Fix basis parser and other tests

pyscf/cc/ccsd.py

@@ -821,7 +821,7 @@ def __init__(self, cc):
         self._scf = cc._scf.as_scanner()
 
     def __call__(self, mol_or_geom, **kwargs):
-        if isinstance(mol_or_geom, gto.Mole):
+        if isinstance(mol_or_geom, gto.MoleBase):
             mol = mol_or_geom
         else:
             mol = self.mol.set_geom_(mol_or_geom, inplace=False)
@@ -934,12 +934,6 @@ class CCSDBase(lib.StreamObject):
     ))
 
     def __init__(self, mf, frozen=None, mo_coeff=None, mo_occ=None):
-        if isinstance(mf, gto.Mole):
-            raise RuntimeError('''
-You see this error message because of the API updates in pyscf v0.10.
-In the new API, the first argument of CC class is HF objects.  Please see
-http://sunqm.net/pyscf/code-rule.html#api-rules for the details of API conventions''')
-
         from pyscf.scf import hf
         if isinstance(mf, hf.KohnShamDFT):
             raise RuntimeError(

pyscf/ci/cisd.py

@@ -23,7 +23,7 @@
 
 from functools import reduce
 import numpy
-from pyscf.gto import Mole
+from pyscf import gto
 from pyscf import lib
 from pyscf.lib import logger
 from pyscf.cc import ccsd
@@ -786,7 +786,7 @@ def __init__(self, ci):
         self._scf = ci._scf.as_scanner()
 
     def __call__(self, mol_or_geom, ci0=None, **kwargs):
-        if isinstance(mol_or_geom, Mole):
+        if isinstance(mol_or_geom, gto.Mole):
             mol = mol_or_geom
         else:
             mol = self.mol.set_geom_(mol_or_geom, inplace=False)

pyscf/df/grad/casscf.py

@@ -34,7 +34,7 @@
 from itertools import product
 import numpy
 from scipy import linalg
-from pyscf.gto import Mole
+from pyscf import gto
 from pyscf import lib
 from pyscf import ao2mo
 from pyscf.lib import logger
@@ -160,7 +160,8 @@ def __init__(self, g):
         lib.GradScanner.__init__(self, g)
 
     def __call__(self, mol_or_geom, **kwargs):
-        if isinstance(mol_or_geom, gto.Mole):
+        if isinstance(mol_or_geom, gto.MoleBase):
+            assert mol_or_geom.__class__ == gto.Mole
             mol = mol_or_geom
         else:
             mol = self.mol.set_geom_(mol_or_geom, inplace=False)

pyscf/df/grad/sacasscf.py

@@ -21,7 +21,7 @@
 import gc
 from functools import reduce
 from scipy import linalg
-from pyscf.gto import Mole
+from pyscf import gto
 from pyscf import mcscf, lib, ao2mo
 from pyscf.grad import lagrange
 from pyscf.grad import rhf as rhf_grad
@@ -331,7 +331,8 @@ def __init__(self, g, state):
             self.state = state
 
     def __call__(self, mol_or_geom, **kwargs):
-        if isinstance(mol_or_geom, Mole):
+        if isinstance(mol_or_geom, gto.MoleBase):
+            assert mol_or_geom.__class__ == gto.Mole
             mol = mol_or_geom
         else:
             mol = self.mol.set_geom_(mol_or_geom, inplace=False)

pyscf/df/incore.py

@@ -46,7 +46,7 @@ def aux_e2(mol, auxmol_or_auxbasis, intor='int3c2e', aosym='s1', comp=None, out=
 
             cintopt = gto.moleintor.make_cintopt(mol._atm, mol._bas, mol._env, 'int3c2e')
     '''
-    if isinstance(auxmol_or_auxbasis, gto.Mole):
+    if isinstance(auxmol_or_auxbasis, gto.MoleBase):
         auxmol = auxmol_or_auxbasis
     else:
         auxbasis = auxmol_or_auxbasis
@@ -76,7 +76,7 @@ def aux_e1(mol, auxmol_or_auxbasis, intor='int3c2e', aosym='s1', comp=None, out=
 
