Add additional file-based interface for LAMMPS (#409)

* Rename lammps interface to lammpslib * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fixes * update notebooks * rename test file * Add file based interface * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add pyiron_lammps as dependency * fix tests * remove internal print * Add new line at end of file * fix old tests * fix old tests * Add more tests * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
pyiron · Feb 24, 2025 · 5382348 · 5382348
1 parent ba274dd
commit 5382348
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diff --git a/.ci_support/environment-docs.yml b/.ci_support/environment-docs.yml
@@ -19,3 +19,4 @@ dependencies:
 - pylammpsmpi =0.2.31
 - jinja2 =3.1.5
 - jupyter-book =1.0.0
+- pyiron_lammps =0.3.2
diff --git a/.ci_support/environment-lammps.yml b/.ci_support/environment-lammps.yml
@@ -8,3 +8,4 @@ dependencies:
 - jinja2 =3.1.5
 - iprpy-data =2023.07.25
 - dynaphopy =1.17.16
+- pyiron_lammps =0.3.2
diff --git a/.ci_support/environment-notebooks.yml b/.ci_support/environment-notebooks.yml
@@ -9,3 +9,4 @@ dependencies:
 - pylammpsmpi =0.2.31
 - jinja2 =3.1.5
 - dynaphopy =1.17.16
+- pyiron_lammps =0.3.2
diff --git a/.ci_support/environment-old.yml b/.ci_support/environment-old.yml
@@ -9,8 +9,8 @@ dependencies:
 - lammps =2022.06.23
 - lxml =4.9.1
 - mendeleev =0.12.0
-- numpy =1.23.5
-- pandas =2.0.0
+- numpy =1.26.0
+- pandas =2.0.3
 - phonopy =2.20.0
 - pylammpsmpi =0.2.1
 - requests =2.24.0
@@ -19,3 +19,4 @@ dependencies:
 - spglib =2.0.2
 - structuretoolkit =0.0.10
 - tqdm =4.44.0
+- pyiron_lammps =0.3.2
diff --git a/atomistics/calculators/__init__.py b/atomistics/calculators/__init__.py
@@ -38,42 +38,42 @@
 
 try:
     from atomistics.calculators.lammps import (
-        calc_molecular_dynamics_langevin_with_lammps,
-        calc_molecular_dynamics_nph_with_lammps,
-        calc_molecular_dynamics_npt_with_lammps,
-        calc_molecular_dynamics_nvt_with_lammps,
-        calc_molecular_dynamics_thermal_expansion_with_lammps,
-        calc_static_with_lammps,
-        evaluate_with_lammps,
-        evaluate_with_lammps_library,
+        calc_molecular_dynamics_langevin_with_lammpslib,
+        calc_molecular_dynamics_nph_with_lammpslib,
+        calc_molecular_dynamics_npt_with_lammpslib,
+        calc_molecular_dynamics_nvt_with_lammpslib,
+        calc_molecular_dynamics_thermal_expansion_with_lammpslib,
+        calc_static_with_lammpslib,
+        evaluate_with_lammpslib,
+        evaluate_with_lammpslib_library_interface,
         get_potential_by_name,
         get_potential_dataframe,
-        optimize_positions_and_volume_with_lammps,
-        optimize_positions_with_lammps,
+        optimize_positions_and_volume_with_lammpslib,
+        optimize_positions_with_lammpslib,
     )
 
     __all__ += [
-        "calc_molecular_dynamics_thermal_expansion_with_lammps",
-        "calc_molecular_dynamics_nph_with_lammps",
-        "calc_molecular_dynamics_npt_with_lammps",
-        "calc_molecular_dynamics_nvt_with_lammps",
-        "calc_molecular_dynamics_langevin_with_lammps",
-        "calc_static_with_lammps",
-        "evaluate_with_lammps",
-        "evaluate_with_lammps_library",
+        "calc_molecular_dynamics_thermal_expansion_with_lammpslib",
+        "calc_molecular_dynamics_nph_with_lammpslib",
+        "calc_molecular_dynamics_npt_with_lammpslib",
+        "calc_molecular_dynamics_nvt_with_lammpslib",
+        "calc_molecular_dynamics_langevin_with_lammpslib",
+        "calc_static_with_lammpslib",
+        "evaluate_with_lammpslib",
+        "evaluate_with_lammpslib_library_interface",
         "get_potential_dataframe",
         "get_potential_by_name",
-        "optimize_positions_and_volume_with_lammps",
-        "optimize_positions_with_lammps",
+        "optimize_positions_and_volume_with_lammpslib",
+        "optimize_positions_with_lammpslib",
     ]
 except ImportError:
     pass
 
