Rename nprim to nexp where appropriate

iodata/basis.py

@@ -118,12 +118,12 @@ class Shell:
     """
 
     exponents: NDArray[float] = attrs.field(validator=validate_shape(("coeffs", 0)))
-    """The array containing the exponents of the primitives, with shape (nprim,)."""
+    """The array containing the exponents of the primitives, with shape (nexp,)."""
 
     coeffs: NDArray[float] = attrs.field(validator=validate_shape(("exponents", 0), ("kinds", 0)))
     """
     The array containing the coefficients of the normalized primitives in each contraction;
-    shape = (nprim, ncon).
+    shape = (nexp, ncon).
     These coefficients assume that the primitives are L2 (orbitals) or L1
     (densities) normalized, but contractions are not necessarily normalized.
     (This depends on the code which generated the contractions.)
@@ -143,8 +143,8 @@ def nbasis(self) -> int:
         return result
 
     @property
-    def nprim(self) -> int:
-        """Number of primitives, also known as the contraction length."""
+    def nexp(self) -> int:
+        """Number of exponents in the contracted shell, also known as the contraction length."""
         return len(self.exponents)
 
     @property

iodata/formats/fchk.py

@@ -157,15 +157,15 @@ def load_one(lit: LineIterator) -> dict:
     # B) Load the orbital basis set
     shell_types = fchk["Shell types"]
     shell_map = fchk["Shell to atom map"] - 1
-    nprims = fchk["Number of primitives per shell"]
+    nexps = fchk["Number of primitives per shell"]
     exponents = fchk["Primitive exponents"]
     ccoeffs_level1 = fchk["Contraction coefficients"]
     ccoeffs_level2 = fchk.get("P(S=P) Contraction coefficients")
 
     shells = []
     counter = 0
     # First loop over all shells
-    for i, n in enumerate(nprims):
+    for i, n in enumerate(nexps):
         if shell_types[i] == -1:
             # Special treatment for SP shell type
             shells.append(
@@ -196,7 +196,7 @@ def load_one(lit: LineIterator) -> dict:
         counter += n
     del shell_map
     del shell_types
-    del nprims
+    del nexps
     del exponents
 
     result["obasis"] = MolecularBasis(shells, CONVENTIONS, "L2")
@@ -645,9 +645,9 @@ def dump_one(f: TextIO, data: IOData):
     # write molecular orbital basis set
     if data.obasis is not None:
         # number of primitives per shell
-        nprims = np.array([shell.nprim for shell in data.obasis.shells])
+        nexps = np.array([shell.nexp for shell in data.obasis.shells])
         exponents = np.array([item for shell in data.obasis.shells for item in shell.exponents])
-        coeffs = np.array([s.coeffs[i][0] for s in data.obasis.shells for i in range(s.nprim)])
+        coeffs = np.array([s.coeffs[i][0] for s in data.obasis.shells for i in range(s.nexp)])
         coordinates = np.array([data.atcoords[shell.icenter] for shell in data.obasis.shells])
         shell_to_atom = np.array([shell.icenter + 1 for shell in data.obasis.shells])
 
@@ -669,14 +669,14 @@ def dump_one(f: TextIO, data: IOData):
         _dump_integer_scalars("Number of basis functions", data.obasis.nbasis, f)
         _dump_integer_scalars("Number of independent functions", data.obasis.nbasis, f)
         _dump_integer_scalars("Number of contracted shells", len(data.obasis.shells), f)
-        _dump_integer_scalars("Number of primitive shells", nprims.sum(), f)
+        _dump_integer_scalars("Number of primitive shells", nexps.sum(), f)
         _dump_integer_scalars("Pure/Cartesian d shells", num_pure_d_shells, f)
         _dump_integer_scalars("Pure/Cartesian f shells", num_pure_f_shells, f)
         _dump_integer_scalars("Highest angular momentum", np.amax(np.abs(shell_types)), f)
-        _dump_integer_scalars("Largest degree of contraction", np.amax(nprims), f)
+        _dump_integer_scalars("Largest degree of contraction", np.amax(nexps), f)
 
         _dump_integer_arrays("Shell types", np.array(shell_types), f)
-        _dump_integer_arrays("Number of primitives per shell", nprims, f)
+        _dump_integer_arrays("Number of primitives per shell", nexps, f)
         _dump_integer_arrays("Shell to atom map", shell_to_atom, f)
 
