Merge pull request #1 from langner/ramon

Merge with master add add deleted test back

Author: rcrehuet

DALTON/DALTON-2015/dalton_atombasis.out

@@ -131,8 +131,29 @@ def testADF_ADF2013_01_stopiter_MoOCl4_sp_adfout(logfile):
     # len(logfile.data.scfvalues[0]) == 11
     assert not hasattr(logfile.data, "scfvalues")
 
+def testADF_ADF2016_fa2_adf_out(logfile):		
+    """This logfile, without symmetry, should get atombasis parsed."""		
+    assert hasattr(logfile.data, "atombasis")		
+    assert [b for ab in logfile.data.atombasis for b in ab] == list(range(logfile.data.nbasis))
+
 # DALTON #
 
+def testDALTON_DALTON_2015_dalton_atombasis_out(logfile):
+    """This logfile didn't parse due to the absence of a line in the basis
+    set section.
+    """
+    assert hasattr(logfile.data, "nbasis")
+    assert logfile.data.nbasis == 37
+    assert hasattr(logfile.data, "atombasis")
+
+def testDALTON_DALTON_2015_dalton_intgrl_out(logfile):
+    """This logfile didn't parse due to the absence of a line in the basis
+    set section.
+    """
+    assert hasattr(logfile.data, "nbasis")
+    assert logfile.data.nbasis == 4
+    assert hasattr(logfile.data, "atombasis")
+
 def testDALTON_DALTON_2015_stopiter_dalton_dft_out(logfile):
     """Check to ensure that an incomplete SCF is handled correctly."""
     assert len(logfile.data.scfvalues[0]) == 8
@@ -155,6 +176,18 @@ def testGAMESS_Firefly8_0_stopiter_firefly_out(logfile):
     """Check to ensure that an incomplete SCF is handled correctly."""
     assert len(logfile.data.scfvalues[0]) == 6
 
+def testGAMESS_Firefly8_1_benzene_am1_log(logfile):
+	"""Molecular orbitals were not parsed (cclib/cclib#228)."""
+	assert hasattr(logfile.data, 'mocoeffs')
+
+def testGAMESS_Firefly8_1_naphtalene_t_0_out(logfile):
+	"""Molecular orbitals were not parsed (cclib/cclib#228)."""
+	assert hasattr(logfile.data, 'mocoeffs')
+
+def testGAMESS_Firefly8_1_naphtalene_t_0_SP_out(logfile):
+	"""Molecular orbitals were not parsed (cclib/cclib#228)."""
+	assert hasattr(logfile.data, 'mocoeffs')
+
 # GAMESS #
 
 def testGAMESS_GAMESS_US2008_N2_UMP2_out(logfile):
@@ -453,16 +486,22 @@ def testMolpro_Molpro2008_ch2o_molpro_casscf_out(logfile):
     assert logfile.data.mocoeffs[0][-2][0] == 0.0
     assert logfile.data.mocoeffs[0][0][-2] == 0.0
 
+    assert isinstance(logfile.data.nocoeffs, numpy.ndarray)
+    assert isinstance(logfile.data.nooccnos, numpy.ndarray)
+    assert logfile.data.nocoeffs.shape == logfile.data.mocoeffs[0].shape
+    assert len(logfile.data.nooccnos) == logfile.data.nmo
+    assert logfile.data.nooccnos[27] == 1.95640
+
 def testMolpro_Molpro2012_CHONHSH_HF_STO_3G_out(logfile):
-	"""Formatting of the basis function is slightly different than expected."""
-	assert len(logfile.data.gbasis) == 7
-	assert len(logfile.data.gbasis[0]) == 3 # C
-	assert len(logfile.data.gbasis[1]) == 3 # N
-	assert len(logfile.data.gbasis[2]) == 3 # O
-	assert len(logfile.data.gbasis[3]) == 5 # S
-	assert len(logfile.data.gbasis[4]) == 1 # H
-	assert len(logfile.data.gbasis[5]) == 1 # H
-	assert len(logfile.data.gbasis[6]) == 1 # H
+    """Formatting of the basis function is slightly different than expected."""
+    assert len(logfile.data.gbasis) == 7
+    assert len(logfile.data.gbasis[0]) == 3 # C
+    assert len(logfile.data.gbasis[1]) == 3 # N
+    assert len(logfile.data.gbasis[2]) == 3 # O
+    assert len(logfile.data.gbasis[3]) == 5 # S
+    assert len(logfile.data.gbasis[4]) == 1 # H
+    assert len(logfile.data.gbasis[5]) == 1 # H
+    assert len(logfile.data.gbasis[6]) == 1 # H
 
