Terachem reqxyz is false when NEB, version in conf.py updated, author…

… info updated

geometric/engine.py

@@ -174,7 +174,7 @@ def set_tcenv():
     os.environ['PATH'] = os.path.join(TCHome,'bin')+":"+os.environ['PATH']
     os.environ['LD_LIBRARY_PATH'] = os.path.join(TCHome,'lib')+":"+os.environ['LD_LIBRARY_PATH']
 
-def load_tcin(f_tcin):
+def load_tcin(f_tcin, reqxyz=True):
     tcdef = OrderedDict()
     tcdef['convthre'] = "3.0e-6"
     tcdef['threall'] = "1.0e-13"
@@ -183,7 +183,7 @@ def load_tcin(f_tcin):
     # tcdef['dftgrid'] = "1"
     # tcdef['precision'] = "mixed"
     # tcdef['threspdp'] = "1.0e-8"
-    tcin = edit_tcin(fin=f_tcin, options={'run':'gradient', 'keep_scr':'yes', 'scrdir':'scr'}, defaults=tcdef)
+    tcin = edit_tcin(fin=f_tcin, reqxyz=reqxyz, options={'run':'gradient', 'keep_scr':'yes', 'scrdir':'scr'}, defaults=tcdef)
     return tcin
 
 #====================================#

geometric/prepare.py

@@ -144,7 +144,7 @@ def get_molecule_engine(**kwargs):
         if engine_str == 'tera':
             logger.info("TeraChem engine selected. Expecting TeraChem input for gradient calculation.\n")
             set_tcenv()
-            tcin = load_tcin(inputf)
+            tcin = load_tcin(inputf, reqxyz=not NEB)
             # The QM-MM interface is designed on the following ideas:
             # 1) We are only optimizing the QM portion of the system
             # (until we implement fast inversion of G matrices and Hessians)
@@ -206,6 +206,8 @@ def get_molecule_engine(**kwargs):
                 M.build_topology()
             elif pdb is not None:
                 M = Molecule(pdb, radii=radii, fragment=frag)
+            elif NEB:
+                M = Molecule(kwargs.get('chain_coords'))
             else:
                 if not os.path.exists(tcin['coordinates']):
                     raise RuntimeError("TeraChem coordinate file does not exist")
@@ -378,8 +380,9 @@ def get_molecule_engine(**kwargs):
 
     if NEB:
         logger.info("\nNudged Elastic Band calculation will be performed.\n")
-        chain_coord = kwargs.get('chain_coords', None)
-        M.load_frames(chain_coord)
+        if engine_str != 'tera':
+            chain_coord = kwargs.get('chain_coords', None)
+            M.load_frames(chain_coord)
         images = kwargs.get('images', 11)
         if images > len(M):
             # HP 5/3/2023 : We can interpolate here if len(M) == 2.

geometric/tests/test_neb.py

@@ -78,8 +78,6 @@ def test_tera_hcn_neb_optimize(localizer, molecule_engine_hcn):
     """
     NEB with TeraChem
     """
-    shutil.copy2(os.path.join(datad, 'hcn_neb_input.xyz'), os.path.join(os.getcwd(), 'hcn_neb_input.xyz'))
-
     M, engine = molecule_engine_hcn('tera', 11)
 
     params = geometric.params.NEBParams(**{"optep": False, "align": False})
@@ -166,17 +164,13 @@ def test_terachem_bigchem(localizer, molecule_engine_hcn):
     """
     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_hcn('tera', 11)
 
     params = geometric.params.NEBParams(**{"align": False, "verbose": 1, "bigchem": True})
     chain = geometric.neb.ElasticBand(
         M, engine=engine, tmpdir=tempfile.mkdtemp(), params=params, plain=0
     )
 
-    os.remove('hcn_neb_input.xyz')
-
     assert chain.coordtype == "cart"
 
     final_chain, optCycle = geometric.neb.OptimizeChain(chain, engine, params)
@@ -296,9 +290,6 @@ def work_queue_cleanup(self):
     @addons.using_terachem
     @addons.using_workqueue
     def test_terachem_work_queue_neb(self, localizer, molecule_engine_hcn):
-
-        shutil.copy2(os.path.join(datad, 'hcn_neb_input.xyz'), os.path.join(os.getcwd(), 'hcn_neb_input.xyz'))
-
         M, engine = molecule_engine_hcn('tera', 11)
         params = geometric.params.NEBParams(**{"optep": False, "align": False, "verbose": 1})
         chain = geometric.neb.ElasticBand(