revert cclib#1405

Part of reverting breaking changes on default
branch (cclib#1482)

cclib/bridge/cclib2pyscf.py

@@ -5,7 +5,7 @@
 
 """Bridge for using cclib data in PySCF (https://github.com/pyscf/pyscf)."""
 
-from cclib.parser.utils import PeriodicTable, find_package
+from cclib.parser.utils import PeriodicTable, convertor, find_package
 
 import numpy as np
 
@@ -85,7 +85,7 @@ def makepyscf_mos(ccdata, mol):
         molecular orbital energies in units of Hartree
     """
     inputattrs = ccdata.__dict__
-    mo_energies = ccdata.moenergies
+    mo_energies = convertor(np.asarray(ccdata.moenergies), "eV", "hartree")
     if "mocoeffs" in inputattrs:
         mol.build()
         s = mol.intor("int1e_ovlp")

cclib/io/moldenwriter.py

@@ -184,7 +184,7 @@ def _mo_from_ccdata(self, mosyms, moenergies, mooccs, mocoeffs):
             for j in range(len(mooccs[i])):
                 restricted_spin_idx = i % len(mocoeffs)
                 lines.append(f" Sym= {mosyms[restricted_spin_idx][j]}")
-                moenergy = moenergies[restricted_spin_idx][j]
+                moenergy = utils.convertor(moenergies[restricted_spin_idx][j], "eV", "hartree")
                 lines.append(f" Ene= {moenergy:10.4f}")
                 lines.append(f" Spin= {spin}")
                 lines.append(f" Occup= {mooccs[i][j]:10.6f}")

cclib/io/wfxwriter.py

@@ -301,10 +301,10 @@ def _mo_energies(self):
         alpha_elctrons = self._no_alpha_electrons()
         beta_electrons = self._no_beta_electrons()
         for mo_energy in self.ccdata.moenergies[0][:alpha_elctrons]:
-            mo_energies.append(WFX_FIELD_FMT % mo_energy)
+            mo_energies.append(WFX_FIELD_FMT % (utils.convertor(mo_energy, "eV", "hartree")))
         if self.ccdata.mult > 1:
             for mo_energy in self.ccdata.moenergies[1][:beta_electrons]:
-                mo_energies.append(WFX_FIELD_FMT % mo_energy)
+                mo_energies.append(WFX_FIELD_FMT % (utils.convertor(mo_energy, "eV", "hartree")))
         return mo_energies
 
     def _mo_spin_types(self):
@@ -451,7 +451,7 @@ def _energy(self) -> str:
             energy = self.ccdata.scfenergies[-1]
         else:
             raise filewriter.MissingAttributeError("scfenergies/mpenergies/ccenergies")
-        return WFX_FIELD_FMT % energy
+        return WFX_FIELD_FMT % (utils.convertor(energy, "eV", "hartree"))
 
     def _virial_ratio(self) -> str:
         """Ratio of kinetic energy to potential energy."""

