''' + rks.RKS.__doc__
-gto.Cell.KS = property(KS)
 
 def KKS(cell, *args, **kwargs):
     if cell.spin == 0:
@@ -112,4 +101,3 @@ def KKS(cell, *args, **kwargs):
 KKS.__doc__ = '''
 A wrap function to create DFT object with k-point sampling (KRKS or KUKS).\n
 ''' + krks.KRKS.__doc__
-gto.Cell.KKS = property(KKS)

pyscf/pbc/dft/kgks.py

@@ -35,6 +35,7 @@ from pyscf.pbc.dft import krks
 from pyscf.pbc.dft import rks
 from pyscf.pbc.dft import multigrid
 from pyscf.pbc.dft.numint2c import KNumInt2C
+from pyscf.dft import gks as mol_ks
 from pyscf import __config__
 
 def get_veff(ks, cell=None, dm=None, dm_last=0, vhf_last=0, hermi=1,
@@ -117,6 +118,8 @@ class KGKS(rks.KohnShamDFT, kghf.KGHF):
     '''GKS class adapted for PBCs with k-point sampling.
     '''
 
+    collinear = mol_ks.GKS.collinear
+    spin_samples = mol_ks.GKS.spin_samples
     get_veff = get_veff
     energy_elec = krks.energy_elec
     get_rho = krks.get_rho

pyscf/pbc/dft/numint.py

@@ -1264,7 +1264,7 @@ class KNumInt(lib.StreamObject, numint.LibXCMixin):
             if isinstance(dms[0], numpy.ndarray) and dms[0].ndim == 2:
                 mo_coeff = [mo_coeff]
                 mo_occ = [mo_occ]
-            nao = cell.nao_nr()
+            nao = dms[0].shape[-1]
             ndms = len(mo_occ)
             def make_rho(idm, ao, non0tab, xctype):
                 return self.eval_rho2(cell, ao, mo_coeff[idm], mo_occ[idm],

pyscf/pbc/dft/numint2c.py

@@ -335,6 +335,7 @@ class KNumInt2C(lib.StreamObject, numint.LibXCMixin):
     collinear_samples = numint2c.NumInt2C.collinear_samples
 
     make_mask = lib.invalid_method('make_mask')
+    eval_ao = staticmethod(pnumint.eval_ao_kpts)
 
     def eval_rho(self, cell, ao_kpts, dm_kpts, non0tab=None, xctype='LDA',
                  hermi=0, with_lapl=True, verbose=None):

pyscf/pbc/lib/kpts.py

@@ -410,7 +410,7 @@ def symmetrize_wavefunction(kpts, psiR_k, mesh):
     '''
     raise RuntimeError('need verification')
     psiR_k = np.asarray(psiR_k, order='C')
-    is_complex = psiR_k.dtype == np.complex
+    is_complex = np.iscomplexobj(psiR_k.dtype)
     nao = psiR_k.shape[1]
     nG = psiR_k.shape[2]
     psiR = np.zeros([kpts.nkpts,nao,nG], dtype = psiR_k.dtype, order='C')

pyscf/pbc/scf/__init__.py

@@ -40,9 +40,6 @@ from pyscf.pbc.lib import kpts as libkpts
 GHF = ghf.GHF
 UHF = uhf.UHF
 ROHF = rohf.ROHF
-gto.Cell.GHF = property(GHF)
-gto.Cell.UHF = property(UHF)
-gto.Cell.ROHF = property(ROHF)
 
 def RHF(cell, *args, **kwargs):
     if cell.spin == 0:
@@ -50,7 +47,6 @@ def RHF(cell, *args, **kwargs):
     else:
         return rohf.ROHF(cell, *args, **kwargs)
 RHF.__doc__ = rhf.RHF.__doc__
-gto.Cell.RHF = property(RHF)
 
 #KRHF = krhf.KRHF  # KRHF supports cell.spin != 0 if number of k-points is even
 def KRHF(cell, *args, **kwargs):
@@ -61,7 +57,6 @@ def KRHF(cell, *args, **kwargs):
         if isinstance(kwargs['kpts'], libkpts.KPoints):
             return khf_ksymm.KRHF(cell, *args, **kwargs)
     return krhf.KRHF(cell, *args, **kwargs)
-gto.Cell.KRHF = property(KRHF)
 
 def KUHF(cell, *args, **kwargs):
     for arg in args:
@@ -71,10 +66,8 @@ def KUHF(cell, *args, **kwargs):
         if isinstance(kwargs['kpts'], libkpts.KPoints):
             return kuhf_ksymm.KUHF(cell, *args, **kwargs)
     return kuhf.KUHF(cell, *args, **kwargs)
-gto.Cell.KUHF = property(KUHF)
 
