add cell to struc (from_ase_atoms) & fix load_grid bug in mgp & repla…

…ce spc_set with 'sort'
mir-group · Jun 16, 2020 · 43dc506 · 43dc506
1 parent 941afad
commit 43dc506
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Showing 4 changed files with 9 additions and 11 deletions.
diff --git a/flare/mgp/map2b.py b/flare/mgp/map2b.py
@@ -29,12 +29,10 @@ def build_bond_struc(self, species_list):
 
         # 2 body (2 atoms (1 bond) config)
         self.spc = []
-        self.spc_set = []
         for spc1_ind, spc1 in enumerate(species_list):
             for spc2 in species_list[spc1_ind:]:
                 species = [spc1, spc2]
-                self.spc.append(species)
-                self.spc_set.append(set(species))
+                self.spc.append(sorted(species))
 
 
     def get_arrays(self, atom_env):
@@ -43,7 +41,7 @@ def get_arrays(self, atom_env):
 
     def find_map_index(self, spc):
         # use set because of permutational symmetry
-        return self.spc_set.index(set(spc))
+        return self.spc.index(sorted(spc))
 
 
 

diff --git a/flare/mgp/map3b.py b/flare/mgp/map3b.py
@@ -30,7 +30,6 @@ def build_bond_struc(self, species_list):
 
         # 2 body (2 atoms (1 bond) config)
         self.spc = []
-        self.spc_set = []
         N_spc = len(species_list)
         for spc1_ind in range(N_spc):
             spc1 = species_list[spc1_ind]
@@ -40,7 +39,6 @@ def build_bond_struc(self, species_list):
                     spc3 = species_list[spc3_ind]
                     species = [spc1, spc2, spc3]
                     self.spc.append(species)
-                    self.spc_set.append(set(species))
 
 
     def get_arrays(self, atom_env):

diff --git a/flare/mgp/mapxb.py b/flare/mgp/mapxb.py
@@ -59,7 +59,6 @@ def __init__(self,
         self.n_sample = n_sample
 
         self.spc = []
-        self.spc_set = []
         self.maps = []
         self.kernel_info = None
         self.hyps_mask = hyps_mask
@@ -170,7 +169,7 @@ def as_dict(self) -> dict:
         out_dict['bounds'] = [m.bounds for m in self.maps]
 
         # rm keys since they are built in the __init__ function
-        key_list = ['singlexbody', 'spc_set']
+        key_list = ['singlexbody', 'spc']
         for key in key_list:
             if out_dict.get(key) is not None:
                 del out_dict[key]
@@ -477,7 +476,7 @@ def build_map(self, GP):
 
             grid_path = f'{self.load_grid}/mgp_grids/{self.bodies}_{self.species_code}'
             y_mean = np.load(f'{grid_path}_mean.npy')
-            y_var = np.load(f'{grid_path}_var.npy')
+            y_var = np.load(f'{grid_path}_var.npy', allow_pickle=True)
 
         self.mean.set_values(y_mean)
         if not self.mean_only:

diff --git a/flare/struc.py b/flare/struc.py
@@ -265,15 +265,18 @@ def from_dict(dictionary: dict) -> 'flare.struc.Structure':
         return struc
 
     @staticmethod
-    def from_ase_atoms(atoms: 'ase.Atoms') -> 'flare.struc.Structure':
+    def from_ase_atoms(atoms: 'ase.Atoms', cell=None) -> 'flare.struc.Structure':
         """
         From an ASE Atoms object, return a FLARE structure
 
         :param atoms: ASE Atoms object
         :type atoms: ASE Atoms object
         :return: A FLARE structure from an ASE atoms object
         """
-        struc = Structure(cell=np.array(atoms.cell),
+
+        if cell is None:
+            cell = np.array(atoms.cell)
+        struc = Structure(cell=cell,
                           positions=atoms.positions,
                           species=atoms.get_chemical_symbols())
         return struc