         _dump_real_arrays("Primitive exponents", exponents, f)
@@ -686,9 +686,9 @@ def dump_one(f: TextIO, data: IOData):
             sp_coeffs = []
             for shell, shell_type in zip(data.obasis.shells, shell_types):
                 if shell_type == -1:
-                    sp_coeffs.extend([shell.coeffs[i][1] for i in range(shell.nprim)])
+                    sp_coeffs.extend([shell.coeffs[i][1] for i in range(shell.nexp)])
                 else:
-                    sp_coeffs.extend([0.0] * shell.nprim)
+                    sp_coeffs.extend([0.0] * shell.nexp)
             _dump_real_arrays("P(S=P) Contraction coefficients", np.array(sp_coeffs), f)
         _dump_real_arrays("Coordinates of each shell", coordinates.flatten(), f)
 

iodata/formats/molden.py

@@ -276,10 +276,10 @@ def _load_helper_obasis(lit: LineIterator) -> MolecularBasis:
                 break
             # Read a new shell
             angmom = angmom_sti(words[0])
-            nprim = int(words[1])
-            exponents = np.zeros(nprim)
-            coeffs = np.zeros((nprim, 1))
-            for iprim in range(nprim):
+            nexp = int(words[1])
+            exponents = np.zeros(nexp)
+            coeffs = np.zeros((nexp, 1))
+            for iprim in range(nexp):
                 words = next(lit).split()
                 exponents[iprim] = float(words[0].replace("D", "E"))
                 coeffs[iprim, 0] = float(words[1].replace("D", "E"))
@@ -528,7 +528,7 @@ def _fix_obasis_turbomole(obasis: MolecularBasis) -> Union[MolecularBasis, None]
         fixed_shells.append(fixed_shell)
         angmom = shell.angmoms[0]
         kind = shell.kinds[0]
-        for iprim in range(shell.nprim):
+        for iprim in range(shell.nexp):
             # Default 1.0: do not to correct anything, unless we know how to correct.
             correction = 1.0
             if angmom == 2 and kind == "c":
@@ -872,7 +872,7 @@ def dump_one(f: TextIO, data: IOData):
         # Write out as a segmented basis. Molden format does not support
         # generalized contractions.
         for iangmom, angmom in enumerate(shell.angmoms):
-            f.write(f" {angmom_its(angmom):1s}  {shell.nprim:3d} 1.00\n")
+            f.write(f" {angmom_its(angmom):1s}  {shell.nexp:3d} 1.00\n")
             for exponent, coeff in zip(shell.exponents, shell.coeffs[:, iangmom]):
                 f.write(f"{exponent:20.10f} {coeff:20.10f}\n")
     f.write("\n")

iodata/formats/mwfn.py

@@ -181,11 +181,11 @@ def _load_helper_shells(lit: LineIterator, nshell: int) -> dict:
 
 
 def _load_helper_section(
-    lit: LineIterator, nprim: int, start: str, skip: int, dtype: np.dtype
+    lit: LineIterator, size: int, start: str, skip: int, dtype: np.dtype
 ) -> NDArray:
     """Read single or multiple line(s) section."""
     section = []
-    while len(section) < nprim:
+    while len(section) < size:
         line = next(lit)
         if not line.startswith(start):
             raise LoadError(f"Expected line to start with {start}. Got line={line}.", lit)

iodata/formats/wfn.py

@@ -565,7 +565,7 @@ def dump_one(f: TextIO, data: IOData) -> None:
         for angmom, kind in zip(shell.angmoms, shell.kinds):
             n = len(data.obasis.conventions[angmom, kind])
             c = raw_coeffs[index_mo_old : index_mo_old + n]
-            for _ in range(shell.nprim):
+            for _ in range(shell.nexp):
                 mo_coeffs[index_mo_new : index_mo_new + n] = c
                 index_mo_new += n
             index_mo_old += n

iodata/formats/wfx.py

@@ -409,7 +409,7 @@ def dump_one(f: TextIO, data: IOData):
         for angmom, kind in zip(shell.angmoms, shell.kinds):
             n = len(data.obasis.conventions[angmom, kind])
             c = raw_coeffs[index_mo_old : index_mo_old + n]
-            for _j in range(shell.nprim):
+            for _j in range(shell.nexp):
                 mo_coeffs[index_mo_new : index_mo_new + n] = c
                 index_mo_new += n
             index_mo_old += n

iodata/test/test_basis.py

@@ -94,11 +94,11 @@ def test_shell_info_propertes():
     assert shells[2].nbasis == 4
     assert shells[3].nbasis == 5
     assert shells[4].nbasis == 6 + 7 + 9
-    assert shells[0].nprim == 6
-    assert shells[1].nprim == 3
-    assert shells[2].nprim == 1
-    assert shells[3].nprim == 2
-    assert shells[4].nprim == 1
+    assert shells[0].nexp == 6
+    assert shells[1].nexp == 3
+    assert shells[2].nexp == 1
+    assert shells[3].nexp == 2
+    assert shells[4].nexp == 1
     assert shells[0].ncon == 1
     assert shells[1].ncon == 2
     assert shells[2].ncon == 2

