made hookean constraint optional

Author: Richard Tran

calculators/prediction_tools.py

@@ -74,7 +74,7 @@ def add_hookean_constraint(image, des_rt = 2., rec_rt = 1., spring_constant=7.5,
     image.set_constraint(cons)
 
 
-def cal_slab_energy(data, calc, traj_output=False, debug=False,refixed=False):
+def cal_slab_energy(data, calc, traj_output=False, debug=False,refixed=False, add_spring=True):
 
     testobj = Atoms(data.atomic_numbers, positions=data.pos, tags=data.tags, 
                     cell=data.cell.squeeze(), pbc=True)
@@ -95,9 +95,10 @@ def cal_slab_energy(data, calc, traj_output=False, debug=False,refixed=False):
             c = FixAtoms(mask=data.fixed)
             testobj.set_constraint(c)
 
-    # added spring constant to prevent massive
-    # surface reconstruction and desorption
-    add_hookean_constraint(testobj)
+    if add_spring:
+        # added spring constant to prevent massive
+        # surface reconstruction and desorption
+        add_hookean_constraint(testobj)
 
     if traj_output == True:
         os.makedirs("./trajs", exist_ok=True)
@@ -120,10 +121,10 @@ def cal_slab_energy(data, calc, traj_output=False, debug=False,refixed=False):
     return unrelax_slab_energy, relax_slab_energy, forces, pos_relaxed
 
 
-def add_info(data, calc, debug=False, traj_output=False,refixed=False):
+def add_info(data, calc, debug=False, traj_output=False,refixed=False, add_spring=True):
 
     unrelax_slab_energy, relax_slab_energy,forces, pos_relaxed = \
-    cal_slab_energy(data, calc, traj_output=traj_output, debug=debug,refixed=refixed)
+    cal_slab_energy(data, calc, traj_output=traj_output, debug=debug,refixed=refixed, add_spring=add_spring)
 
     data.y = relax_slab_energy
     data.unrelax_energy = unrelax_slab_energy
@@ -140,7 +141,7 @@ class MyThread(threading.Thread):
     max_threads = 8
     thread_limiter = threading.BoundedSemaphore(max_threads)
 
-    def __init__(self, datalist, pathname, gpus=0, debug=False, skip_ads=None,refixed=False):
+    def __init__(self, datalist, pathname, gpus=0, debug=False, skip_ads=None,refixed=False, add_spring=True):
 
         threading.Thread.__init__(self)
 
@@ -149,6 +150,7 @@ def __init__(self, datalist, pathname, gpus=0, debug=False, skip_ads=None,refixe
         self.gpus=gpus
         self.debug = debug
         self.refixed=refixed
+        self.add_spring = add_spring
 
         # Make a list of rid that have already been done and converged to be skipped
         if os.path.isfile(pathname):
@@ -182,7 +184,7 @@ def run(self):
                     continue
                 # run predictions here
                 try:
-                    data = add_info(data, calc, debug=self.debug,refixed= self.refixed)
+                    data = add_info(data, calc, debug=self.debug,refixed= self.refixed, add_spring=self.add_spring)
                 except RuntimeError:
                     continue
                 data_list_E.append(data)

calculators/run_predictions_from_lmdb.py

@@ -26,7 +26,8 @@ def read_options():
                         help="Number of GPUs available")
     parser.add_argument("-a", "--remove_ads", dest="remove_ads", type=str, default=None, 
                         help="Adsorbate to omit")
-
+    parser.add_argument("-s", "--add_spring", dest="add_spring", type=str, default=True, 
+                        help="Whether or not to add Hookean constraints")
 
     args = parser.parse_args()
 
@@ -51,7 +52,7 @@ def read_options():
                 lp = range(int(len(input_lmdb)/args.number_of_threads)*j, 
                            int(len(input_lmdb)/args.number_of_threads)*(1+j))
                 thread = MyThread([input_lmdb[ii] for ii in lp], output_lmdb, 
-                                  args.gpus, debug=args.debug, skip_ads=args.remove_ads)
+                                  args.gpus, debug=args.debug, skip_ads=args.remove_ads, add_spring=args.add_spring)
                 thread.start()
                 sys.stdout = open(os.devnull, "w")