pyscf 2.6.0__py3-none-macosx_11_0_arm64.whl → 2.6.2__py3-none-macosx_11_0_arm64.whl

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/numpy_helper.py

@@ -1144,7 +1144,7 @@ class NPArrayWithTag(numpy.ndarray):
 
     # Whenever the contents of the array were modified (through ufunc), the tag
     # should be expired. Overwrite the output of ufunc to restore ndarray type.
-    def __array_wrap__(self, out, context=None):
+    def __array_wrap__(self, out, context=None, return_scalar=False):
         if out.ndim == 0:  # if ufunc returns a scalar
             return out[()]
         else:

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/dfmp2.py

@@ -62,7 +62,7 @@ def kernel(mp, mo_energy=None, mo_coeff=None, eris=None, with_t2=WITH_T2,
     for i in range(nocc):
         buf = numpy.dot(Lov[:,i*nvir:(i+1)*nvir].T,
                         Lov).reshape(nvir,nocc,nvir)
-        gi = numpy.array(buf, copy=False)
+        gi = numpy.asarray(buf)
         gi = gi.reshape(nvir,nocc,nvir).transpose(1,0,2)
         t2i = gi/lib.direct_sum('jb+a->jba', eia, eia[i])
         edi = numpy.einsum('jab,jab', t2i, gi) * 2

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/eom_kccsd_uhf.py

@@ -1238,7 +1238,7 @@ if __name__ == '__main__':
     r1, r2 = eom_kgccsd.spin2spatial_ip_doublet(spin_r1_ip, spin_r2_ip, kconserv, kshift, orbspin)
     vector = myeom.amplitudes_to_vector(r1, r2, kshift)
     vector = myeom.matvec(vector, kshift=kshift, imds=imds)
-    Hr1, Hr2 = myeom.vector_to_amplitudes(vector, nkpts, (nmoa, nmob), (nocca, noccb))
+    Hr1, Hr2 = myeom.vector_to_amplitudes(vector, 0, nkpts, (nmoa, nmob), (nocca, noccb))
     Hr1a, Hr1b = Hr1
     Hr2aaa, Hr2baa, Hr2abb, Hr2bbb = Hr2
     print('ip Hr1a',   abs(lib.fp(Hr1a)   - (-0.34462696543560045-1.6104596956729178j)))
@@ -1263,7 +1263,7 @@ if __name__ == '__main__':
 
     vector = myeom.amplitudes_to_vector(r1, r2, kshift)
     vector = myeom.matvec(vector, kshift=kshift, imds=imds)
-    Hr1, Hr2 = myeom.vector_to_amplitudes(vector, nkpts, (nmoa, nmob), (nocca, noccb))
+    Hr1, Hr2 = myeom.vector_to_amplitudes(vector, 0, nkpts, (nmoa, nmob), (nocca, noccb))
     Hr1a, Hr1b = Hr1
     Hr2aaa, Hr2aba, Hr2bab, Hr2bbb = Hr2
 

pyscf/pbc/cc/kccsd_rhf_ksymm.py

@@ -326,6 +326,7 @@ def add_vvvv_(cc, Ht2, t1, t2, eris):
         get_Wvvvv = lambda ka, kb, kc: _Wvvvv[ka, kb, kc]
 
     kakb, igroup = np.unique(kqrts.kqrts_ibz[:,2:], axis=0, return_inverse=True)
+    igroup = igroup.ravel()
     for i in range(np.amax(igroup) + 1):
         ka, kb = kakb[i]
         idx = np.where(igroup==i)[0]

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:

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/multigrid/multigrid.py

@@ -294,8 +294,8 @@ def eval_rho(cell, dm, shls_slice=None, hermi=0, xctype='LDA', kpts=None,
                 dm_i = dm_i.real
             has_imag = dm_i.dtype == numpy.complex128
             if has_imag:
-                dmR = numpy.array(dm_i.real, order='C')
-                dmI = numpy.array(dm_i.imag, order='C')
+                dmR = numpy.asarray(dm_i.real, order='C')
+                dmI = numpy.asarray(dm_i.imag, order='C')
             else:
                 # make a copy because the dm may be overwritten in the
                 # NUMINT_rho_drv inplace

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/mp/kmp2_ksymm.py

@@ -54,6 +54,7 @@ def kernel(mp, mo_energy, mo_coeff, verbose=logger.NOTE, with_t2=WITH_T2):
 
     kijab, weight, k4_bz2ibz = kd.make_k4_ibz(sym='s2')
     _, igroup = np.unique(kijab[:,:2], axis=0, return_index=True)
+    igroup = igroup.ravel()
     igroup = list(igroup) + [len(kijab)]
 
     emp2_ss = emp2_os = 0.

