Merge branch 'master' of https://github.com/pyscf/pyscf

pulling from master of pyscf

pyscf/cc/gccsd.py

@@ -362,6 +362,7 @@ def _make_eris_incore(mycc, mo_coeff=None, ao2mofn=None):
             mo = mo_a + mo_b
             eri = ao2mo.kernel(mycc._scf._eri, mo)
             if eri.size == nmo**4:  # if mycc._scf._eri is a complex array
+                eri = eri.reshape(nmo**2, nmo**2)
                 sym_forbid = (orbspin[:,None] != orbspin).ravel()
             else:  # 4-fold symmetry
                 sym_forbid = (orbspin[:,None] != orbspin)[np.tril_indices(nmo)]

pyscf/dft/rks.py

@@ -539,5 +539,4 @@ def to_gpu(self):
         obj = lib.to_gpu(hf.SCF.reset(self.view(RKS)))
         # Attributes only defined in gpu4pyscf.RKS
         obj.screen_tol = 1e-14
-        obj.disp = None
         return obj

pyscf/dft/uks.py

@@ -203,5 +203,4 @@ def to_gpu(self):
         obj = lib.to_gpu(SCF.reset(self.view(UKS)))
         # Attributes only defined in gpu4pyscf.RKS
         obj.screen_tol = 1e-14
-        obj.disp = None
         return obj

pyscf/grad/mp2.py

@@ -241,12 +241,16 @@ def converged(self):
 
 
 def _shell_prange(mol, start, stop, blksize):
+    l = mol._bas[start:stop,gto.ANG_OF]
+    if mol.cart:
+        dims = (l+1)*(l+2)//2 * mol._bas[start:stop,gto.NCTR_OF]
+    else:
+        dims = (l*2+1) * mol._bas[start:stop,gto.NCTR_OF]
     nao = 0
     ib0 = start
-    for ib in range(start, stop):
-        now = (mol.bas_angular(ib)*2+1) * mol.bas_nctr(ib)
+    for ib, now in zip(range(start, stop), dims):
         nao += now
-        if nao > blksize and nao > now:
+        if nao > blksize:
             yield (ib0, ib, nao-now)
             ib0 = ib
             nao = now

pyscf/grad/test/test_mp2.py

@@ -153,6 +153,14 @@ def test_symmetrize(self):
         g = mol.RHF.run().MP2().run().Gradients().kernel()
         self.assertAlmostEqual(lib.fp(g), 0.049987975650731625, 6)
 
+    # issue 1985
+    def test_cart_gto(self):
+        mol1 = mol.copy()
+        mol1.cart = True
+        mol1.basis = '6-31g*'
+        g = mol.RHF.run().MP2().run().Gradients().kernel()
+        self.assertAlmostEqual(lib.fp(g), -0.03568120792884476, 6)
+
 
 if __name__ == "__main__":
     print("Tests for MP2 gradients")

pyscf/gto/mole.py

@@ -419,7 +419,7 @@ def str2atm(line):
     return list(zip(z, c.tolist()))
 
 #TODO: sort exponents
-def format_basis(basis_tab):
+def format_basis(basis_tab, sort_basis=True):
     '''Convert the input :attr:`Mole.basis` to the internal data format.
 
     ``{ atom: [(l, ((-exp, c_1, c_2, ..),
@@ -457,10 +457,16 @@ def format_basis(basis_tab):
     fmt_basis = {}
     for atom, atom_basis in basis_tab.items():
         symb = _atom_symbol(atom)
-        fmt_basis[symb] = basis_converter(symb, atom_basis)
-
-        if len(fmt_basis[symb]) == 0:
+        _basis = basis_converter(symb, atom_basis)
+        if len(_basis) == 0:
             raise BasisNotFoundError('Basis not found for  %s' % symb)
+
+        # Sort basis accroding to angular momentum. This is important for method
+        # decontract_basis, which assumes that basis functions with the same
+        # angular momentum are grouped together. Related to issue #1620 #1770
+        if sort_basis:
+            _basis = sorted([b for b in _basis if b], key=lambda b: b[0])
+        fmt_basis[symb] = _basis
     return fmt_basis
 
 def _generate_basis_converter():
@@ -503,11 +509,6 @@ def converter(symb, raw_basis):
                     _basis.extend(nparray_to_list(rawb))
         else:
             _basis = nparray_to_list(raw_basis)
-
-        # Sort basis accroding to angular momentum. This is important for method
-        # decontract_basis, which assumes that basis functions with the same
-        # angular momentum are grouped together. Related to issue #1620 #1770
-        _basis = sorted([b for b in _basis if b], key=lambda b: b[0])
         return _basis
     return converter
 
@@ -654,6 +655,8 @@ def _to_full_contraction(mol, bas_idx):
             bas_idx = ib0 + numpy.where(mol._bas[ib0:ib1,ANG_OF] == l)[0]
             if len(bas_idx) == 0:
                 continue
+            if bas_idx[0] + len(bas_idx) != bas_idx[-1] + 1:
+                raise NotImplementedError('Discontinuous bases of same angular momentum')
 
             mol_exps, b_coeff = _to_full_contraction(mol, bas_idx)
             nprim, nc = b_coeff.shape
@@ -2523,11 +2526,13 @@ def build(self, dump_input=True, parse_arg=ARGPARSE,
         if self.verbose >= logger.WARN:
             self.check_sanity()
 
