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

pyscf/__init__.py

@@ -35,7 +35,7 @@ to try out the package::
 
 '''
 
-__version__ = '2.6.0'
+__version__ = '2.6.1'
 
 import os
 import sys

pyscf/adc/__init__.py

@@ -70,8 +70,6 @@ def UADC(mf, frozen=None, mo_coeff=None, mo_occ=None):
 UADC.__doc__ = uadc.UADC.__doc__
 
 def RADC(mf, frozen=None, mo_coeff=None, mo_occ=None):
-    __doc__ = radc.RADC.__doc__
-
     if not (frozen is None or frozen == 0):
         raise NotImplementedError
 

pyscf/ao2mo/nrr_outcore.py

@@ -95,11 +95,11 @@ def general(mol, mo_coeffs, erifile, dataname='eri_mo',
 
     if isinstance(erifile, str):
         if h5py.is_hdf5(erifile):
-            feri = h5py.File(erifile, 'a')
+            feri = lib.H5FileWrap(erifile, 'a')
             if dataname in feri:
                 del(feri[dataname])
         else:
-            feri = h5py.File(erifile, 'w')
+            feri = lib.H5FileWrap(erifile, 'w')
     else:
         assert(isinstance(erifile, h5py.Group))
         feri = erifile
@@ -250,7 +250,7 @@ def half_e1(mol, mo_coeffs, swapfile,
     log.debug('step1: (ij,kl) = (%d,%d), mem cache %.8g MB, iobuf %.8g MB',
               nij_pair, nao_pair, mem_words*16/1e6, iobuf_words*16/1e6)
 
-    fswap = h5py.File(swapfile, 'w')
+    fswap = lib.H5FileWrap(swapfile, 'w')
     for icomp in range(comp):
         fswap.create_group(str(icomp))  # for h5py old version
 

pyscf/ao2mo/outcore.py

@@ -238,11 +238,11 @@ def general(mol, mo_coeffs, erifile, dataname='eri_mo',
 
     if isinstance(erifile, str):
         if h5py.is_hdf5(erifile):
-            feri = h5py.File(erifile, 'a')
+            feri = lib.H5FileWrap(erifile, 'a')
             if dataname in feri:
                 del (feri[dataname])
         else:
-            feri = h5py.File(erifile, 'w')
+            feri = lib.H5FileWrap(erifile, 'w')
     else:
         assert (isinstance(erifile, h5py.Group))
         feri = erifile
@@ -431,7 +431,7 @@ def half_e1(mol, mo_coeffs, swapfile,
     if isinstance(swapfile, h5py.Group):
         fswap = swapfile
     else:
-        fswap = lib.H5TmpFile(swapfile)
+        fswap = lib.H5FileWrap(swapfile, 'a')
     for icomp in range(comp):
         fswap.create_group(str(icomp)) # for h5py old version
 

pyscf/ao2mo/r_outcore.py

@@ -74,11 +74,11 @@ def general(mol, mo_coeffs, erifile, dataname='eri_mo',
 
     if isinstance(erifile, str):
         if h5py.is_hdf5(erifile):
-            feri = h5py.File(erifile, 'a')
+            feri = lib.H5FileWrap(erifile, 'a')
             if dataname in feri:
                 del (feri[dataname])
         else:
-            feri = h5py.File(erifile, 'w')
+            feri = lib.H5FileWrap(erifile, 'w')
     else:
         assert (isinstance(erifile, h5py.Group))
         feri = erifile
@@ -214,7 +214,7 @@ def half_e1(mol, mo_coeffs, swapfile,
     log.debug('step1: (ij,kl) = (%d,%d), mem cache %.8g MB, iobuf %.8g MB',
               nij_pair, nao_pair, mem_words*16/1e6, iobuf_words*16/1e6)
 