iodata/test/test_fchk.py

@@ -69,7 +69,7 @@ def test_load_fchk_hf_sto3g_num():
     assert shell0.kinds == ["c"]
     assert_allclose(shell0.exponents, np.array([1.66679134e02, 3.03608123e01, 8.21682067e00]))
     assert_allclose(shell0.coeffs, np.array([[1.54328967e-01], [5.35328142e-01], [4.44634542e-01]]))
-    assert shell0.nprim == 3
+    assert shell0.nexp == 3
     assert shell0.ncon == 1
     assert shell0.nbasis == 1
     shell1 = mol.obasis.shells[1]
@@ -87,11 +87,11 @@ def test_load_fchk_hf_sto3g_num():
             ]
         ),
     )
-    assert shell1.nprim == 3
+    assert shell1.nexp == 3
     assert shell1.ncon == 2
     assert shell1.nbasis == 4
     shell2 = mol.obasis.shells[2]
-    assert shell2.nprim == 3
+    assert shell2.nexp == 3
     assert shell2.ncon == 1
     assert shell2.nbasis == 1
     assert mol.obasis.primitive_normalization == "L2"
@@ -123,7 +123,7 @@ def test_load_fchk_h_sto3g_num():
     assert mol.title == "h_sto3g"
     assert len(mol.obasis.shells) == 1
     assert mol.obasis.nbasis == 1
-    assert mol.obasis.shells[0].nprim == 3
+    assert mol.obasis.shells[0].nexp == 3
     assert len(mol.atcoords) == len(mol.atnums)
     assert mol.atcoords.shape[1] == 3
     assert len(mol.atnums) == 1

iodata/test/test_molden.py

@@ -154,19 +154,19 @@ def test_load_molden_low_nh3_molden_cart():
         assert shell.icenter == 3
 
     shell0 = obasis.shells[0]
-    assert shell0.nprim == 8
+    assert shell0.nexp == 8
     assert shell0.exponents.shape == (8,)
     assert_allclose(shell0.exponents[4], 0.2856000000e02)
     assert shell0.coeffs.shape == (8, 1)
     assert_allclose(shell0.coeffs[4, 0], 0.2785706633e00)
     shell7 = obasis.shells[7]
-    assert shell7.nprim == 1
+    assert shell7.nexp == 1
     assert shell7.exponents.shape == (1,)
     assert_allclose(shell7.exponents, [0.8170000000e00])
     assert_allclose(shell7.coeffs, [[1.0]])
     assert shell7.coeffs.shape == (1, 1)
     shell19 = obasis.shells[19]
-    assert shell19.nprim == 3
+    assert shell19.nexp == 3
     assert shell19.exponents.shape == (3,)
     assert_allclose(shell19.exponents, [0.1301000000e02, 0.1962000000e01, 0.4446000000e00])
     assert_allclose(shell19.coeffs, [[0.3349872639e-01], [0.2348008012e00], [0.8136829579e00]])

iodata/test/test_molekel.py

@@ -122,7 +122,7 @@ def test_load_mkl_ethanol():
     # assert_allclose(mol.obasis.shells[-1].coeffs[-1, -1], 0.181380684)
     assert_equal([shell.icenter for shell in mol.obasis.shells[:5]], [0, 0, 1, 1, 1])
     assert_equal([shell.angmoms[0] for shell in mol.obasis.shells[:5]], [0, 0, 0, 0, 1])
-    assert_equal([shell.nprim for shell in mol.obasis.shells[:5]], [3, 1, 6, 3, 3])
+    assert_equal([shell.nexp for shell in mol.obasis.shells[:5]], [3, 1, 6, 3, 3])
     assert_equal(mol.mo.coeffs.shape, (39, 39))
     assert_equal(mol.mo.energies.shape, (39,))
     assert_equal(mol.mo.occs.shape, (39,))

iodata/test/test_mwfn.py

@@ -40,16 +40,16 @@ def test_load_mwfn_ch3_rohf_g03():
     assert_equal(mol.mo.occs.max(), 2.0)
     assert_equal(mol.extra["full_virial_ratio"], 2.00174844)
     assert_equal(mol.extra["nindbasis"], 8)
-    assert_equal(np.sum([shell.nprim * shell.nbasis for shell in mol.obasis.shells]), 24)
+    assert_equal(np.sum([shell.nexp * shell.nbasis for shell in mol.obasis.shells]), 24)
     assert_equal(len(mol.obasis.shells), 6)
-    assert_equal(np.sum([shell.nprim for shell in mol.obasis.shells]), 18)
+    assert_equal(np.sum([shell.nexp for shell in mol.obasis.shells]), 18)
     assert_equal(mol.charge, 0.0)
     assert_equal(mol.nelec, 9)
     assert_equal(mol.natom, 4)
     assert_equal(mol.energy, -3.90732095e01)
     assert_allclose([shell.angmoms[0] for shell in mol.obasis.shells], [0, 0, 1, 0, 0, 0])
     assert_allclose([shell.icenter for shell in mol.obasis.shells], [0, 0, 0, 1, 2, 3])
-    assert_allclose([shell.nprim for shell in mol.obasis.shells], [3, 3, 3, 3, 3, 3])
+    assert_allclose([shell.nexp for shell in mol.obasis.shells], [3, 3, 3, 3, 3, 3])
     exponents1 = np.array([7.16168373e01, 1.30450963e01, 3.53051216e00])
     exponents2 = np.array([2.94124936e00, 6.83483096e-01, 2.22289916e-01])
     exponents3 = np.array([2.94124936e00, 6.83483096e-01, 2.22289916e-01])