added traceback to bfgslinesearch_constrainted

bfgslinesearch_constrained.py

@@ -6,6 +6,8 @@ from ase.ga.utilities import get_mic_distance
 
 from utils import check_valid_bondlengths
 
+import traceback
+
 
 class BFGSLineSearch_constrained(BFGSLineSearch):
     def __init__(self, atoms, pos_init=None, restart=None, logfile='-', maxstep=.2,

gofee.py

@@ -185,6 +185,7 @@ class GOFEE():
             self.comm.barrier()
 
     def initialize(self):
+        self.get_initial_structures()
         self.steps = 0
 
     def get_initial_structures(self):
@@ -198,22 +199,14 @@ class GOFEE():
         they are generated by heavily rattling the supplied structures.
         """
         
-        # Collect potentially supplied structures and evaluate
-        # energies and forces if not present.
-        structures_init = []
+        # Collect potentially supplied structures.
         if self.structures is not None:
             for a in self.structures:
                 a.info = {'origin': 'PreSupplied'}
-                calc = a.get_calculator()
-                if isinstance(calc, SinglePointCalculator):
-                    if 'energy' in calc.results and 'forces' in calc.results:
-                        # Add without evaluating.
-                        structures_init.append(a)
-                        continue
-                a = self.evaluate(a)
-                structures_init.append(a)
+        else:
+            self.structures = []
         
-        Nremaining = self.Ninit - len(structures_init)
+        Nremaining = self.Ninit - len(self.structures)
         
         if Nremaining > 0 and self.startgenerator is None:
             # Initialize rattle-mutation for all atoms.
@@ -227,21 +220,33 @@ class GOFEE():
                 a = self.startgenerator.get_new_candidate()
             else:
                 # Perform two times rattle of all atoms.
-                a0 = structures_init[i % len(structures_init)]
+                a0 = self.structures[i % len(self.structures)]
                 a = rattle.get_new_candidate([a])
                 a = rattle.get_new_candidate([a])
+            self.structures.append(a)
+                
+    def evaluate_initial_structures(self):
+        structures_init = []
+        for a in self.structures:
+            calc = a.get_calculator()
+            if isinstance(calc, SinglePointCalculator):
+                if 'energy' in calc.results and 'forces' in calc.results:
+                    # Write without evaluating.
+                    structures_init.append(a)
+                    continue
             a = self.evaluate(a)
             structures_init.append(a)
-        
+
         for a in structures_init:
             self.write(a)
         self.gpr.memory.save_data(structures_init)
         self.population.add(structures_init)
-                
+
     def run(self):
         """ Method to run the search.
         """
-        self.get_initial_structures()
+        if self.steps == 0:
+            self.evaluate_initial_structures()
 
         while self.steps < self.max_steps:
             self.print_master('\n ### steps: {} ###\n'.format(self.steps))

surrogate/gpr.py

@@ -80,7 +80,7 @@ class GPR():
         if kernel is 'single':
             self.kernel = gauss_kernel()
         elif kernel is 'double':
-            self.kernel = double_gauss_kernel(Nsplit_eta=self.descriptor.Nelements_2body)
+            self.kernel = double_gauss_kernel()
         else:
             self.kernel = kernel