Merge branch 'main' into feature_website [ci skip]

Author: lohedges

.github/workflows/main.yaml

@@ -46,7 +46,7 @@ jobs:
           ref: ${{ github.event.pull_request.head.sha }}
         if: github.event_name == 'pull_request'
 #
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: conda-incubator/setup-miniconda@v3
         with:
           auto-update-conda: true
           python-version: ${{ matrix.python-version }}

.gitignore

@@ -29,3 +29,7 @@ results/
 
 # VSCode config
 .vscode/
+
+# Local test input.
+tests/input/deepmd
+tests/input/rascal

README.md

@@ -8,3 +8,5 @@
 (Mascot courtesy [Nictrain123](https://www.deviantart.com/nictrain123/art/Simply-Emily-774815887) ![CC BY 3.0](https://licensebuttons.net/l/by/3.0/80x15.png).)
 
 See the [website](https://chemle.github.io/emle-engine) for full documentation.
+
+We thank EPSRC for funding (grant code EP/V011421/1).

bin/emle-analyze

@@ -3,7 +3,7 @@
 #######################################################################
 # EMLE-Engine: https://github.com/chemle/emle-engine
 #
-# Copyright: 2023-2024
+# Copyright: 2023-2025
 #
 # Authors: Lester Hedges   <[email protected]>
 #          Kirill Zinovjev <[email protected]>
@@ -36,14 +36,19 @@ parser.add_argument(
 parser.add_argument(
     "--backend",
     type=str,
-    choices=["deepmd", "ani2x"],
-    help="Gas phase ML backend ('deepmd' or 'ani2x')",
+    choices=["torchani", "mace", "deepmd"],
+    help="Gas phase ML backend",
 )
 parser.add_argument(
     "--deepmd-model",
     type=str,
     metavar="name.pb",
-    help="Deepmd model file (for backend='deepmd')",
+    help="DeePMD model file (for backend='deepmd')",
+)
+parser.add_argument(
+    "--mace-model",
+    type=str,
+    help="MACE model file (for backend='mace')",
 )
 parser.add_argument(
     "--qm-xyz", type=str, metavar="name.xyz", required=True, help="QM xyz file"
@@ -64,19 +69,28 @@ args = parser.parse_args()
 
 import scipy.io
 
-from emle.models._emle import EMLE
+from emle.models import EMLE
+from emle._analyzer import EMLEAnalyzer
 from emle._orca_parser import ORCAParser
-from emle._analyzer import EMLEAnalyzer, ANI2xBackend, DeepMDBackend
-
 
 if args.backend == "deepmd" and not args.deepmd_model:
     parser.error("--deepmd-model is required when backend='deepmd'")
+if args.backend == "mace" and not args.mace_model:
+    parser.error("--mace-model is required when backend='mace'")
 
 backend = None
-if args.backend == "ani2x":
-    backend = ANI2xBackend()
+if args.backend == "torchani":
+    from emle._models import ANI2xEMLE
+
+    backend = ANI2xEMLE()
+elif args.backend == "mace":
+    from emle._models import MACEEMLE
+
+    backend = MACEEMLE(mace_model=args.mace_model)
 elif args.backend == "deepmd":
-    backend = DeepMDBackend(args.deepmd_model)
+    from emle._backends import DeepMD
+
+    backend = DeepMD(args.deepmd_model)
 
 emle_base = EMLE(model=args.emle_model)._emle_base
 

bin/emle-server

@@ -3,7 +3,7 @@
 #######################################################################
 # EMLE-Engine: https://github.com/chemle/emle-engine
 #
-# Copyright: 2023-2024
+# Copyright: 2023-2025
 #
 # Authors: Lester Hedges   <[email protected]>
 #          Kirill Zinovjev <[email protected]>
@@ -30,6 +30,7 @@ import time
 
 from glob import glob
 
+from emle import _supported_backends
 from emle._socket import Socket
 
 
@@ -92,6 +93,14 @@ try:
     ani2x_model_index = int(os.getenv("EMLE_ANI2X_MODEL_INDEX"))
 except:
     ani2x_model_index = None
+try:
+    mace_model = os.getenv("EMLE_MACE_MODEL")
+except:
+    mace_model = None
+try:
+    ace_model = os.getenv("EMLE_ACE_MODEL")
+except:
+    ace_model = None
 rascal_model = os.getenv("EMLE_RASCAL_MODEL")
 parm7 = os.getenv("EMLE_PARM7")
 try:
@@ -147,6 +156,8 @@ env = {
     "pc_xyz_file": pc_xyz_file,
     "qm_xyz_frequency": qm_xyz_frequency,
     "ani2x_model_index": ani2x_model_index,
+    "mace_model": mace_model,
+    "ace_model": ace_model,
     "rascal_model": rascal_model,
     "lambda_interpolate": lambda_interpolate,
     "interpolate_steps": interpolate_steps,
@@ -225,8 +236,9 @@ parser.add_argument(
 parser.add_argument(
     "--backend",
     type=str,
+    nargs="*",
     help="the in vacuo backend",
-    choices=["torchani", "deepmd", "orca", "sander", "sqm", "xtb"],
+    choices=_supported_backends,
     required=False,
 )
 parser.add_argument(
@@ -248,6 +260,24 @@ parser.add_argument(
     choices=["cpu", "cuda"],
     required=False,
 )
+parser.add_argument(
+    "--ani2x-model-index",
+    type=int,
+    help="the index of the ANI2x model to use",
+    required=False,
+)
+parser.add_argument(
+    "--mace-model",
+    type=str,
+    help="name of the MACE-OFF23 model, or path to the MACE model file",
+    required=False,
+)
+parser.add_argument(
+    "--ace-model",
+    type=str,
+    help="path to the ACE model file",
+    required=False,
+)
 parser.add_argument(
     "--deepmd-model",
     type=str,

bin/emle-train

@@ -3,7 +3,7 @@
 #######################################################################
 # EMLE-Engine: https://github.com/chemle/emle-engine
 #
-# Copyright: 2023-2024
+# Copyright: 2023-2025
 #
 # Authors: Lester Hedges   <[email protected]>
 #          Kirill Zinovjev <[email protected]>

bin/orca

@@ -3,7 +3,7 @@
 #######################################################################
 # EMLE-Engine: https://github.com/chemle/emle-engine
 #
-# Copyright: 2023-2024
+# Copyright: 2023-2025
 #
 # Authors: Lester Hedges   <[email protected]>
 #          Kirill Zinovjev <[email protected]>

emle/__init__.py

@@ -1,7 +1,7 @@
 ######################################################################
 # EMLE-Engine: https://github.com/chemle/emle-engine
 #
-# Copyright: 2023-2024
+# Copyright: 2023-2025
 #
 # Authors: Lester Hedges   <[email protected]>
 #          Kirill Zinovjev <[email protected]>
@@ -32,6 +32,19 @@
 molecular systems.
 """
 
+# List of supported backends.
+_supported_backends = [
+    "torchani",
+    "mace",
+    "ace",
+    "deepmd",
+    "orca",
+    "rascal",
+    "sqm",
+    "sander",
+    "xtb",
+]
+
 from ._version import get_versions
 
 __version__ = get_versions()["version"]