Merge pull request #41 from kzinovjev/emle-analyze-fix

Emle analyze fix

README.md

@@ -427,7 +427,7 @@ decomposition of the in vacuo electronic density of the QM region with
 [horton](https://theochem.github.io/horton/2.1.1/index.html). Usage:
 ```
 emle-analyze --qm-xyz qm.xyz \
-             --pc.xyz pc.xyz \
+             --pc-xyz pc.xyz \
              --emle-model model.mat \
              --orca-tarball orca.tar \
              --backend [deepmd, ani2x]
@@ -464,7 +464,7 @@ with `--deepmd-model`.
 Training of custom EMLE models can be performed with `emle-train` tool. It
 requires a tarball with the reference QM calculations with the same naming
 convention as the one for `emle-analyze` script, with the difference that only
-gas phase calculations are required and dipolar polarizabilies must be present.
+gas phase calculations are required and dipolar polarizabilities must be present.
 Simple usage:
 ```
 emle-train --orca-tarball orca.tar model.mat

bin/emle-analyze

@@ -80,11 +80,11 @@ if args.backend == "mace" and not args.mace_model:
 
 backend = None
 if args.backend == "torchani":
-    from emle._models import ANI2xEMLE
+    from emle.models import ANI2xEMLE
 
     backend = ANI2xEMLE()
 elif args.backend == "mace":
-    from emle._models import MACEEMLE
+    from emle.models import MACEEMLE
 
     backend = MACEEMLE(mace_model=args.mace_model)
 elif args.backend == "deepmd":

emle/_analyzer.py

@@ -124,7 +124,8 @@ def __init__(
         )
         self.alpha = self._get_mol_alpha(self.A_thole, self.atomic_numbers)
 
-        mesh_data = emle_base._get_mesh_data(qm_xyz_bohr, pc_xyz_bohr, self.s)
+        mask = (self.atomic_numbers > 0).unsqueeze(-1)
+        mesh_data = emle_base._get_mesh_data(qm_xyz_bohr, pc_xyz_bohr, self.s, mask)
         self.e_static = (
             emle_base.get_static_energy(
                 self.q_core, self.q_val, self.pc_charges, mesh_data
@@ -133,7 +134,7 @@ def __init__(
         )
         self.e_induced = (
             emle_base.get_induced_energy(
-                self.A_thole, self.pc_charges, self.s, mesh_data
+                self.A_thole, self.pc_charges, self.s, mesh_data, mask
             )
             * _HARTREE_TO_KCAL_MOL
         )
@@ -155,6 +156,7 @@ def __init__(
             "q_val",
             "q_total",
             "alpha",
+            "e_backend"    
             "e_static",
             "e_induced",
             "e_static_mbis",
@@ -184,7 +186,7 @@ def _parse_qm_xyz(filename):
         """
 
         atoms = _ase_io.read(filename, index=":")
-        atomic_numbers = _pad_to_max([_.get_atomic_numbers() for _ in atoms], -1)
+        atomic_numbers = _pad_to_max([_.get_atomic_numbers() for _ in atoms], 0)
         xyz = _np.array([_.get_positions() for _ in atoms])
         return atomic_numbers, xyz