     The same arguments as function aux_e2 can be input to aux_e1.
     '''
-    if isinstance(auxmol_or_auxbasis, gto.Mole):
+    if isinstance(auxmol_or_auxbasis, gto.MoleBase):
         auxmol = auxmol_or_auxbasis
     else:
         auxbasis = auxmol_or_auxbasis
@@ -96,7 +96,7 @@ def aux_e1(mol, auxmol_or_auxbasis, intor='int3c2e', aosym='s1', comp=None, out=
 def fill_2c2e(mol, auxmol_or_auxbasis, intor='int2c2e', comp=None, hermi=1, out=None):
     '''2-center 2-electron AO integrals for auxiliary basis (auxmol)
     '''
-    if isinstance(auxmol_or_auxbasis, gto.Mole):
+    if isinstance(auxmol_or_auxbasis, gto.MoleBase):
         auxmol = auxmol_or_auxbasis
     else:
         auxbasis = auxmol_or_auxbasis

pyscf/grad/casci.py

@@ -27,7 +27,7 @@
 
 from functools import reduce
 import numpy
-from pyscf.gto import Mole
+from pyscf import gto
 from pyscf import lib
 from pyscf import ao2mo
 from pyscf.lib import logger
@@ -226,7 +226,8 @@ def __init__(self, g, state):
             self.state = state
 
     def __call__(self, mol_or_geom, state=None, **kwargs):
-        if isinstance(mol_or_geom, Mole):
+        if isinstance(mol_or_geom, gto.MoleBase):
+            assert mol_or_geom.__class__ == gto.Mole
             mol = mol_or_geom
         else:
             mol = self.mol.set_geom_(mol_or_geom, inplace=False)

pyscf/grad/casscf.py

@@ -30,7 +30,7 @@
 
 from functools import reduce
 import numpy
-from pyscf.gto import Mole
+from pyscf import gto
 from pyscf import lib
 from pyscf import ao2mo
 from pyscf.lib import logger
@@ -171,7 +171,8 @@ def __init__(self, g):
         lib.GradScanner.__init__(self, g)
 
     def __call__(self, mol_or_geom, **kwargs):
-        if isinstance(mol_or_geom, Mole):
+        if isinstance(mol_or_geom, gto.MoleBase):
+            assert mol_or_geom.__class__ == gto.Mole
             mol = mol_or_geom
         else:
             mol = self.mol.set_geom_(mol_or_geom, inplace=False)

pyscf/grad/ccsd.py

@@ -25,7 +25,7 @@
 import numpy
 from functools import reduce
 from pyscf import lib
-from pyscf.gto import Mole
+from pyscf import gto
 from pyscf.lib import logger
 from pyscf.cc import ccsd
 from pyscf.cc import _ccsd
@@ -231,7 +231,8 @@ def __init__(self, g):
         lib.GradScanner.__init__(self, g)
 
     def __call__(self, mol_or_geom, **kwargs):
-        if isinstance(mol_or_geom, Mole):
+        if isinstance(mol_or_geom, gto.MoleBase):
+            assert mol_or_geom.__class__ == gto.Mole
             mol = mol_or_geom
         else:
             mol = self.mol.set_geom_(mol_or_geom, inplace=False)

pyscf/grad/cisd.py

@@ -21,7 +21,7 @@
 '''
 
 import numpy
-from pyscf.gto import Mole
+from pyscf import gto
 from pyscf import lib
 from pyscf.lib import logger
 from pyscf.ci import cisd
@@ -89,7 +89,8 @@ def __init__(self, g, state):
             self.state = state
 
     def __call__(self, mol_or_geom, state=None, **kwargs):
-        if isinstance(mol_or_geom, Mole):
+        if isinstance(mol_or_geom, gto.MoleBase):
+            assert mol_or_geom.__class__ == gto.Mole
             mol = mol_or_geom
         else:
             mol = self.mol.set_geom_(mol_or_geom, inplace=False)