 try:
     from atomistics.calculators.lammps.phonon import (
-        calc_molecular_dynamics_phonons_with_lammps,
+        calc_molecular_dynamics_phonons_with_lammpslib,
     )
 
-    __all__ += ["calc_molecular_dynamics_phonons_with_lammps"]
+    __all__ += ["calc_molecular_dynamics_phonons_with_lammpslib"]
 except ImportError:
     pass
diff --git a/atomistics/calculators/lammps/__init__.py b/atomistics/calculators/lammps/__init__.py
@@ -1,14 +1,14 @@
-from atomistics.calculators.lammps.calculator import (
-    calc_molecular_dynamics_langevin_with_lammps,
-    calc_molecular_dynamics_nph_with_lammps,
-    calc_molecular_dynamics_npt_with_lammps,
-    calc_molecular_dynamics_nvt_with_lammps,
-    calc_molecular_dynamics_thermal_expansion_with_lammps,
-    calc_static_with_lammps,
-    evaluate_with_lammps,
-    evaluate_with_lammps_library,
-    optimize_positions_and_volume_with_lammps,
-    optimize_positions_with_lammps,
+from atomistics.calculators.lammps.libcalculator import (
+    calc_molecular_dynamics_langevin_with_lammpslib,
+    calc_molecular_dynamics_nph_with_lammpslib,
+    calc_molecular_dynamics_npt_with_lammpslib,
+    calc_molecular_dynamics_nvt_with_lammpslib,
+    calc_molecular_dynamics_thermal_expansion_with_lammpslib,
+    calc_static_with_lammpslib,
+    evaluate_with_lammpslib,
+    evaluate_with_lammpslib_library_interface,
+    optimize_positions_and_volume_with_lammpslib,
+    optimize_positions_with_lammpslib,
 )
 from atomistics.calculators.lammps.potential import (
     get_potential_by_name,
@@ -17,27 +17,27 @@
 
 try:
     from atomistics.calculators.lammps.phonon import (
-        calc_molecular_dynamics_phonons_with_lammps,
+        calc_molecular_dynamics_phonons_with_lammpslib,
     )
 
     __all__ = [
-        "calc_molecular_dynamics_phonons_with_lammps",
+        "calc_molecular_dynamics_phonons_with_lammpslib",
     ]
 except ImportError:
     __all__ = []
 
 
 __all__ += [
-    "calc_molecular_dynamics_thermal_expansion_with_lammps",
-    "calc_molecular_dynamics_nph_with_lammps",
-    "calc_molecular_dynamics_npt_with_lammps",
-    "calc_molecular_dynamics_nvt_with_lammps",
-    "calc_molecular_dynamics_langevin_with_lammps",
-    "calc_static_with_lammps",
-    "evaluate_with_lammps",
-    "evaluate_with_lammps_library",
-    "optimize_positions_and_volume_with_lammps",
-    "optimize_positions_with_lammps",
+    "calc_molecular_dynamics_thermal_expansion_with_lammpslib",
+    "calc_molecular_dynamics_nph_with_lammpslib",
+    "calc_molecular_dynamics_npt_with_lammpslib",
+    "calc_molecular_dynamics_nvt_with_lammpslib",
+    "calc_molecular_dynamics_langevin_with_lammpslib",
+    "calc_static_with_lammpslib",
+    "evaluate_with_lammpslib",
+    "evaluate_with_lammpslib_library_interface",
+    "optimize_positions_and_volume_with_lammpslib",
+    "optimize_positions_with_lammpslib",
     "get_potential_dataframe",
     "get_potential_by_name",
 ]