cclib/parser/data.py

@@ -28,13 +28,13 @@ class ccData:
         atommasses -- atom masses (array[1], daltons)
         atomnos -- atomic numbers (array[1])
         atomspins -- atomic spin densities (dict of arrays[1])
-        ccenergies -- molecular energies with Coupled-Cluster corrections (array[2], hartree)
+        ccenergies -- molecular energies with Coupled-Cluster corrections (array[2], eV)
         charge -- net charge of the system (integer)
         coreelectrons -- number of core electrons in atom pseudopotentials (array[1])
-        dispersionenergies -- dispersion energy corrections (array[1], hartree)
+        dispersionenergies -- dispersion energy corrections (array[1], eV)
         enthalpy -- sum of electronic and thermal enthalpies (float, hartree/particle)
         entropy -- entropy (float, hartree/(particle*kelvin))
-        etenergies -- energies of electronic transitions (array[1], hartree)
+        etenergies -- energies of electronic transitions (array[1], 1/cm)
         etoscs -- oscillator strengths of electronic transitions (array[1])
         etdips -- electric transition dipoles of electronic transitions (array[2], ebohr)
         etveldips -- velocity-gauge electric transition dipoles of electronic transitions (array[2], ebohr)
@@ -55,10 +55,10 @@ class ccData:
         homos -- molecular orbital indices of HOMO(s) (array[1])
         metadata -- various metadata about the package and computation (dict)
         mocoeffs -- molecular orbital coefficients (list of arrays[2])
-        moenergies -- molecular orbital energies (list of arrays[1], hartree)
+        moenergies -- molecular orbital energies (list of arrays[1], eV)
         moments -- molecular multipole moments (list of arrays[], a.u.)
         mosyms -- orbital symmetries (list of lists)
-        mpenergies -- molecular electronic energies with Møller-Plesset corrections (array[2], hartree)
+        mpenergies -- molecular electronic energies with Møller-Plesset corrections (array[2], eV)
         mult -- multiplicity of the system (integer)
         natom -- number of atoms (integer)
         nbasis -- number of basis functions (integer)
@@ -78,7 +78,7 @@ class ccData:
         scanenergies -- energies of potential energy surface (list)
         scannames -- names of variables scanned (list of strings)
         scanparm -- values of parameters in potential energy surface (list of tuples)
-        scfenergies -- molecular electronic energies after SCF (Hartree-Fock, DFT) (array[1], hartree)
+        scfenergies -- molecular electronic energies after SCF (Hartree-Fock, DFT) (array[1], eV)
         scftargets -- targets for convergence of the SCF (array[2])
         scfvalues -- current values for convergence of the SCF (list of arrays[2])
         temperature -- temperature used for Thermochemistry (float, kelvin)

cclib/parser/logfileparser.py

@@ -211,6 +211,28 @@ def parse(self, progress=None, fupdate=0.05, cupdate=0.002):
             if attr not in _nodelete:
                 self.__delattr__(attr)
 
+        # Convert from atomic units to convenience units.
+        for attr in ("ccenergies", "dispersionenergies", "mpenergies", "scfenergies"):
+            if hasattr(data, attr):
+                setattr(data, attr, utils.convertor(getattr(data, attr), "hartree", "eV"))
+        for attr in ("etenergies",):
+            if hasattr(data, attr):
+                setattr(data, attr, utils.convertor(getattr(data, attr), "hartree", "wavenumber"))
+        for attr in ("scanenergies",):
+            if hasattr(data, attr):
+                setattr(
+                    data,
+                    attr,
+                    utils.convertor(numpy.asarray(getattr(data, attr)), "hartree", "eV").tolist(),
+                )
+        for attr in ("moenergies",):
+            if hasattr(data, attr):
+                setattr(
+                    data,
+                    attr,
+                    [utils.convertor(elem, "hartree", "eV") for elem in getattr(data, attr)],
+                )
+
         # Perform final checks on values of attributes.
         data.check_values(logger=self.logger)
 

cclib/parser/turbomoleparser.py

@@ -765,6 +765,7 @@ def extract(self, inputfile, line):
                 info = re.match(
                     r".*eigenvalue=(?P<moenergy>[0-9D\.+-]{20})\s+nsaos=(?P<count>\d+).*", line
                 )
+                assert info is not None
                 eigenvalue = utils.float(info.group("moenergy"))
 
                 moenergies.append(eigenvalue)

doc/sphinx/data_notes.rst

@@ -149,7 +149,7 @@ However, in *all* cases the dispersion energy for a given geometry will also be
 etenergies
 ----------
 
-This is a rank 1 array that contains the energies of electronic transitions from a reference state to the excited states of the molecule, in hartree. There should be as many elements to this array as there are excited states calculated. Any type of excited state calculation should provide output that can be parsed into this attribute.
+This is a rank 1 array that contains the energies of electronic transitions from a reference state to the excited states of the molecule, in ``cm<sup>-1</sup>``. There should be as many elements to this array as there are excited states calculated. Any type of excited state calculation should provide output that can be parsed into this attribute.
 
 etoscs
 ------
@@ -389,7 +389,7 @@ Note: For restricted calculation, ``mocoeffs`` is still a list, but it only cont
 moenergies
 ----------
 
-A list of rank 1 arrays containing the molecular orbital energies in hartree. The list is of length 1 for restricted calculations, but length 2 for unrestricted calculations.
+A list of rank 1 arrays containing the molecular orbital energies in eV. The list is of length 1 for restricted calculations, but length 2 for unrestricted calculations.
 