-    fswap = h5py.File(swapfile, 'w')
+    fswap = lib.H5FileWrap(swapfile, 'w')
     for icomp in range(comp):
         fswap.create_group(str(icomp))  # for h5py old version
 

pyscf/ao2mo/semi_incore.py

@@ -140,11 +140,11 @@ def general(eri, mo_coeffs, erifile, dataname='eri_mo',
 
     if isinstance(erifile, str):
         if h5py.is_hdf5(erifile):
-            feri = h5py.File(erifile, 'a')
+            feri = lib.H5FileWrap(erifile, 'a')
             if dataname in feri:
                 del (feri[dataname])
         else:
-            feri = h5py.File(erifile,'w',libver='latest')
+            feri = lib.H5FileWrap(erifile,'w', libver='latest')
     else:
         assert (isinstance(erifile, h5py.Group))
         feri = erifile

pyscf/df/df_jk.py

@@ -200,6 +200,8 @@ class _DFHF:
                 return uks.Hessian(self)
             else:
                 return uhf.Hessian(self)
+        elif isinstance(self, scf.rohf.ROHF):
+            raise NotImplementedError
         elif isinstance(self, scf.rhf.RHF):
             if isinstance(self, scf.hf.KohnShamDFT):
                 return rks.Hessian(self)

pyscf/df/incore.py

@@ -28,7 +28,9 @@ from pyscf import __config__
 
 
 MAX_MEMORY = getattr(__config__, 'df_outcore_max_memory', 2000)  # 2GB
-LINEAR_DEP_THR = getattr(__config__, 'df_df_DF_lindep', 1e-9)
+# LINEAR_DEP_THR cannot be below 1e-7,
+# see qchem default setting in https://manual.q-chem.com/5.4/sec_Basis_Customization.html
+LINEAR_DEP_THR = getattr(__config__, 'df_df_DF_lindep', 1e-7)
 
 
 # This function is aliased for backward compatibility.

pyscf/df/outcore.py

@@ -27,12 +27,11 @@ from pyscf.lib import logger
 from pyscf import ao2mo
 from pyscf.ao2mo import _ao2mo
 from pyscf.ao2mo.outcore import _load_from_h5g
-from pyscf.df.incore import _eig_decompose
+from pyscf.df.incore import _eig_decompose, LINEAR_DEP_THR
 from pyscf.df.addons import make_auxmol
 from pyscf import __config__
 
 MAX_MEMORY = getattr(__config__, 'df_outcore_max_memory', 2000)  # 2GB
-LINEAR_DEP_THR = getattr(__config__, 'df_df_DF_lindep', 1e-12)
 
 #
 # for auxe1 (P|ij)
@@ -303,11 +302,11 @@ def _create_h5file(erifile, dataname):
         erifile = erifile.name
 
     if h5py.is_hdf5(erifile):
-        feri = h5py.File(erifile, 'a')
+        feri = lib.H5FileWrap(erifile, 'a')
         if dataname in feri:
             del (feri[dataname])
     else:
-        feri = h5py.File(erifile, 'w')
+        feri = lib.H5FileWrap(erifile, 'w')
     return feri
 
 del (MAX_MEMORY)

pyscf/dft/__init__.py

@@ -66,7 +66,6 @@ def KS(mol, xc='LDA,VWN'):
 KS.__doc__ = '''
 A wrap function to create DFT object (RKS or UKS).\n
 ''' + rks.RKS.__doc__
-gto.Mole.KS = gto.Mole.DFT = property(KS)
 DFT = KS
 
 def RKS(mol, xc='LDA,VWN'):
@@ -78,7 +77,6 @@ def RKS(mol, xc='LDA,VWN'):
     else:
         return ROKS(mol, xc)
 RKS.__doc__ = rks.RKS.__doc__
-gto.Mole.RKS = property(RKS)
 
 def ROKS(mol, xc='LDA,VWN'):
     if not mol.symmetry or mol.groupname == 'C1':
@@ -86,7 +84,6 @@ def ROKS(mol, xc='LDA,VWN'):
     else:
         return rks_symm.ROKS(mol, xc)
 ROKS.__doc__ = roks.ROKS.__doc__
-gto.Mole.ROKS = property(ROKS)
 
