Bump pyiron-lammps from 0.3.3 to 0.4.0 (#412)

* Bump pyiron-lammps from 0.3.3 to 0.4.0

Bumps [pyiron-lammps](https://github.com/pyiron/pyiron_lammps) from 0.3.3 to 0.4.0.
- [Release notes](https://github.com/pyiron/pyiron_lammps/releases)
- [Commits](pyiron/pyiron_lammps@pyiron_lammps-0.3.3...pyiron_lammps-0.4.0)

---
updated-dependencies:
- dependency-name: pyiron-lammps
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>

* Update environment.yml

* Update environment-docs.yml

* Update environment-lammps.yml

* Update environment-notebooks.yml

* Update filecalculator.py

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Jan Janssen <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.ci_support/environment-docs.yml

@@ -19,4 +19,4 @@ dependencies:
 - pylammpsmpi =0.2.31
 - jinja2 =3.1.5
 - jupyter-book =1.0.0
-- pyiron_lammps =0.3.3
+- pyiron_lammps =0.4.0

.ci_support/environment-lammps.yml

@@ -8,4 +8,4 @@ dependencies:
 - jinja2 =3.1.5
 - iprpy-data =2023.07.25
 - dynaphopy =1.17.16
-- pyiron_lammps =0.3.3
+- pyiron_lammps =0.4.0

.ci_support/environment-notebooks.yml

@@ -9,4 +9,4 @@ dependencies:
 - pylammpsmpi =0.2.31
 - jinja2 =3.1.5
 - dynaphopy =1.17.16
-- pyiron_lammps =0.3.3
+- pyiron_lammps =0.4.0

atomistics/calculators/lammps/filecalculator.py

@@ -3,8 +3,8 @@
 import pandas
 from ase.atoms import Atoms
 from jinja2 import Template
-from pyiron_lammps.output import parse_lammps_output as _parse_lammps_output
-from pyiron_lammps.structure import write_lammps_datafile as _write_lammps_datafile
+from pyiron_lammps import parse_lammps_output_files as _parse_lammps_output_files
+from pyiron_lammps import write_lammps_structure as _write_lammps_structure
 
 from atomistics.calculators.interface import get_quantities_from_tasks
 from atomistics.calculators.lammps.commands import (
@@ -56,13 +56,13 @@ def _lammps_file_initialization(structure):
 def _write_lammps_input_file(
     working_directory, structure, potential_dataframe, input_template
 ):
-    _write_lammps_datafile(
+    _write_lammps_structure(
         structure=structure,
-        el_eam_lst=potential_dataframe["Species"],
+        potential_elements=potential_dataframe["Species"],
         bond_dict=None,
         units="metal",
         file_name="lammps.data",
-        cwd=working_directory,
+        working_directory=working_directory,
     )
     input_str = (
         "".join(_lammps_file_initialization(structure=structure))
@@ -111,7 +111,7 @@ def optimize_positions_and_volume_with_lammpsfile(
         input_template=input_template,
     )
     executable_function(working_directory)
-    output = _parse_lammps_output(
+    output = _parse_lammps_output_files(
         working_directory=working_directory,
         structure=structure,
         potential_elements=potential_dataframe["Species"],
@@ -155,7 +155,7 @@ def optimize_positions_with_lammpsfile(
         input_template=input_template,
     )
     executable_function(working_directory)
-    output = _parse_lammps_output(
+    output = _parse_lammps_output_files(
         working_directory=working_directory,
         structure=structure,
         potential_elements=potential_dataframe["Species"],
@@ -189,7 +189,7 @@ def calc_static_with_lammpsfile(
         input_template=input_template,
     )
     executable_function(working_directory)
-    output = _parse_lammps_output(
+    output = _parse_lammps_output_files(
         working_directory=working_directory,
         structure=structure,
         potential_elements=potential_dataframe["Species"],

binder/environment.yml

@@ -15,4 +15,4 @@ dependencies:
 - jinja2 =3.1.5
 - dynaphopy =1.17.16
 - tqdm =4.67.1
-- pyiron_lammps =0.3.3
+- pyiron_lammps =0.4.0

pyproject.toml

@@ -49,14 +49,14 @@ lammps = [
     "pylammpsmpi==0.2.31",
     "jinja2==3.1.5",
     "pandas==2.2.3",
-    "pyiron_lammps==0.3.3",
+    "pyiron_lammps==0.4.0",
 ]
 lammps_phonons = [
     "pylammpsmpi==0.2.31",
     "jinja2==3.1.5",
     "pandas==2.2.3",
     "dynaphopy==1.17.16",
-    "pyiron_lammps==0.3.3",
+    "pyiron_lammps==0.4.0",
 ]
 experimental = [
     "lxml==5.3.1",