 **GAMESS-UK**: similar to `mocoeffs`_, the directive `FORMAT HIGH`_ needs to be used if you want all of the eigenvalues printed.
 
@@ -568,7 +568,7 @@ A list of lists where each list contains the values scanned for each parameter i
 scfenergies
 -----------
 
-An array containing the converged SCF energies of the calculation, in hartree. For an optimisation log file, there will be as many elements in this array as there were optimisation steps.
+An array containing the converged SCF energies of the calculation, in eV. For an optimisation log file, there will be as many elements in this array as there were optimisation steps.
 
 If a dispersion correction of any form was used, it is part of the SCF energy and, in the event that it is separable, such as with D3 and similar empirical corrections, it is also available separately under `dispersionenergies`_.
 

test/bridge/testpyscf.py

@@ -6,7 +6,7 @@
 from test.test_data import getdatafile
 
 from cclib.bridge import cclib2pyscf
-from cclib.parser.utils import find_package
+from cclib.parser.utils import convertor, find_package
 
 import numpy as np
 
@@ -31,7 +31,7 @@ def test_makepyscf(self) -> None:
         mhf = dft.RKS(pyscfmol)
         mhf.xc = "b3lyp"
         en = mhf.kernel()
-        assert abs(en - refen) < 5.0e-5
+        assert abs(convertor(en, "hartree", "eV") - refen) < convertor(5.0e-5, "hartree", "eV")
         # check that default basis is returned if basis is not present.
         del self.data.gbasis
         pyscfmol2 = cclib2pyscf.makepyscf(self.data)
@@ -40,15 +40,15 @@ def test_makepyscf(self) -> None:
     def test_makepyscf_mos(self) -> None:
         pyscfmol = cclib2pyscf.makepyscf(self.data)
         mo_coeff, mo_occ, mo_syms, mo_energies = cclib2pyscf.makepyscf_mos(self.data, pyscfmol)
-        assert np.allclose(mo_energies, self.data.moenergies)
+        assert np.allclose(mo_energies, convertor(np.array(self.data.moenergies), "eV", "hartree"))
         # check first MO coefficient
         assert np.allclose(mo_coeff[0][0], self.data.mocoeffs[0][0][0])
         # check a random middle MO coefficient
         assert np.allclose(mo_coeff[0][10], self.data.mocoeffs[0][10][0])
         # test unrestricted code.
         pyscfmol = cclib2pyscf.makepyscf(self.udata)
         mo_coeff, mo_occ, mo_syms, mo_energies = cclib2pyscf.makepyscf_mos(self.udata, pyscfmol)
-        assert np.allclose(mo_energies, self.udata.moenergies)
+        assert np.allclose(mo_energies, convertor(np.array(self.udata.moenergies), "eV", "hartree"))
         # check first MO coefficient
         assert np.allclose(mo_coeff[0][0][0], self.udata.mocoeffs[0][0][0])
         # check a random middle MO coefficient

test/data/testCC.py

@@ -5,6 +5,8 @@
 
 """Test coupled cluster logfiles"""
 
+from cclib.parser import utils
+
 import numpy
 import pytest
 
@@ -33,7 +35,9 @@ def testenergycc2(self, data) -> None:
         e_scf = data.scfenergies[0]
         e_cc = data.ccenergies[0]
         e_corr = e_cc - e_scf
-        assert pytest.approx(e_corr, rel=self.rel_thresh) == self.corr_energy
+        assert pytest.approx(e_corr, rel=self.rel_thresh) == utils.convertor(
+            self.corr_energy, "hartree", "eV"
+        )
 
 
 class GenericCCDTest(GenericCCTest):
@@ -45,7 +49,9 @@ def testenergyccd(self, data) -> None:
         e_scf = data.scfenergies[0]
         e_cc = data.ccenergies[0]
         e_corr = e_cc - e_scf
-        assert pytest.approx(e_corr, rel=self.rel_thresh) == self.corr_energy
+        assert pytest.approx(e_corr, rel=self.rel_thresh) == utils.convertor(
+            self.corr_energy, "hartree", "eV"
+        )
 