 def UKS(mol, xc='LDA,VWN'):
     if not mol.symmetry or mol.groupname == 'C1':
@@ -94,7 +91,6 @@ def UKS(mol, xc='LDA,VWN'):
     else:
         return uks_symm.UKS(mol, xc)
 UKS.__doc__ = uks.UKS.__doc__
-gto.Mole.UKS = property(UKS)
 
 def GKS(mol, xc='LDA,VWN'):
     if not mol.symmetry or mol.groupname == 'C1':
@@ -102,7 +98,6 @@ def GKS(mol, xc='LDA,VWN'):
     else:
         return gks_symm.GKS(mol, xc)
 GKS.__doc__ = gks.GKS.__doc__
-gto.Mole.GKS = property(GKS)
 
 def DKS(mol, xc='LDA,VWN'):
     from pyscf.scf import dhf
@@ -110,12 +105,8 @@ def DKS(mol, xc='LDA,VWN'):
         return dks.RDKS(mol, xc=xc)
     else:
         return dks.UDKS(mol, xc=xc)
-
 UDKS = dks.UDKS
 RDKS = dks.RDKS
-gto.Mole.DKS = property(DKS)
-gto.Mole.UDKS = property(UDKS)
-gto.Mole.RDKS = property(RDKS)
 
 def X2C(mol, *args):
     '''X2C Kohn-Sham'''
@@ -126,4 +117,3 @@ def X2C(mol, *args):
     else:
         return dft.UKS(mol, *args)
 X2C_KS = X2C
-gto.Mole.X2C_KS = property(X2C)

pyscf/geomopt/__init__.py

@@ -22,6 +22,6 @@ def optimize(method, *args, **kwargs):
     except ImportError as e1:
         try:
             from . import berny_solver as geom
-        except ImportError as e2:
+        except ImportError:
             raise e1
     return geom.optimize(method, *args, **kwargs)

pyscf/grad/rhf.py

@@ -474,3 +474,4 @@ Grad = Gradients
 from pyscf import scf
 # Inject to RHF class
 scf.hf.RHF.Gradients = lib.class_as_method(Gradients)
+scf.rohf.ROHF.Gradients = lib.invalid_method('Gradients')

pyscf/grad/rks.py

@@ -622,3 +622,4 @@ Grad = Gradients
 
 from pyscf import dft
 dft.rks.RKS.Gradients = dft.rks_symm.RKS.Gradients = lib.class_as_method(Gradients)
+dft.roks.ROKS.Gradients = lib.invalid_method('Gradients')

pyscf/gto/__init__.py

@@ -24,5 +24,4 @@ from pyscf.gto.moleintor import getints, getints_by_shell
 from pyscf.gto.eval_gto import eval_gto
 from pyscf.gto import ecp
 
-parse = basis.parse
 #import pyscf.gto.mole.cmd_args

pyscf/gto/basis/__init__.py

@@ -531,7 +531,6 @@ def _convert_contraction(contr_string):
 def _truncate(basis, contr_scheme, symb, split_name):
     # keep only first n_keep contractions for each l
     contr_b = []
-    b_index = 0
     for l, n_keep in enumerate(contr_scheme):
         n_saved = 0
         if n_keep > 0:

pyscf/gto/eval_gto.py

@@ -82,8 +82,14 @@ def eval_gto(mol, eval_name, coords, comp=None, shls_slice=None, non0tab=None,
             If provided, results are written into this array.
 
     Returns:
-        2D array of shape (N,nao) Or 3D array of shape (\*,N,nao) to store AO
-        values on grids.
+        An 2D to 4D array for AO values on grids.
+        If eval_name is scalar functions, such as GTOval and GTOval_ip_cart,
+        the shape of the return is (N,nao) for GTOval, and (*,N,nao) for other
+        functions.
+        If eval_name is spinor functions, such as GTOval_spinor and GTOval_sp_spinor,
+        the shape of the return is (2,N,nao) for GTOval_spinor, and (2,*,N,nao)
+        for other functions. The leading dimension 2 represents the spin-up and
+        spin-down components of the spinor basis.
 