pyscf/grad/mp2.py

@@ -24,7 +24,7 @@
 import numpy
 from pyscf import lib
 from functools import reduce
-from pyscf.gto import Mole
+from pyscf import gto
 from pyscf.lib import logger
 from pyscf.grad import rhf as rhf_grad
 from pyscf.scf import cphf
@@ -224,7 +224,8 @@ def __init__(self, g):
         lib.GradScanner.__init__(self, g)
 
     def __call__(self, mol_or_geom, **kwargs):
-        if isinstance(mol_or_geom, Mole):
+        if isinstance(mol_or_geom, gto.MoleBase):
+            assert mol_or_geom.__class__ == gto.Mole
             mol = mol_or_geom
         else:
             mol = self.mol.set_geom_(mol_or_geom, inplace=False)

pyscf/grad/rhf.py

@@ -254,7 +254,8 @@ def __init__(self, g):
         lib.GradScanner.__init__(self, g)
 
     def __call__(self, mol_or_geom, **kwargs):
-        if isinstance(mol_or_geom, gto.Mole):
+        if isinstance(mol_or_geom, gto.MoleBase):
+            assert mol_or_geom.__class__ == gto.Mole
             mol = mol_or_geom
         else:
             mol = self.mol.set_geom_(mol_or_geom, inplace=False)

pyscf/grad/sacasscf.py

@@ -19,7 +19,7 @@
 from functools import reduce
 from itertools import product
 from scipy import linalg
-from pyscf.gto import Mole
+from pyscf import gto
 from pyscf.grad import lagrange
 from pyscf.mcscf.addons import StateAverageMCSCFSolver, StateAverageFCISolver
 from pyscf.mcscf.addons import StateAverageMixFCISolver, state_average_mix_
@@ -374,7 +374,8 @@ def __init__(self, g, state):
         self._converged = False
 
     def __call__(self, mol_or_geom, **kwargs):
-        if isinstance(mol_or_geom, Mole):
+        if isinstance(mol_or_geom, gto.MoleBase):
+            assert mol_or_geom.__class__ == gto.Mole
             mol = mol_or_geom
         else:
             mol = self.mol.set_geom_(mol_or_geom, inplace=False)

pyscf/grad/tdrhf.py

@@ -22,7 +22,7 @@
 
 from functools import reduce
 import numpy
-from pyscf.gto import Mole
+from pyscf import gto
 from pyscf import lib
 from pyscf.lib import logger
 from pyscf.grad import rhf as rhf_grad
@@ -207,7 +207,8 @@ def __init__(self, g, state):
             self.state = state
 
     def __call__(self, mol_or_geom, state=None, **kwargs):
-        if isinstance(mol_or_geom, Mole):
+        if isinstance(mol_or_geom, gto.MoleBase):
+            assert mol_or_geom.__class__ == gto.Mole
             mol = mol_or_geom
         else:
             mol = self.mol.set_geom_(mol_or_geom, inplace=False)

pyscf/gto/basis/__init__.py

@@ -608,27 +608,27 @@ def load(filename_or_basisname, symb, optimize=OPTIMIZE_CONTRACTION):
         try:
             return parse_nwchem.parse(filename_or_basisname, symb,
                                       optimize=optimize)
-        except IndexError:
-            raise BasisNotFoundError(filename_or_basisname)
         except BasisNotFoundError as basis_err:
             pass
+        except Exception:
+            raise BasisNotFoundError(filename_or_basisname)
 
         try:
             return parse_nwchem.parse(filename_or_basisname, optimize=optimize)
-        except IndexError:
-            raise BasisNotFoundError(f'Invalid basis {filename_or_basisname}')
         except BasisNotFoundError:
             pass
+        except Exception:
+            raise BasisNotFoundError(f'Invalid basis {filename_or_basisname}')
 
         try:
             return parse_cp2k.parse(filename_or_basisname, optimize=optimize)
-        except IndexError:
-            raise BasisNotFoundError(f'Invalid basis {filename_or_basisname}')
         except BasisNotFoundError:
             pass
+        except Exception:
+            raise BasisNotFoundError(f'Invalid basis {filename_or_basisname}')
 