 
 class GenericCCSDTest(GenericCCTest):
@@ -57,7 +63,9 @@ def testenergyccsd(self, data) -> None:
         e_scf = data.scfenergies[0]
         e_cc = data.ccenergies[0]
         e_corr = e_cc - e_scf
-        assert pytest.approx(e_corr, rel=self.rel_thresh) == self.corr_energy
+        assert pytest.approx(e_corr, rel=self.rel_thresh) == utils.convertor(
+            self.corr_energy, "hartree", "eV"
+        )
 
 
 class GenericCCSDPTTest(GenericCCTest):
@@ -69,7 +77,9 @@ def testenergyccsdpt(self, data) -> None:
         e_scf = data.scfenergies[0]
         e_cc = data.ccenergies[0]
         e_corr = e_cc - e_scf
-        assert pytest.approx(e_corr, rel=self.rel_thresh) == self.corr_energy
+        assert pytest.approx(e_corr, rel=self.rel_thresh) == utils.convertor(
+            self.corr_energy, "hartree", "eV"
+        )
 
 
 class DALTONCCSDPTTest(GenericCCSDPTTest):

test/data/testGeoOpt.py

@@ -5,6 +5,8 @@
 
 """Test geometry optimization logfiles in cclib"""
 
+from cclib.parser import utils
+
 import numpy
 from common import get_minimum_carbon_separation
 from skip import skipForLogfile, skipForParser
@@ -23,8 +25,8 @@ class GenericGeoOptTest:
     extrascfs = 0
 
     # Approximate B3LYP energy of dvb after SCF in STO-3G.
-    b3lyp_energy = -380.90674109218116
-    b3lyp_tolerance = 1.4699729516340807
+    scfenergy = -380.90674109218116
+    scfenergy_tolerance = 1.4699729516340807
 
     @skipForParser("Molcas", "The parser is still being developed so we skip this test")
     @skipForParser("MOPAC", "The success status is not parsed yet")
@@ -100,11 +102,9 @@ def testscfvaluetype(self, data) -> None:
 
     def testscfenergy(self, data) -> None:
         """Is the SCF energy close to target?"""
-        scf = data.scfenergies[-1]
-        ref = self.b3lyp_energy
-        tol = self.b3lyp_tolerance
-        msg = f"Final SCF energy: {scf:f} not {int(ref)} +- {int(tol)}eV"
-        assert abs(scf - ref) < 40, msg
+        assert abs(
+            data.scfenergies[-1] - utils.convertor(self.scfenergy, "hartree", "eV")
+        ) < utils.convertor(self.scfenergy_tolerance, "hartree", "eV")
 
     @skipForParser("xTB", "Not implemented yet")
     def testscfenergydim(self, data) -> None:
@@ -231,8 +231,8 @@ class ADFGeoOptTest(GenericGeoOptTest):
     extracoords = 1
     extrascfs = 1
 
-    b3lyp_energy = -5.144905330719283
-    b3lyp_tolerance = 0.03674932379085202
+    scfenergy = -5.144905330719283
+    scfenergy_tolerance = 0.03674932379085202
 
 
 class DALTONGeoOptTest(GenericGeoOptTest):
@@ -307,8 +307,8 @@ class MOPACGeoOptTest(GenericGeoOptTest):
     """Customized geometry optimization unittest for MOPAC."""
 
     # The geometry optimization unit test logfile uses a PM7 Hamiltonian.
-    b3lyp_energy = 0.08166294233283113
-    b3lyp_tolerance = 1.6e-5
+    scfenergy = 0.08166294233283113
+    scfenergy_tolerance = 1.6e-5
 
 
 class NWChemGeoOptTest(GenericGeoOptTest):
@@ -335,7 +335,7 @@ class OrcaGeoOptTest(GenericGeoOptTest):
     #   2) gradient is overachieved and displacement is reasonable (3 x tolerance)
     #   3) displacement is overachieved and gradient is reasonable (3 x tolerance)
     #   4) energy, gradients and angles are converged (displacements not considered)
-    # All these exceptions are signaleld in the output with some comments, and here
+    # All these exceptions are signaled in the output with some comments, and here
     # we include the first three exceptions for the pruposes of the unit test.
     def testgeoconverged(self, data) -> None:
         """Has the geometry converged and set optdone to True?"""
@@ -387,9 +387,8 @@ def testgeoconverged(self, data) -> None:
 class XTBGeoOptTest(GenericGeoOptTest):
     """Customized restricted single point unittest"""
 