     Examples:
 
@@ -95,6 +101,9 @@ def eval_gto(mol, eval_name, coords, comp=None, shls_slice=None, non0tab=None,
     >>> ao_value = mol.eval_gto("GTOval_ig_sph", coords)
     >>> print(ao_value.shape)
     (3, 100, 24)
+    >>> ao_a, ao_b = mol.eval_gto("GTOval_spinor", coords)
+    >>> print(ao_a.shape)
+    (100, 24)
     '''
     eval_name, comp = _get_intor_and_comp(mol, eval_name, comp)
 

pyscf/gto/mole.py

@@ -3189,7 +3189,7 @@ class MoleBase(lib.StreamObject):
             return self._env[ptr:ptr+3].copy()
 
     def atom_coords(self, unit='Bohr'):
-        '''np.asarray([mol.atom_coords(i) for i in range(mol.natm)])'''
+        '''np.asarray([mol.atom_coord(i) for i in range(mol.natm)])'''
         ptr = self._atm[:,PTR_COORD]
         c = self._env[numpy.vstack((ptr,ptr+1,ptr+2)).T].copy()
         if not is_au(unit):
@@ -3840,7 +3840,7 @@ def _parse_nuc_mod(str_or_int_or_fn):
 def _update_from_cmdargs_(mol):
     try:
         # Detect whether in Ipython shell
-        __IPYTHON__  # noqa:
+        __IPYTHON__  # noqa: F821
         return
     except Exception:
         pass

pyscf/hessian/dispersion.py

@@ -46,7 +46,7 @@ def get_dispersion(hessobj, disp=None, with_3body=None):
     if with_3body is not None:
         with_3body = disp_with_3body
 
-    if mf.disp[:2].upper() == 'D3':
+    if disp_version[:2].upper() == 'D3':
         logger.info(mf, "Calc dispersion correction with DFTD3.")
         logger.info(mf, f"Parameters: xc={method}, version={disp_version}, atm={with_3body}")
         logger.warn(mf, "DFTD3 does not support analytical Hessian, using finite difference")
@@ -57,21 +57,21 @@ def get_dispersion(hessobj, disp=None, with_3body=None):
             for j in range(3):
                 coords[i,j] += eps
                 mol.set_geom_(coords, unit='Bohr')
-                d3_model = dftd3.DFTD3Dispersion(mol, xc=method, version=mf.disp, atm=with_3body)
+                d3_model = dftd3.DFTD3Dispersion(mol, xc=method, version=disp_version, atm=with_3body)
                 res = d3_model.get_dispersion(grad=True)
                 g1 = res.get('gradient')
 
                 coords[i,j] -= 2.0*eps
                 mol.set_geom_(coords, unit='Bohr')
-                d3_model = dftd3.DFTD3Dispersion(mol, xc=method, version=mf.disp, atm=with_3body)
+                d3_model = dftd3.DFTD3Dispersion(mol, xc=method, version=disp_version, atm=with_3body)
                 res = d3_model.get_dispersion(grad=True)
                 g2 = res.get('gradient')
 
                 coords[i,j] += eps
                 h_disp[i,:,j,:] = (g1 - g2)/(2.0*eps)
-            return h_disp
+        return h_disp
 
-    elif mf.disp[:2].upper() == 'D4':
+    elif disp_version[:2].upper() == 'D4':
         logger.info(mf, "Calc dispersion correction with DFTD4.")
         logger.info(mf, f"Parameters: xc={method}, atm={with_3body}")
         logger.warn(mf, "DFTD4 does not support analytical Hessian, using finite difference.")