-        self._atom = self.format_atom(self.atom, unit=self.unit)
+        if self.atom:
+            self._atom = self.format_atom(self.atom, unit=self.unit)
         uniq_atoms = {a[0] for a in self._atom}
 
-        _basis = _parse_default_basis(self.basis, uniq_atoms)
-        self._basis = self.format_basis(_basis)
+        if self.basis:
+            _basis = _parse_default_basis(self.basis, uniq_atoms)
+            self._basis = self.format_basis(_basis)
         env = self._env[:PTR_ENV_START]
         self._atm, self._bas, self._env = \
                 self.make_env(self._atom, self._basis, env, self.nucmod,
@@ -2643,30 +2648,12 @@ def _build_symmetry(self, *args, **kwargs):
                            for ir in self.irrep_id]
         return self
 
-    @lib.with_doc(format_atom.__doc__)
-    def format_atom(self, atom, origin=0, axes=None, unit='Ang'):
-        return format_atom(atom, origin, axes, unit)
-
-    @lib.with_doc(format_basis.__doc__)
-    def format_basis(self, basis_tab):
-        return format_basis(basis_tab)
-
-    @lib.with_doc(format_pseudo.__doc__)
-    def format_pseudo(self, pseudo_tab):
-        return format_pseudo(pseudo_tab)
-
-    @lib.with_doc(format_ecp.__doc__)
-    def format_ecp(self, ecp_tab):
-        return format_ecp(ecp_tab)
-
-    @lib.with_doc(expand_etb.__doc__)
-    def expand_etb(self, l, n, alpha, beta):
-        return expand_etb(l, n, alpha, beta)
-
-    @lib.with_doc(expand_etbs.__doc__)
-    def expand_etbs(self, etbs):
-        return expand_etbs(etbs)
-    etbs = expand_etbs
+    format_atom = staticmethod(format_atom)
+    format_basis = staticmethod(format_basis)
+    format_pseudo = staticmethod(format_pseudo)
+    format_ecp = staticmethod(format_ecp)
+    expand_etb = staticmethod(expand_etb)
+    expand_etbs = etbs = staticmethod(expand_etbs)
 
     @lib.with_doc(make_env.__doc__)
     def make_env(self, atoms, basis, pre_env=[], nucmod={}, nucprop=None):
@@ -3713,7 +3700,7 @@ def __getattr__(self, key):
                      '_repr_mimebundle_'):
             # https://github.com/mewwts/addict/issues/26
             # https://github.com/jupyter/notebook/issues/2014
-            raise AttributeError
+            raise AttributeError(f'Mole object has no attribute {key}')
 
         # Import all available modules. Some methods are registered to other
         # classes/modules when importing modules in __all__.
@@ -3734,8 +3721,10 @@ def __getattr__(self, key):
                 if xc in dft.XC:
                     mf.xc = xc
                     key = 'TDDFT'
-        else:
+        elif 'CI' in key or 'CC' in key or 'CAS' in key or 'MP' in key:
             mf = scf.HF(self)
+        else:
+            raise AttributeError(f'Mole object has no attribute {key}')
 
         method = getattr(mf, key)
 

pyscf/lib/CMakeLists.txt

@@ -222,7 +222,7 @@ if(ENABLE_XCFUN AND BUILD_XCFUN)
     GIT_REPOSITORY https://github.com/dftlibs/xcfun.git
     GIT_TAG a89b783
     # This patch adds the xcfun derivative order up to 5
-    PATCH_COMMAND git apply ${PROJECT_SOURCE_DIR}/libxcfun.patch
+    PATCH_COMMAND git apply --reject ${PROJECT_SOURCE_DIR}/libxcfun.patch
     PREFIX ${PROJECT_BINARY_DIR}/deps
     INSTALL_DIR ${PROJECT_SOURCE_DIR}/deps
     CMAKE_ARGS -DCMAKE_BUILD_TYPE=RELEASE -DBUILD_SHARED_LIBS=1

pyscf/lib/misc.py

@@ -1340,7 +1340,10 @@ def to_gpu(method):
     gpu4pyscf objects.
     '''
     import cupy
+    from pyscf import gto
     for key, val in method.__dict__.items():
+        if isinstance(val, gto.MoleBase):
+            continue
         if isinstance(val, numpy.ndarray):
             setattr(method, key, cupy.asarray(val))
         elif hasattr(val, 'to_gpu'):

pyscf/lo/boys.py

@@ -115,7 +115,10 @@ def dipole_integral(mol, mo_coeff, charge_center=None):
     return dip
 
 def atomic_init_guess(mol, mo_coeff):
-    s = mol.intor_symmetric('int1e_ovlp')
+    if getattr(mol, 'pbc_intor', None):
+        s = mol.pbc_intor('int1e_ovlp', hermi=1)
+    else:
+        s = mol.intor_symmetric('int1e_ovlp')
     c = orth.orth_ao(mol, s=s)
     mo = reduce(numpy.dot, (c.conj().T, s, mo_coeff))
 # Find the AOs which have largest overlap to MOs