 KROHF = krohf.KROHF
-gto.Cell.KROHF = property(KROHF)
 
 #KGHF = kghf.KGHF
 def KGHF(cell, *args, **kwargs):
@@ -85,7 +78,6 @@ def KGHF(cell, *args, **kwargs):
         if isinstance(kwargs['kpts'], libkpts.KPoints):
             return kghf_ksymm.KGHF(cell, *args, **kwargs)
     return kghf.KGHF(cell, *args, **kwargs)
-gto.Cell.KGHF = property(KGHF)
 
 newton = newton_ah.newton
 
@@ -94,14 +86,12 @@ def HF(cell, *args, **kwargs):
         return rhf.RHF(cell, *args, **kwargs)
     else:
         return uhf.UHF(cell, *args, **kwargs)
-gto.Cell.HF = property(HF)
 
 def KHF(cell, *args, **kwargs):
     if cell.spin == 0:
         return KRHF(cell, *args, **kwargs)
     else:
         return KUHF(cell, *args, **kwargs)
-gto.Cell.KHF = property(KHF)
 
 
 def KS(cell, *args, **kwargs):

pyscf/pbc/scf/ghf.py

@@ -100,6 +100,7 @@ def get_jk(mf, cell=None, dm=None, hermi=0, kpt=None, kpts_band=None,
 class GHF(pbchf.SCF):
     '''GHF class for PBCs.
     '''
+    _keys = {'with_soc'}
 
     def __init__(self, cell, kpt=np.zeros(3),
                  exxdiv=getattr(__config__, 'pbc_scf_SCF_exxdiv', 'ewald')):

pyscf/pbc/scf/hf.py

@@ -789,7 +789,7 @@ class SCF(mol_hf.SCF):
     def dump_chk(self, envs):
         if self.chkfile:
             mol_hf.SCF.dump_chk(self, envs)
-            with h5py.File(self.chkfile, 'a') as fh5:
+            with lib.H5FileWrap(self.chkfile, 'a') as fh5:
                 fh5['scf/kpt'] = self.kpt
         return self
 

pyscf/pbc/scf/kghf.py

@@ -186,6 +186,8 @@ def _cast_mol_init_guess(fn):
 class KGHF(khf.KSCF):
     '''GHF class for PBCs.
     '''
+    _keys = {'with_soc'}
+
     def __init__(self, cell, kpts=np.zeros((1,3)),
                  exxdiv=getattr(__config__, 'pbc_scf_SCF_exxdiv', 'ewald')):
         khf.KSCF.__init__(self, cell, kpts, exxdiv)

pyscf/pbc/scf/khf.py

@@ -614,7 +614,7 @@ class KSCF(pbchf.SCF):
     def dump_chk(self, envs):
         if self.chkfile:
             mol_hf.SCF.dump_chk(self, envs)
-            with h5py.File(self.chkfile, 'a') as fh5:
+            with lib.H5FileWrap(self.chkfile, 'a') as fh5:
                 fh5['scf/kpts'] = self.kpts
         return self
 

pyscf/pbc/scf/khf_ksymm.py

@@ -245,7 +245,7 @@ class KsymAdaptedKSCF(khf.KSCF):
     def dump_chk(self, envs):
         if self.chkfile:
             mol_hf.SCF.dump_chk(self, envs)
-            with h5py.File(self.chkfile, 'a') as fh5:
+            with lib.H5FileWrap(self.chkfile, 'a') as fh5:
                 fh5['scf/kpts'] = self.kpts.kpts_ibz #FIXME Shall we rebuild kpts? If so, more info is needed.
         return self
 

pyscf/scf/__init__.py

@@ -130,7 +130,6 @@ def HF(mol, *args):
 HF.__doc__ = '''
 A wrap function to create SCF class (RHF or UHF).\n
 ''' + hf.SCF.__doc__
-gto.Mole.HF = property(HF)
 
 def RHF(mol, *args):
     if mol.spin == 0:
@@ -141,7 +140,6 @@ def RHF(mol, *args):
     else:
         return ROHF(mol, *args)
 RHF.__doc__ = hf.RHF.__doc__
-gto.Mole.RHF = property(RHF)
 
 def ROHF(mol, *args):
     if mol.nelectron == 1:
@@ -154,7 +152,6 @@ def ROHF(mol, *args):
     else:
         return hf_symm.ROHF(mol, *args)
 ROHF.__doc__ = rohf.ROHF.__doc__
-gto.Mole.ROHF = property(ROHF)
 