-    def testscfenergy(self, data) -> None:
-        """Is the SCF energy within the target?"""
-        assert abs(data.scfenergies[-1] - -26.438242468348) < 1.0e-6
+    scfenergy = -26.438242468348
+    scfenergy_tolerance = 1.0e-6
 
 
 class TurbomoleKeepGeoOptTest(GenericGeoOptTest):

test/data/testSP.py

@@ -7,6 +7,8 @@
 
 import datetime
 
+from cclib.parser import utils
+
 import numpy
 import packaging
 from common import get_minimum_carbon_separation
@@ -271,7 +273,9 @@ def testscfvaluetype(self, data) -> None:
     @skipForParser("NBO", "attribute not implemented in this version")
     def testscfenergy(self, data) -> None:
         """Is the SCF energy within the target?"""
-        assert abs(data.scfenergies[-1] - self.scfenergy) < self.scfenergy_delta
+        assert abs(
+            data.scfenergies[-1] - utils.convertor(self.scfenergy, "hartree", "eV")
+        ) < utils.convertor(self.scfenergy_delta, "hartree", "eV")
 
     @skipForParser("FChk", "Formatted Checkpoint files do not have a section for SCF convergence")
     @skipForParser("GAMESSDAT", "Scftargets probably do not exist in the file")
@@ -308,7 +312,9 @@ def testtypemoenergies(self, data) -> None:
     @skipForParser("xTB", "not implemented yet")
     def testfirstmoenergy(self, data) -> None:
         """Is the lowest energy molecular orbital within the target?"""
-        assert abs(data.moenergies[0][0] - self.moenergy) < self.moenergy_delta
+        assert abs(
+            data.moenergies[0][0] - utils.convertor(self.moenergy, "hartree", "eV")
+        ) < utils.convertor(self.moenergy_delta, "hartree", "eV")
 
     @skipForParser("DALTON", "mocoeffs not implemented yet")
     @skipForLogfile(
@@ -738,21 +744,23 @@ class TurbomoleHFSPTest(TurbomoleSPTest, GenericHFSPTest):
 class XTBSPTest(GenericSPTest):
     """Customized restricted single point unittest"""
 
-    def testscfenergy(self, data) -> None:
-        """Is the SCF energy within the target?"""
-        assert abs(data.scfenergies[-1] - -26.425939358406) < 1.0e-6
+    scfenergy = -26.425939358406
+    scfenergy_delta = 1.0e-6
 
 
 class GenericDispersionTest:
     """Generic single-geometry dispersion correction unittest"""
 
     # Q-Chem 5.4
     dispersionenergy = -0.0147199319
+    dispersionenergy_delta = 2.0e-7
 
     def testdispersionenergies(self, data) -> None:
         """Is the dispersion energy parsed correctly?"""
         assert len(data.dispersionenergies) == 1
-        assert abs(data.dispersionenergies[0] - self.dispersionenergy) < 2.0e-7
+        assert abs(
+            data.dispersionenergies[0] - utils.convertor(self.dispersionenergy, "hartree", "eV")
+        ) < utils.convertor(self.dispersionenergy_delta, "hartree", "eV")
 
 
 class FireflyDispersionTest(GenericDispersionTest):

test/data/testScan.py

@@ -41,7 +41,9 @@ def testscanenergies(self, data) -> None:
         assert isinstance(data.scanenergies, list)
 
         # This checks the order of magnitude, and unit conversion if nothing else.
-        numpy.testing.assert_array_less(numpy.array(data.scanenergies), -378)
+        numpy.testing.assert_array_less(
+            numpy.array(data.scanenergies), cclib.parser.utils.convertor(-378, "hartree", "eV")
+        )
 
     @skipForParser("ORCA", "Not implemented")
     @skipForParser("Jaguar", "Not implemented")