         # Last, a trial to access Basis Set Exchange database
-        from pyscf.basis import bse
+        from pyscf.gto.basis import bse
         if bse.basis_set_exchange is not None:
             try:
                 bse_obj = bse.basis_set_exchange.api.get_basis(

pyscf/gto/basis/bse.py

@@ -5,6 +5,7 @@
 '''
 
 try:
+    import basis_set_exchange
     from basis_set_exchange import lut, manip, sort
 except ImportError:
     basis_set_exchange = None

pyscf/gto/basis/parse_cp2k.py

@@ -61,33 +61,49 @@ def load(basisfile, symb, optimize=False):
     return _parse(search_seg(basisfile, symb), optimize)
 
 def _parse(blines, optimize=False):
-    header_ln = blines.pop(0)  # noqa: F841
-    nsets = int(blines.pop(0))
+    blines_iter = iter(blines)
+    try:
+        header_ln = next(blines_iter)  # noqa: F841
+        nsets = int(next(blines_iter))
+    except Exception:
+        raise BasisNotFoundError('Not basis data')
+
     basis = []
-    for n in range(nsets):
-        comp = [int(p) for p in blines.pop(0).split()]
-        lmin, lmax, nexps, ncontractions = comp[1], comp[2], comp[3], comp[4:]
-        basis_n = [[l] for l in range(lmin,lmax+1)]
-        for nexp in range(nexps):
-            line = blines.pop(0)
-            dat = line.split()
-            try:
-                bfun = [float(x) for x in dat]
-            except ValueError:
-                if DISABLE_EVAL:
-                    raise ValueError('Failed to parse basis %s' % line)
-                else:
-                    bfun = eval(','.join(dat))
-            exp = bfun.pop(0)
-            for i,l in enumerate(range(lmin,lmax+1)):
-                cl = [exp]
-                for c in range(ncontractions[i]):
-                    cl.append(bfun.pop(0))
-                basis_n[i].append(tuple(cl))
-        basis.extend(basis_n)
+    try:
+        for n in range(nsets):
+            comp = [int(p) for p in next(blines_iter).split()]
+            lmin, lmax, nexps, ncontractions = comp[1], comp[2], comp[3], comp[4:]
+            basis_n = [[l] for l in range(lmin,lmax+1)]
+            for nexp in range(nexps):
+                line = next(blines_iter)
+                dat = line.split()
+                try:
+                    bfun = [float(x) for x in dat]
+                except ValueError:
+                    if DISABLE_EVAL:
+                        raise ValueError('Failed to parse %s' % line)
+                    else:
+                        bfun = eval(','.join(dat))
+
+                if len(bfun) != sum(ncontractions) + 1:
+                    raise ValueError('Basis data incomplete')
+
+                bfun_iter = iter(bfun)
+                exp = next(bfun_iter)
+                for i,l in enumerate(range(lmin,lmax+1)):
+                    cl = [exp]
+                    for c in range(ncontractions[i]):
+                        cl.append(next(bfun_iter))
+                    basis_n[i].append(cl)
+            basis.extend(basis_n)
+    except StopIteration:
+        raise ValueError('Basis data incomplete')
+
     basis_sorted = []
     for l in range(MAXL):
         basis_sorted.extend([b for b in basis if b[0] == l])
+    if not basis_sorted:
+        raise BasisNotFoundError('Basis data not found')
 
     if optimize:
         basis_sorted = parse_nwchem.optimize_contraction(basis_sorted)

pyscf/gto/basis/parse_molpro.py

@@ -24,6 +24,7 @@
 
 import re
 import numpy
+import numpy as np
 
 try:
     from pyscf.gto.basis.parse_nwchem import optimize_contraction