 def testMolpro_Molpro2012_dvb_gopt_unconverged_out(logfile):
     """An unconverged geometry optimization to test for empty optdone (see #103 for details)."""
@@ -548,6 +587,12 @@ def testORCA_ORCA2_9_job_out(logfile):
     """
     assert all([abs(sum(v)-1.0) < 0.0001 for k, v in logfile.data.atomspins.items()])
 
+def testORCA_ORCA2_9_qmspeedtest_hf_out(logfile):
+	"""Check precision of SCF energies (cclib/cclib#210)."""
+	energy = logfile.data.scfenergies[-1]
+	expected = -17542.5188694
+	assert abs(energy - expected) < 10**-6
+
 def testORCA_ORCA3_0_dvb_gopt_unconverged_out(logfile):
     """An unconverged geometry optimization to test for empty optdone (see #103 for details)."""
     assert hasattr(logfile.data, 'optdone') and not logfile.data.optdone

DALTON/DALTON-2015/dalton_intgrl.out

@@ -33,18 +33,24 @@ ADF/ADF2013.01/stopiter_dvb_un_sp.adfout
 ADF/ADF2013.01/stopiter_dvb_un_sp_c.adfout
 ADF/ADF2013.01/stopiter_MoOCl4-sp.adfout
 ADF/ADF2014.01/dvb_gopt_b_fullscf.out
+ADF/ADF2016/fa2.adf.out
 DALTON/DALTON-2013/C_bigbasis.aug-cc-pCVQZ.out
 DALTON/DALTON-2013/b3lyp_energy_dvb_sp_nosym.out
 DALTON/DALTON-2013/dvb_sp_hf_nosym.out
 DALTON/DALTON-2013/sp_b3lyp_dvb.out
 DALTON/DALTON-2013/td_b3lyp_dvb.out
+DALTON/DALTON-2015/dalton_atombasis.out
+DALTON/DALTON-2015/dalton_intgrl.out
 DALTON/DALTON-2015/stopiter_dalton_dft.out
 DALTON/DALTON-2015/stopiter_dalton_hf.out
 GAMESS/Firefly7.1/firefly-FailStationary.out
 GAMESS/Firefly7.1/triazole_tddft_c1_b3lyp_631Gdp_sp.out
 GAMESS/Firefly8.0/dvb_gopt_a_unconverged.out
 GAMESS/Firefly8.0/h2o.log
 GAMESS/Firefly8.0/stopiter_firefly.out
+GAMESS/Firefly8.1/benzene_am1.log
+GAMESS/Firefly8.1/naphtalene_t_0.out
+GAMESS/Firefly8.1/naphtalene_t_0_SP.out
 GAMESS/GAMESS-US2003/bv6010sup1molecule_4.inp.cml_.log
 GAMESS/GAMESS-US2004/exam01.out
 GAMESS/GAMESS-US2004/ex.out
@@ -237,6 +243,7 @@ ORCA/ORCA2.8/dvb_td.out
 ORCA/ORCA2.9/job.out
 ORCA/ORCA2.9/PCB_1_122.out
 ORCA/ORCA2.9/prova.out
+ORCA/ORCA2.9/qmspeedtest_hf.out
 ORCA/ORCA3.0/benzene_td_singlets.out
 ORCA/ORCA3.0/CuI-MePY2-CH3CN_optxes.out
 ORCA/ORCA3.0/dvb_gopt_unconverged.out
@@ -267,6 +274,7 @@ QChem/QChem4.2/dvb_gopt_unconverged.out
 QChem/QChem4.2/dvb_sp_multipole_10.out
 QChem/QChem4.2/dvb_sp_omp.out
 QChem/QChem4.2/dvb_sp_unconverged.out
+QChem/QChem4.2/opt_ZZZZ_+1.000.out
 QChem/QChem4.2/print_frgm_false_opt.out
 QChem/QChem4.2/print_frgm_true_opt.out
 QChem/QChem4.2/print_frgm_false_sp.out