pyscf/hessian/rhf.py

@@ -618,6 +618,7 @@ class Hessian(HessianBase):
 # Inject to RHF class
 from pyscf import scf
 scf.hf.RHF.Hessian = lib.class_as_method(Hessian)
+scf.rohf.ROHF.Hessian = lib.invalid_method('Hessian')
 
 
 if __name__ == '__main__':

pyscf/hessian/rks.py

@@ -593,3 +593,4 @@ class Hessian(rhf_hess.HessianBase):
 
 from pyscf import dft
 dft.rks.RKS.Hessian = dft.rks_symm.RKS.Hessian = lib.class_as_method(Hessian)
+dft.roks.ROKS.Hessian = dft.rks_symm.ROKS.Hessian = lib.invalid_method('Hessian')

pyscf/lib/chkfile.py

@@ -105,6 +105,7 @@ def dump(chkfile, key, value):
     >>> f['symm/Ci/op']
     <HDF5 dataset "op": shape (2,), type "|S1">
     '''
+    from pyscf.lib import H5FileWrap
     def save_as_group(key, value, root):
         if isinstance(value, dict):
             root1 = root.create_group(key)
@@ -126,14 +127,14 @@ def dump(chkfile, key, value):
                     save_as_group('%06d'%k, v, root1)
 
     if h5py.is_hdf5(chkfile):
-        with h5py.File(chkfile, 'r+') as fh5:
+        with H5FileWrap(chkfile, 'r+') as fh5:
             if key in fh5:
                 del (fh5[key])
             elif key + '__from_list__' in fh5:
                 del (fh5[key+'__from_list__'])
             save_as_group(key, value, fh5)
     else:
-        with h5py.File(chkfile, 'w') as fh5:
+        with H5FileWrap(chkfile, 'w') as fh5:
             save_as_group(key, value, fh5)
 dump_chkfile_key = save = dump
 

pyscf/lib/linalg_helper.py

@@ -33,7 +33,7 @@ from pyscf import __config__
 
 SAFE_EIGH_LINDEP = getattr(__config__, 'lib_linalg_helper_safe_eigh_lindep', 1e-15)
 DAVIDSON_LINDEP = getattr(__config__, 'lib_linalg_helper_davidson_lindep', 1e-14)
-DSOLVE_LINDEP = getattr(__config__, 'lib_linalg_helper_dsolve_lindep', 1e-15)
+DSOLVE_LINDEP = getattr(__config__, 'lib_linalg_helper_dsolve_lindep', 1e-13)
 MAX_MEMORY = getattr(__config__, 'lib_linalg_helper_davidson_max_memory', 2000)  # 2GB
 
 # sort by similarity has problem which flips the ordering of eigenvalues when

pyscf/lib/misc.py

@@ -23,6 +23,7 @@ Some helper functions
 import os
 import sys
 import time
+import random
 import platform
 import warnings
 import tempfile
@@ -1111,8 +1112,52 @@ class call_in_background:
         if self.executor is not None:
             self.executor.shutdown(wait=True)
 
+class H5FileWrap(h5py.File):
+    '''
+    A wrapper for h5py.File that allows global options to be set by
+    the user via lib.param.H5F_WRITE_KWARGS, which is imported
+    upon startup from the user's configuration file.
+
+    These options are, as the name suggests, not used when the
+    HDF5 file is opened in read-only mode.
+
+    Example:
+
+    >>> with temporary_env(lib.param, H5F_WRITE_KWARGS={'driver': 'core'}):
+    ...     with lib.H5TmpFile() as f:
+    ...         print(f.driver)
+    core
+    '''
+    def __init__(self, filename, mode, *args, **kwargs):
+        if mode != 'r':
+            options = param.H5F_WRITE_KWARGS.copy()
+            options.update(kwargs)
+        else:
+            options = kwargs
+        super().__init__(filename, mode, *args, **options)
+
+    def _finished(self):
+        '''
+        Close the file and flush it if it is open.
+        Flushing explicitly should not be necessary:
+        this is intended to avoid a bug that unpredictably
+        causes outcore DF to hang on an NFS filesystem.
+        '''
+        try:
+            if super().id:
+                super().flush()
+            super().close()
+        except AttributeError:  # close not defined in old h5py
+            pass
+        except ValueError:  # if close() is called twice
+            pass
+        except ImportError:  # exit program before de-referring the object
+            pass
+
+    def __del__(self):
+        self._finished()
 
-class H5TmpFile(h5py.File):
+class H5TmpFile(H5FileWrap):
     '''Create and return an HDF5 temporary file.
 