pyscf/pbc/mpicc/kccsd_rhf.py

@@ -3276,4 +3276,4 @@ class _IMDS:
         self.WvvvoR1  = self.fint2['WvvvoR1' ]
 
 def _cp(a):
-    return np.array(a, copy=False, order='C')
+    return np.array(a, order='C')

pyscf/pbc/mpicc/kintermediates_rhf.py

@@ -187,7 +187,7 @@ def cc_Woooo(cc,t1,t2,eris,feri2=None):
             for iterkl, kl in enumerate(ranges1):
                 for iterki, ki in enumerate(ranges2):
                     kj = kconserv[kk,ki,kl]
-                    oooo_tmp[iterkk,iterkl,iterki] = np.array(eris.oooo[kk,kl,ki],copy=True)
+                    oooo_tmp[iterkk,iterkl,iterki] = np.array(eris.oooo[kk,kl,ki], copy=True)
                     oooo_tmp[iterkk,iterkl,iterki] += einsum('klic,jc->klij',eris.ooov[kk,kl,ki],t1[kj])
                     oooo_tmp[iterkk,iterkl,iterki] += einsum('klcj,ic->klij',eris.ooov[kl,kk,kj].transpose(1,0,3,2),t1[ki])
 
@@ -233,7 +233,7 @@ def cc_Wvvvv(cc,t1,t2,eris,feri2=None):
             for kc in ranges1:
                 for kb in range(ka+1):
                     kd = kconserv[ka,kc,kb]
-                    vvvv_tmp = np.array(eris.vvvv[ka,kb,kc],copy=True)
+                    vvvv_tmp = np.array(eris.vvvv[ka,kb,kc], copy=True)
                     vvvv_tmp += einsum('akcd,kb->abcd',eris.ovvv[kb,ka,kd].transpose(1,0,3,2),-t1[kb])
                     vvvv_tmp += einsum('kbcd,ka->abcd',eris.ovvv[ka,kb,kc],-t1[ka])
                     Wvvvv[ka,kb,kc] = vvvv_tmp
@@ -336,7 +336,7 @@ def cc_Wvovo(cc,t1,t2,eris,feri2=None):
             for iterkk, kk in enumerate(ranges1):
                 for iterkc, kc in enumerate(ranges2):
                     ki = kconserv[ka,kc,kk]
-                    vovo_tmp[iterka,iterkk,iterkc] = np.array(eris.ovov[kk,ka,ki]).transpose(1,0,3,2)
+                    vovo_tmp[iterka,iterkk,iterkc] = np.asarray(eris.ovov[kk,ka,ki]).transpose(1,0,3,2)
                     vovo_tmp[iterka,iterkk,iterkc] -= einsum('lkci,la->akci',eris.ooov[kk,ka,ki].transpose(1,0,3,2),t1[ka])
                     vovo_tmp[iterka,iterkk,iterkc] += einsum('akcd,id->akci',eris.ovvv[kk,ka,ki].transpose(1,0,3,2),t1[ki])
                     # Beginning of change
@@ -391,7 +391,7 @@ def cc_Wovov(cc,t1,t2,eris,feri2=None):
             for iterka, ka in enumerate(ranges1):
                 for iterki, ki in enumerate(ranges2):
                     kc = kconserv[kk,ki,ka]
-                    ovov_tmp[iterkk,iterka,iterki] = np.array(eris.ovov[kk,ka,ki],copy=True)
+                    ovov_tmp[iterkk,iterka,iterki] = np.asarray(eris.ovov[kk,ka,ki])
                     ovov_tmp[iterkk,iterka,iterki] -= einsum('lkci,la->kaic',eris.ooov[kk,ka,ki].transpose(1,0,3,2),t1[ka])
                     ovov_tmp[iterkk,iterka,iterki] += einsum('akcd,id->kaic',eris.ovvv[kk,ka,ki].transpose(1,0,3,2),t1[ki])
                     # Beginning of change
@@ -1308,7 +1308,7 @@ def Wovoo(cc,t1,t2,eris,fint=None):
                 for iterki,ki in enumerate(ranges2):
                     kj = kconserv[kk,ki,kb]
 
-                    ovoo_tmp[iterkk,iterkb,iterki] = np.array(eris.ovoo[kk,kb,ki],copy=True)
+                    ovoo_tmp[iterkk,iterkb,iterki] = np.asarray(eris.ovoo[kk,kb,ki])
                     ovoo_tmp[iterkk,iterkb,iterki] += einsum('kbid,jd->kbij',WW1ovov_kbi[iterkk,iterkb,iterki], t1[kj])
                     ovoo_tmp[iterkk,iterkb,iterki] += einsum('klij,lb->kbij', WWoooo_kbi[iterkk,iterkb,iterki],-t1[kb])
                     #ovoo_tmp[iterkk,iterkb,iterki] += einsum('kbcj,ic->kbij',WW1ovvo_kbi[iterkk,iterkb,iterki],t1[ki])
@@ -1550,4 +1550,4 @@ def WvoovR1(cc,t1,t2,eris,fint=None):
     return Wkaci
 
 def _cp(a):
-    return np.array(a, copy=False, order='C')
+    return np.array(a, 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