[WIP] Add support for LAMMPS mliappy

calphy/helpers.py

@@ -21,20 +21,22 @@
 sarath.menon@ruhr-uni-bochum.de/yury.lysogorskiy@icams.rub.de
 """
 
-import os
-import shutil
-import warnings
 import logging
-import numpy as np
 from collections import Counter, defaultdict
 
-from pylammpsmpi import LammpsLibrary
-from lammps import lammps
-from ase.io import read, write
-
+import numpy as np
 import pyscal3.core as pc
 from pyscal3.trajectory import Trajectory
 
+from pylammpsmpi import LammpsLibrary
+
+try:
+    import lammps.mliap  # noqa: F401
+
+    has_mliap = True
+except ImportError:
+    has_mliap = False
+
 
 class LammpsScript:
     """Collect LAMMPS commands instead of executing them.
@@ -115,6 +117,11 @@ def create_object(
         if "-screen" not in cmdargs:
             cmdargs.extend(["-screen", "none"])
         lmp = LammpsLibrary(cores=cores, working_directory=directory, cmdargs=cmdargs)
+        if has_mliap:
+            if "-k" in cmdargs or "-kokkos" in cmdargs:
+                lmp.lmp.activate_mliappy_kokkos()
+            else:
+                lmp.lmp.activate_mliappy()
 
     commands = [
         ["units", "metal"],

environment-nolammps.yml

@@ -12,9 +12,9 @@ dependencies:
   - pyyaml
   - mendeleev
   - openmpi 
-  - numpy
+  - numpy >=2.0.0
   - mpi4py
-  - pylammpsmpi
+  - pylammpsmpi >0.4.1
   - matplotlib
   - tqdm
   - pydantic >=2.3.0

environment.yml

@@ -9,9 +9,9 @@ dependencies:
   - mendeleev
   - lammps
   - openmpi
-  - numpy
+  - numpy >=2.0.0
   - mpi4py
-  - pylammpsmpi
+  - pylammpsmpi >0.4.1
   - matplotlib
   - tqdm
   - pydantic >=2.3.0

pyproject.toml

@@ -31,9 +31,9 @@ dependencies = [
     "mendeleev",
     "tqdm",
     "scipy",
-    "pydantic>=2",
+    "pydantic>=2.3.0",
     "pyscal3",
-    "pylammpsmpi",
+    "pylammpsmpi>0.4.1"
 ]
 
 [project.optional-dependencies]