 def UHF(mol, *args):
     if mol.nelectron == 1:
@@ -167,7 +164,6 @@ def UHF(mol, *args):
     else:
         return uhf_symm.UHF(mol, *args)
 UHF.__doc__ = uhf.UHF.__doc__
-gto.Mole.UHF = property(UHF)
 
 def GHF(mol, *args):
     if mol.nelectron == 1:
@@ -180,7 +176,6 @@ def GHF(mol, *args):
     else:
         return ghf_symm.GHF(mol, *args)
 GHF.__doc__ = ghf.GHF.__doc__
-gto.Mole.GHF = property(GHF)
 
 def DHF(mol, *args):
     if mol.nelectron == 1:
@@ -190,7 +185,6 @@ def DHF(mol, *args):
     else:
         return dhf.DHF(mol, *args)
 DHF.__doc__ = dhf.DHF.__doc__
-gto.Mole.DHF = property(DHF)
 
 
 def X2C(mol, *args):
@@ -201,7 +195,6 @@ def X2C(mol, *args):
     else:
         return x2c.UHF(mol, *args)
 X2C_HF = X2C
-gto.Mole.X2C = gto.Mole.X2C_HF = property(X2C)
 
 def sfx2c1e(mf):
     '''spin-free (the scalar part) X2C with 1-electron X-matrix'''

pyscf/scf/chkfile.py

@@ -17,6 +17,7 @@
 #
 
 import h5py
+from pyscf.lib import H5FileWrap
 from pyscf.lib.chkfile import load_chkfile_key, load
 from pyscf.lib.chkfile import dump_chkfile_key, dump, save
 from pyscf.lib.chkfile import load_mol, save_mol
@@ -28,7 +29,7 @@ def dump_scf(mol, chkfile, e_tot, mo_energy, mo_coeff, mo_occ,
              overwrite_mol=True):
     '''save temporary results'''
     if h5py.is_hdf5(chkfile) and not overwrite_mol:
-        with h5py.File(chkfile, 'a') as fh5:
+        with H5FileWrap(chkfile, 'a') as fh5:
             if 'mol' not in fh5:
                 fh5['mol'] = mol.dumps()
     else:

pyscf/scf/hf.py

@@ -1569,6 +1569,12 @@ class SCF(lib.StreamObject):
         self._opt = {None: None}
         self._eri = None # Note: self._eri requires large amount of memory
 
+    def __getattr__(self, key):
+        '''Accessing methods post-HF methods or mean-field properties'''
+        # Import all available modules, then retry accessing the attribute
+        from pyscf import __all__  # noqa
+        return object.__getattribute__(self, key)
+
     def check_sanity(self):
         s1e = self.get_ovlp()
         cond = lib.cond(s1e)

pyscf/scf/ucphf.py

@@ -91,7 +91,7 @@ def solve_nos1(fvind, mo_energy, mo_occ, h1,
 
 # h1 shape is (:,nvir+nocc,nocc)
 def solve_withs1(fvind, mo_energy, mo_occ, h1, s1,
-                 max_cycle=20, tol=1e-9, hermi=False, verbose=logger.WARN,
+                 max_cycle=50, tol=1e-9, hermi=False, verbose=logger.WARN,
                  level_shift=0):
     '''For field dependent basis. First order overlap matrix is non-zero.
     The first order orbitals are set to

pyscf/solvent/__init__.py

@@ -12,7 +12,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from pyscf.solvent import ddcosmo, pcm
+from pyscf.solvent import ddcosmo
 
 def ddCOSMO(method_or_mol, solvent_obj=None, dm=None):
     '''Initialize ddCOSMO model.

{pyscf-2.6.0.dist-info → pyscf-2.6.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pyscf
-Version: 2.6.0
+Version: 2.6.1
 Summary: PySCF: Python-based Simulations of Chemistry Framework
 Author-email: Qiming Sun <osirpt.sun@gmail.com>
 Maintainer-email: Qiming Sun <osirpt.sun@gmail.com>
@@ -76,9 +76,9 @@ Python-based Simulations of Chemistry Framework
 [![Build Status](https://github.com/pyscf/pyscf/workflows/CI/badge.svg)](https://github.com/pyscf/pyscf/actions?query=workflow%3ACI)
 [![codecov](https://codecov.io/gh/pyscf/pyscf/branch/master/graph/badge.svg)](https://codecov.io/gh/pyscf/pyscf)
 
-2024-06-01
+2024-06-17
 
-* [Stable release 2.6.0](https://github.com/pyscf/pyscf/releases/tag/v2.6.0)
+* [Stable release 2.6.1](https://github.com/pyscf/pyscf/releases/tag/v2.6.1)
 * [Changelog](../master/CHANGELOG)
 * [Documentation](http://www.pyscf.org)
 * [Installation](#installation)