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

pyscf/__init__.py

@@ -35,7 +35,7 @@ to try out the package::
 
 '''
 
-__version__ = '2.6.0'
+__version__ = '2.6.2'
 
 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/cc/ccsd_lambda.py

@@ -364,7 +364,7 @@ def update_lambda(mycc, t1, t2, l1, l2, eris=None, imds=None):
     return l1new, l2new
 
 def _cp(a):
-    return numpy.array(a, copy=False, order='C')
+    return numpy.asarray(a, order='C')
 
 
 if __name__ == '__main__':

pyscf/cc/dfccsd.py

@@ -191,7 +191,7 @@ def _make_df_eris(cc, mo_coeff=None):
     return eris
 
 def _cp(a):
-    return numpy.array(a, copy=False, order='C')
+    return numpy.asarray(a, order='C')
 
 if __name__ == '__main__':
     from pyscf import gto

pyscf/cc/rccsd_lambda.py

@@ -69,7 +69,7 @@ def make_intermediates(mycc, t1, t2, eris):
     oooo = np.asarray(eris.oooo)
     woooo  = lib.einsum('icjl,kc->ikjl', ovoo, t1)
     woooo += lib.einsum('jcil,kc->iljk', ovoo, t1)
-    woooo += oooo.copy()
+    woooo += oooo
     woooo += lib.einsum('icjd,klcd->ikjl', ovov, tau)
 
     theta = t2*2 - t2.transpose(0,1,3,2)

pyscf/cc/rccsd_slow.py

@@ -1047,7 +1047,7 @@ class _IMDS:
         raise NotImplementedError
 
 def _cp(a):
-    return np.array(a, copy=False, order='C')
+    return np.asarray(a, order='C')
 
 
 if __name__ == '__main__':

pyscf/ci/cisd.py

@@ -1141,7 +1141,7 @@ scf.hf.RHF.CISD = lib.class_as_method(RCISD)
 scf.rohf.ROHF.CISD = None
 
 def _cp(a):
-    return numpy.array(a, copy=False, order='C')
+    return numpy.asarray(a, order='C')
 
 
 if __name__ == '__main__':

pyscf/ci/ucisd.py

@@ -976,4 +976,4 @@ from pyscf import scf
 scf.uhf.UHF.CISD = lib.class_as_method(CISD)
 
 def _cp(a):
-    return numpy.array(a, copy=False, order='C')
+    return numpy.asarray(a, order='C')

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/dft/gen_grid.py

@@ -366,7 +366,7 @@ def arg_group_grids(mol, coords, box_size=GROUP_BOX_SIZE):
     box_ids[box_ids[:,2] > boxes[2], 2] = boxes[2]
     rev_idx, counts = numpy.unique(box_ids, axis=0, return_inverse=True,
                                    return_counts=True)[1:3]
-    return rev_idx.argsort(kind='stable')
+    return rev_idx.ravel().argsort(kind='stable')
 
 def _load_conf(mod, name, default):
     var = getattr(__config__, name, None)

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/ccsd.py

@@ -416,7 +416,7 @@ def _load_block_tril(h5dat, row0, row1, nao, out=None):
     return out
 
 def _cp(a):
-    return numpy.array(a, copy=False, order='C')
+    return numpy.asarray(a, order='C')
 
 class Gradients(rhf_grad.GradientsBase):
 

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/grad/uccsd.py

@@ -485,7 +485,7 @@ def _rdm2_mo2ao(mycc, d2, mo_coeff, fsave=None):
         return fsave
 
 def _cp(a):
-    return numpy.array(a, copy=False, order='C')
+    return numpy.asarray(a, order='C')
 
 class Gradients(ccsd_grad.Gradients):
     grad_elec = grad_elec

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/diis.py

@@ -217,7 +217,7 @@ class DIIS:
         if nd < self.min_space:
             return x
 
-        dt = numpy.array(self.get_err_vec(self._head-1), copy=False)
+        dt = numpy.asarray(self.get_err_vec(self._head-1))
         if self._H is None:
             self._H = numpy.zeros((self.space+1,self.space+1), dt.dtype)
             self._H[0,1:] = self._H[1:,0] = 1

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
@@ -1477,15 +1477,12 @@ def _qr(xs, dot, lindep=1e-14):
     xs = (r.T).dot(qs)
     '''
     nvec = len(xs)
-    dtype = xs[0].dtype
-    qs = numpy.empty((nvec,xs[0].size), dtype=dtype)
-    rmat = numpy.empty((nvec,nvec), order='F', dtype=dtype)
+    xs = qs = numpy.array(xs, copy=True)
+    rmat = numpy.eye(nvec, order='F', dtype=xs.dtype)
 
     nv = 0
     for i in range(nvec):
-        xi = numpy.array(xs[i], copy=True)
-        rmat[:,nv] = 0
-        rmat[nv,nv] = 1
+        xi = xs[i]
         for j in range(nv):
             prod = dot(qs[j].conj(), xi)
             xi -= qs[j] * prod