update

gofee.py

@@ -155,9 +155,8 @@ class GOFEE():
                 Ei = a.get_potential_energy()
                 Fi = a.get_forces()
                 self.gpr.memory.save_data([a])
-                self.trajectory.write(a, energy=Ei, forces=Fi)
-                #self.population.add_structure(a, Ei, Fi)
-                self.population.add_structure(a)
+                self.trajectory.write(a)
+                self.population.add(a)
                 
     def run(self):
         self.initialize_search()
@@ -169,18 +168,30 @@ class GOFEE():
             relaxed_candidates = self.get_surrogate_relaxed_candidates()
 
             kappa = self.kappa
-            anew = self.select_with_acquisition(relaxed_candidates, kappa)
-            self.print_master('aq done')
-            anew = self.evaluate(anew)
-            self.print_master('sp done')
-            if self.dualpoint:
-                adp = self.get_dualpoint(anew)
-                adp = self.evaluate(adp)
-            self.print_master('dp done')
-            self.gpr.memory.save_data([anew, adp])
+            a_add = []
+            for _ in range(5):
+                try:
+                    anew = self.select_with_acquisition(relaxed_candidates, kappa)
+                    self.print_master('aq done')
+                    anew = self.evaluate(anew)
+                    a_add.append(anew)
+                    self.print_master('sp done')
+                    if self.dualpoint:
+                        adp = self.get_dualpoint(anew)
+                        adp = self.evaluate(adp)
+                        a_add.append(adp)
+                    self.print_master('dp done')
+                    break
+                except Exception as err:
+                    kappa /=2
+                    if self.master:
+                        traceback.print_exc(file=sys.stderr)
+            self.gpr.memory.save_data(a_add)
             self.counter += 1 + int(self.dualpoint)
 
             # Add structure to population
+            self.population.add(a_add)
+            """
             E = anew.get_potential_energy()
             if self.dualpoint:
                 Edp = adp.get_potential_energy()
@@ -190,8 +201,9 @@ class GOFEE():
                     self.population.add_structure(anew)
             else:
                 self.population.add_structure(anew)
-            
+            """
             if self.master:
+                print('info:', anew.info)
                 print('anew pred:', anew.info['key_value_pairs']['Epred'], anew.info['key_value_pairs']['Epred_std'])
                 print('E_true:', anew.get_potential_energy(), adp.get_potential_energy())
                 print('pop:', [a.get_potential_energy() for a in self.population.pop])

population.py

 import numpy as np
 from ase.calculators.singlepoint import SinglePointCalculator
-
+from ase import Atoms
 
 class population():
 
@@ -40,16 +40,22 @@ class population():
         for k in sorted(structures2remove)[::-1]:
             del self.pop[k]
             del self.pop_MLrelaxed[k]
-        
-    def add_structure(self, a, E=None, F=None):
+
+    def add(self, structures):
+        if isinstance(structures, Atoms):
+            self.__add_structure(structures)
+        elif isinstance(structures, list):
+            assert isinstance(structures[0], Atoms)
+            for a in structures:
+                self.__add_structure(a)
+            
+    def __add_structure(self, a):
         self.remove_duplicate_structures()
 
-        if E is None:
-            assert 'energy' in a.get_calculator().results
-            E = a.get_potential_energy()
-        if F is None:
-            assert 'forces' in a.get_calculator().results
-            F = a.get_forces()
+        assert 'energy' in a.get_calculator().results
+        E = a.get_potential_energy()
+        assert 'forces' in a.get_calculator().results
+        F = a.get_forces()
         
         if E > self.largest_energy and len(self.pop) == self.pop_size:
             return