Merge pull request #230 from ahurta92/adrian-Dipole

NWCHEM: Adrian dipole/homo/lumo changes

qcengine/programs/nwchem/harvester.py

@@ -614,9 +614,7 @@ def harvest_outfile_pass(outtext):
  if mobj:
  psivar["N ALPHA ELECTRONS"] = mobj.group(2)
  psivar["N BETA ELECTRONS"] = mobj.group(3)
-
  if psivar["N ALPHA ELECTRONS"] == psivar["N BETA ELECTRONS"]:
-
  # get HOMO and LUMO energy
  mobj = re.search(
  r"Vector"
@@ -629,34 +627,30 @@ def harvest_outfile_pass(outtext):
  + r"E="
  + r"([+-]?\s?\d+[.]\d+)"
  + r"[D]"
- + r"([+-])"
- + r"[0]"
- + r"(\d+)",
+ + r"([+-]0\d)",
  outtext,
  re.MULTILINE,
  )
  if mobj:
- homo = float(mobj.group(1)) * (10 ** (-1 * float(mobj.group(3))))
+ homo = float(mobj.group(1)) * (10 ** (int(mobj.group(2))))
  psivar["HOMO"] = np.array([round(homo, 10)])
- mobj = re.search(
- r"Vector"
- + r"\s+"
- + r"%d" % (psivar["N ALPHA ELECTRONS"] + 1)
- + r"\s+"
- + r"Occ="
- + r".*"
- + r"\s+"
- + r"E="
- + r"([+-]?\s?\d+[.]\d+)"
- + r"[D]"
- + r"([+-])"
- + r"[0]"
- + r"(\d+)",
- outtext,
- re.MULTILINE,
- )
+ mobj = re.search(
+ r"Vector"
+ + r"\s+"
+ + r"%d" % (psivar["N ALPHA ELECTRONS"] + 1)
+ + r"\s+"
+ + r"Occ="
+ + r".*"
+ + r"\s+"
+ + r"E="
+ + r"([+-]?\s?\d+[.]\d+)"
+ + r"[D]"
+ + r"([+-]0\d)",
+ outtext,
+ re.MULTILINE,
+ )
  if mobj:
- lumo = float(mobj.group(1)) * (10 ** (-1 * float(mobj.group(3))))
+ lumo = float(mobj.group(1)) * (10 ** (int(mobj.group(2))))
  psivar["LUMO"] = np.array([round(lumo, 10)])
 
  mobj = re.search(r"AO basis - number of functions:\s+(\d+)\s+number of shells:\s+(\d+)", outtext, re.MULTILINE)

qcengine/programs/tests/test_nwchem.py

@@ -142,3 +142,45 @@ def test_dipole(h20):
  assert compare_values(-0.00, float(res["extras"]["qcvars"]["DIPOLE MOMENT"][0]), atol=1e-3)
  assert compare_values(-0.00, float(res["extras"]["qcvars"]["DIPOLE MOMENT"][1]), atol=1e-3)
  assert compare_values(-0.272949872, float(res["extras"]["qcvars"]["DIPOLE MOMENT"][2]), atol=1e-5)
+
+
+@pytest.fixture
+def h20v2():
+ water = """
+O 0 0 0
+H 0 0 1
+H 0 1 0
+ """
+ return qcel.models.Molecule.from_data(water)
+
+
+@using("nwchem")
+def test_homo_lumo(h20v2):
+ # Run NH2
+ resi = {
+ "molecule": h20v2,
+ "driver": "energy",
+ "model": {"method": "dft", "basis": "3-21g"},
+ "keywords": {"dft__xc": "b3lyp"},
+ }
+ res = qcng.compute(resi, "nwchem", raise_error=True, return_dict=True)
+
+ # Make sure the calculation completed successfully
+ assert compare_values(-75.968095, res["return_result"], atol=1e-3)
+ assert res["driver"] == "energy"
+ assert "provenance" in res
+ assert res["success"] is True
+
+ # Check the other status information
+ assert res["extras"]["qcvars"]["N ALPHA ELECTRONS"] == "5"
+ assert res["extras"]["qcvars"]["N ATOMS"] == "3"
+ assert res["extras"]["qcvars"]["N BASIS"] == "13"
+
+ # Make sure the properties parsed correctly
+ assert compare_values(-75.968095, res["properties"]["return_energy"], atol=1e-3)
+ assert res["properties"]["calcinfo_natom"] == 3
+ assert res["properties"]["calcinfo_nalpha"] == 5
+ assert res["properties"]["calcinfo_nbasis"] == 13
+ # Make sure Dipole Moment and center of charge parsed correctly
+ assert compare_values(-0.2636515, float(res["extras"]["qcvars"]["HOMO"][0]), atol=1e-5)
+ assert compare_values(0.08207131, float(res["extras"]["qcvars"]["LUMO"][0]), atol=1e-5)