Merge pull request #171 from leila-pujal/screening_ovlp_iodata

Extend screening overlap to IOData wrapper

gbasis/contractions.py

@@ -141,7 +141,7 @@ def __init__(
  "spherical" or "p".
  icenter : np.int64 or None (optional)
  Index for the atomic center for the contraction
- ovr_tol : float
+ tol : float
  Tolerance used in overlap screening.
  ovr_screen : boolean
  Flag used for activating overlap screening.

gbasis/parsers.py

@@ -214,7 +214,7 @@ def make_contractions(basis_dict, atoms, coords, coord_types, tol=1e-20, overlap
  if not isinstance(tol, float):
  raise TypeError("Tolerance must be provided as a float.")
  if not isinstance(overlap, bool):
- raise TypeError("Tolerance must be provided as True or False.")
+ raise TypeError("Overlap must be provided as True or False.")
  if len(atoms) != coords.shape[0]:
  raise ValueError("Number of atoms must be equal to the number of rows in the coordinates.")
 

gbasis/wrappers.py

@@ -3,13 +3,17 @@
 import numpy as np
 
 
-def from_iodata(mol):
+def from_iodata(mol, tol=1e-20, overlap=False):
  """Return basis set stored within the `IOData` instance in `iodata`.
 
  Parameters
  ----------
  mol : iodata.iodata.IOData
  `IOData` instance from `iodata` module.
+ tol : float
+ Tolerance used in overlap screening.
+ overlap : bool
+ Flag for performing overlap screening between contractions.
 
  Returns
  -------
@@ -114,6 +118,10 @@ def angmom_components_sph(self):
  "Only L2 normalization scheme is supported in `gbasis`. Given `IOData` instance uses "
  "primitive normalization scheme, {}".format(molbasis.primitive_normalization)
  )
+ if not isinstance(tol, float):
+ raise TypeError("Tolerance must be provided as a float.")
+ if not isinstance(overlap, bool):
+ raise TypeError("Overlap must be provided as True or False.")
 
  basis = []
  for shell in molbasis.shells:
@@ -133,6 +141,8 @@ def angmom_components_sph(self):
  shell.exponents,
  shell.kinds[0],
  icenter=shell.icenter,
+ tol=tol,
+ ovr_screen=overlap,
  )
  )
 

tests/test_wrappers.py

@@ -18,6 +18,8 @@ def test_from_iodata():
  coord_types = [type for type in [shell.coord_type for shell in basis]]
 
  assert coord_types == ["cartesian"] * 5
+ assert basis[0].ovr_screen == False
+ assert basis[0].ovr_tol == 1e-20
  assert all(isinstance(i, GeneralizedContractionShell) for i in basis)
  assert basis[0].angmom == 0
  assert np.allclose(basis[0].coord, mol.atcoords[0])
@@ -28,6 +30,8 @@ def test_from_iodata():
  assert np.allclose(basis[0].norm_cont, 1.0)
 
  assert basis[1].angmom == 0
+ assert basis[1].ovr_screen == False
+ assert basis[1].ovr_tol == 1e-20
  assert np.allclose(basis[1].coord, mol.atcoords[0])
  assert np.allclose(basis[1].exps, np.array([5.033151319, 1.169596125, 0.3803889600]))
  assert np.allclose(
@@ -36,6 +40,8 @@ def test_from_iodata():
  assert np.allclose(basis[1].norm_cont, 1.0)
 
  assert basis[2].angmom == 1
+ assert basis[2].ovr_screen == False
+ assert basis[2].ovr_tol == 1e-20
  assert np.allclose(basis[2].coord, mol.atcoords[0])
  assert np.allclose(basis[2].exps, np.array([5.033151319, 1.169596125, 0.3803889600]))
  assert np.allclose(
@@ -44,6 +50,8 @@ def test_from_iodata():
  assert np.allclose(basis[2].norm_cont, 1.0)
 
  assert basis[3].angmom == 0
+ assert basis[3].ovr_screen == False
+ assert basis[3].ovr_tol == 1e-20
  assert np.allclose(basis[3].coord, mol.atcoords[1])
  assert np.allclose(basis[3].exps, np.array([3.425250914, 0.6239137298, 0.1688554040]))
  assert np.allclose(
@@ -52,6 +60,8 @@ def test_from_iodata():
  assert np.allclose(basis[3].norm_cont, 1.0)
 
  assert basis[4].angmom == 0
+ assert basis[4].ovr_screen == False
+ assert basis[4].ovr_tol == 1e-20
  assert np.allclose(basis[4].coord, mol.atcoords[2])
  assert np.allclose(basis[4].exps, np.array([3.425250914, 0.6239137298, 0.1688554040]))
  assert np.allclose(
@@ -114,6 +124,27 @@ def test_from_iodata():
  basis, coord_types = from_iodata(mol)
 
 
+def test_from_iodata_ovlp():
+ """Test gbasis.wrapper.from_iodata only for the ovr_screen and tol attributes"""
+ pytest.importorskip("iodata")
+ from iodata import load_one
+
+ mol = load_one(find_datafile("data_iodata_water_sto3g_hf_g03.fchk"))
+
+ basis = from_iodata(mol, tol=0.001, overlap=True)
+
+ assert basis[0].ovr_screen == True
+ assert basis[0].ovr_tol == 0.001
+ assert basis[1].ovr_screen == True
+ assert basis[1].ovr_tol == 0.001
+ assert basis[2].ovr_screen == True
+ assert basis[2].ovr_tol == 0.001
+ assert basis[3].ovr_screen == True
+ assert basis[3].ovr_tol == 0.001
+ assert basis[4].ovr_screen == True
+ assert basis[4].ovr_tol == 0.001
+
+
 def test_from_pyscf():
  """Test gbasis.wrapper.from_pyscf."""
  pytest.importorskip("pyscf")