minor change in test_neb.py and wq command for Psi4 engine is fixed

geometric/engine.py

@@ -1451,7 +1451,7 @@ def calc_wq_new(self, coords, dirname):
         out_files = [('%s/run.out' % dirname, 'run.out'), ('%s/run.log' % dirname, 'run.log')]
         # We will assume that the number of threads on the worker is 1, as this maximizes efficiency
         # in the limit of large numbers of jobs, although it may be controlled via environment variables.
-        queue_up_src_dest(wq, 'psi4 input.dat > run.log 2>&1', in_files, out_files, verbose=False)
+        queue_up_src_dest(wq, 'psi4 input.dat run.out 2>&1', in_files, out_files, verbose=False)
 
     def number_output(self, dirname, calcNum):
         if not os.path.exists(os.path.join(dirname, 'run.out')):

geometric/tests/conftest.py

@@ -17,7 +17,7 @@
 datad = addons.datad
 
 @pytest.fixture
-def molecule_engine_neb():
+def molecule_engine_hcn_neb():
     """Return the Molecule and Engine for an NEB Calculation."""
     input_ext = {'psi4': 'psi4in', 'qchem': 'qcin', 'tera': 'tcin'}
     def get_molecule_engine(engine: str, images: int):

geometric/tests/test_neb.py

@@ -14,28 +14,28 @@
 datad = addons.datad
 exampled = addons.exampled
 
-def test_hcn_neb_input(localizer, molecule_engine_neb):
+def test_hcn_neb_input(localizer, molecule_engine_hcn_neb):
     """
     Test lengths of input chains
     """
     chain_M = geometric.molecule.Molecule(os.path.join(datad, "hcn_neb_input.xyz"))
     nimg = 7
 
-    M1, engine = molecule_engine_neb('psi4', nimg)
+    M1, engine = molecule_engine_hcn_neb('psi4', nimg)
 
     # The number of images can't exceed the maximum number of images in the input chain
-    M2, engine = molecule_engine_neb('psi4', 9999)
+    M2, engine = molecule_engine_hcn_neb('psi4', 9999)
 
     assert nimg == len(M1)
     assert len(M2) == len(chain_M)
 
 
 @addons.using_psi4
-def test_hcn_neb_optimize_1(localizer, molecule_engine_neb):
+def test_hcn_neb_optimize_1(localizer, molecule_engine_hcn_neb):
     """
     Optimize a HCN chain without alignment
     """
-    M, engine = molecule_engine_neb('psi4', 11)
+    M, engine = molecule_engine_hcn_neb('psi4', 11)
 
     params = geometric.params.NEBParams(**{"optep": True, "align": False, "verbose": 1})
     chain = geometric.neb.ElasticBand(
@@ -52,11 +52,11 @@ def test_hcn_neb_optimize_1(localizer, molecule_engine_neb):
 
 
 @addons.using_psi4
-def test_hcn_neb_optimize_2(localizer, molecule_engine_neb):
+def test_hcn_neb_optimize_2(localizer, molecule_engine_hcn_neb):
     """
     Optimize a HCN chain with alignment
     """
-    M, engine = molecule_engine_neb('psi4', 11)
+    M, engine = molecule_engine_hcn_neb('psi4', 11)
 
     # maxg and avgg are increased here to make them converge faster after the alignment
     params = geometric.params.NEBParams(**{"verbose": 1, "maxg": 3.0, "avgg": 2.0})
@@ -75,11 +75,11 @@ def test_hcn_neb_optimize_2(localizer, molecule_engine_neb):
 
 @addons.using_psi4
 @addons.using_bigchem
-def test_psi4_bigchem(localizer, molecule_engine_neb):
+def test_psi4_bigchem(localizer, molecule_engine_hcn_neb):
     """
     Optimize a HCN chain without alignment with BigChem and Psi4
     """
-    M, engine = molecule_engine_neb('psi4', 11)
+    M, engine = molecule_engine_hcn_neb('psi4', 11)
 
     params = geometric.params.NEBParams(**{"align": False, "verbose": 1, "bigchem": True})
     chain = geometric.neb.ElasticBand(
@@ -98,11 +98,11 @@ def test_psi4_bigchem(localizer, molecule_engine_neb):
 
 @addons.using_qchem
 @addons.using_bigchem
-def test_qchem_bigchem(localizer, molecule_engine_neb):
+def test_qchem_bigchem(localizer, molecule_engine_hcn_neb):
     """
     Optimize a HCN chain without alignment with BigChem and QChem
     """
-    M, engine = molecule_engine_neb('qchem', 11)
+    M, engine = molecule_engine_hcn_neb('qchem', 11)
 
     params = geometric.params.NEBParams(**{"align": False, "verbose": 1, "bigchem": True})
     chain = geometric.neb.ElasticBand(
@@ -120,13 +120,13 @@ def test_qchem_bigchem(localizer, molecule_engine_neb):
 
 @addons.using_terachem
 @addons.using_bigchem
-def test_terachem_bigchem(localizer, molecule_engine_neb):
+def test_terachem_bigchem(localizer, molecule_engine_hcn_neb):
     """
     Optimize a HCN chain without alignment with BigChem and TeraChem
     """
     shutil.copy2(os.path.join(datad, 'hcn_neb_input.xyz'), os.path.join(os.getcwd(), 'hcn_neb_input.xyz'))
 
-    M, engine = molecule_engine_neb('tera', 11)
+    M, engine = molecule_engine_hcn_neb('tera', 11)
 
     params = geometric.params.NEBParams(**{"align": False, "verbose": 1, "bigchem": True})
     chain = geometric.neb.ElasticBand(
@@ -159,8 +159,8 @@ def work_queue_cleanup(self):
 
     @addons.using_psi4
     @addons.using_workqueue
-    def test_psi4_work_queue_neb(self, localizer, molecule_engine_neb):
-        M, engine = molecule_engine_neb('psi4', 11)
+    def test_psi4_work_queue_neb(self, localizer, molecule_engine_hcn_neb):
+        M, engine = molecule_engine_hcn_neb('psi4', 11)
         params = geometric.params.NEBParams(**{"optep": True, "align": False, "verbose": 1})
         chain = geometric.neb.ElasticBand(
             M, engine=engine, tmpdir=tempfile.mkdtemp(), params=params, plain=0