     Kwargs:
@@ -1130,22 +1175,40 @@ class H5TmpFile(h5py.File):
     >>> from pyscf import lib
     >>> ftmp = lib.H5TmpFile()
     '''
-    def __init__(self, filename=None, mode='a', *args, **kwargs):
+    def __init__(self, filename=None, mode='a', prefix='', suffix='',
+                 dir=param.TMPDIR, *args, **kwargs):
+        self.delete_on_close = False
         if filename is None:
-            with tempfile.NamedTemporaryFile(dir=param.TMPDIR) as tmpf:
-                h5py.File.__init__(self, tmpf.name, mode, *args, **kwargs)
-        else:
-            h5py.File.__init__(self, filename, mode, *args, **kwargs)
+            filename = H5TmpFile._gen_unique_name(dir, pre=prefix, suf=suffix)
+            self.delete_on_close = True
+        super().__init__(filename, mode, *args, **kwargs)
+
+    # Python 3 stdlib does not have a way to just generate
+    # temporary file names.
+    @staticmethod
+    def _gen_unique_name(directory, pre='', suf=''):
+        absdir = os.path.abspath(directory)
+        random.seed()
+        for seq in range(10000):
+            name = ''.join(random.choices('abcdefghijklmnopqrstuvwxyz0123456789', k=8))
+            filename = os.path.join(absdir, pre + name + suf)
+            try:
+                f = open(filename, 'x')
+            except FileExistsError:
+                continue    # try again
+            f.close()
+            return filename
+        raise FileExistsError("No usable temporary file name found")
+
+    def close(self):
+        filename = self.filename
+        self._finished()
+        if self.delete_on_close:
+            if os.path.exists(filename):
+                os.remove(filename)
+    def __exit__(self, type, value, traceback):
+        self.close()
 
-    def __del__(self):
-        try:
-            self.close()
-        except AttributeError:  # close not defined in old h5py
-            pass
-        except ValueError:  # if close() is called twice
-            pass
-        except ImportError:  # exit program before de-referring the object
-            pass
 
 def fingerprint(a):
     '''Fingerprint of numpy array'''
@@ -1249,6 +1312,20 @@ class light_speed(temporary_env):
         temporary_env.__enter__(self)
         return self.c
 
+class h5filewrite_options(temporary_env):
+    '''Within the context of this macro, extra keyword arguments are
+    passed to h5py.File() whenever an HDF5 file is opened for writing.
+
+    Examples:
+
+    >>> with h5filewrite_options(alignment_interval=4096, alignment_threshold=4096):
+    ...     f = lib.H5FileWrap('mydata.h5', 'w')
+    >>> print(h5py.h5p.PropFAID.get_alignment(f.id.get_access_plist()))
+    (4096, 4096)
+    '''
+    def __init__(self, **kwargs):
+        super().__init__(param, H5F_WRITE_KWARGS=kwargs)
+
 def repo_info(repo_path):
     '''
     Repo location, version, git branch and commit ID

pyscf/lib/parameters.py

@@ -53,6 +53,7 @@ OUTPUT_DIGITS = getattr(__config__, 'OUTPUT_DIGITS', 5)
 OUTPUT_COLS   = getattr(__config__, 'OUTPUT_COLS', 5)
 LOOSE_ZERO_TOL = getattr(__config__, 'LOOSE_ZERO_TOL', 1e-9)
 LARGE_DENOM = getattr(__config__, 'LARGE_DENOM', 1e14)
+H5F_WRITE_KWARGS = getattr(__config__, 'H5F_WRITE_KWARGS', {})
 
