Merge branch 'main' into feature_website

Author: lohedges

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":

bin/emle-stop

@@ -5,13 +5,17 @@ if [ -f "emle_pid.txt" ]; then
     # Get the PID.
     pid=$(cat emle_pid.txt)
 
+    # Try to kill the emle-server process.
     echo "Stopping emle-server: PID $pid"
     timeout -vk 5 10 kill $pid > /dev/null 2>&1
 
 else
     # Try to kill all of the emle-server processes.
     echo "Stopping all emle-server processes..."
-    timeout -vk 5 10 killall emle-server > /dev/null 2>&1
+    for pid in $(ps -ef | grep emle-server | grep -v grep | awk '{print $2}'); do
+        echo "Stopping emle-server: PID $pid"
+        timeout -vk 5 10 kill $pid > /dev/null 2>&1
+    done
 fi
 
 echo "Done!"

demo/demo.sh

@@ -18,4 +18,5 @@ name=emle
 sander -O -i ../$name.in -o $name.out -p ../$PARM -c ../$CRD -r $name.ncrst -x $name.nc
 
 # Stop any running emle-server processes.
+cd ..
 emle-stop

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
 

tests/conftest.py

@@ -1,8 +1,5 @@
-import os
 import pytest
 import psutil
-import shlex
-import subprocess
 
 
 @pytest.fixture(autouse=True)