 L_MAX = 8
 ANGULAR = 'spdfghik'

pyscf/mcscf/chkfile.py

@@ -20,6 +20,7 @@
 #
 
 import h5py
+from pyscf.lib import H5FileWrap
 from pyscf.lib.chkfile import load
 from pyscf.lib.chkfile import dump, save
 from pyscf.lib.chkfile import load_mol, save_mol
@@ -45,11 +46,11 @@ def dump_mcscf(mc, chkfile=None, key='mcscf',
     #if ci_vector is None: ci_vector = mc.ci
 
     if h5py.is_hdf5(chkfile):
-        fh5 = h5py.File(chkfile, 'a')
+        fh5 = H5FileWrap(chkfile, 'a')
         if key in fh5:
             del (fh5[key])
     else:
-        fh5 = h5py.File(chkfile, 'w')
+        fh5 = H5FileWrap(chkfile, 'w')
 
     if 'mol' not in fh5:
         fh5['mol'] = mc.mol.dumps()

pyscf/mp/ump2.py

@@ -303,7 +303,7 @@ def make_fno(mp, thresh=1e-6, pct_occ=None, nvir_act=None, t2=None, eris=None):
     masks = _mo_splitter(mp)
 
     if nvir_act is not None:
-        if isinstance(nvir_act, (int,numpy.int)):
+        if isinstance(nvir_act, (int, numpy.integer)):
             nvir_act = [nvir_act]*2
 
     no_frozen = []

pyscf/mrpt/nevpt2.py

@@ -990,7 +990,7 @@ def trans_e1_outcore(mc, mo, max_memory=None, ioblk_size=256, tmpdir=None,
     time1 = [logger.process_clock(), logger.perf_counter()]
     ao_loc = numpy.array(mol.ao_loc_nr(), dtype=numpy.int32)
     cvcvfile = tempfile.NamedTemporaryFile(dir=tmpdir)
-    with h5py.File(cvcvfile.name, 'w') as f5:
+    with lib.H5TmpFile(cvcvfile.name, 'w') as f5:
         cvcv = f5.create_dataset('eri_mo', (ncore*nvir,ncore*nvir), 'f8')
         ppaa, papa, pacv = _trans(mo, ncore, ncas, load_buf, cvcv, ao_loc)[:3]
     time0 = logger.timer(mol, 'trans_cvcv', *time0)

pyscf/pbc/adc/__init__.py

@@ -19,7 +19,6 @@ from pyscf.pbc.adc import kadc_rhf_ip
 from pyscf.pbc.adc import kadc_rhf_ea
 
 def KRADC(mf, frozen=None, mo_coeff=None, mo_occ=None):
-    from pyscf.pbc.adc import kadc_rhf
     if not isinstance(mf, scf.khf.KRHF):
         mf = mf.to_rhf()
     return kadc_rhf.RADC(mf, frozen, mo_coeff, mo_occ)

pyscf/pbc/cc/kccsd_t_rhf.py

@@ -357,7 +357,7 @@ def check_read_success(filename, **kwargs):
         mode = kwargs.get('mode', 'r')
         if not os.path.isfile(filename):
             return False
-        f = h5py.File(filename, mode=mode, **kwargs)
+        f = lib.H5FileWrap(filename, mode=mode, **kwargs)
         return f.attrs.get('completed', False)
     write_complete = check_write_complete(filename, **kwargs)
     return False and write_complete

pyscf/pbc/df/outcore.py

@@ -48,9 +48,9 @@ def aux_e1(cell, auxcell_or_auxbasis, erifile, intor='int3c2e', aosym='s2ij', co
     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:
@@ -169,9 +169,9 @@ def _aux_e2(cell, auxcell_or_auxbasis, erifile, intor='int3c2e', aosym='s2ij', c
     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: