diff --git a/.ci_support/environment-docs.yml b/.ci_support/environment-docs.yml index a51b44a2..65308618 100644 --- a/.ci_support/environment-docs.yml +++ b/.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 diff --git a/.ci_support/environment-lammps.yml b/.ci_support/environment-lammps.yml index 690f8ce6..c114249f 100644 --- a/.ci_support/environment-lammps.yml +++ b/.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 diff --git a/.ci_support/environment-notebooks.yml b/.ci_support/environment-notebooks.yml index e2f85c06..d7f2dc49 100644 --- a/.ci_support/environment-notebooks.yml +++ b/.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 diff --git a/atomistics/calculators/lammps/filecalculator.py b/atomistics/calculators/lammps/filecalculator.py index c6368165..2c1dd75b 100644 --- a/atomistics/calculators/lammps/filecalculator.py +++ b/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"], diff --git a/binder/environment.yml b/binder/environment.yml index 5e5adfe3..1c8fdc28 100644 --- a/binder/environment.yml +++ b/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 diff --git a/pyproject.toml b/pyproject.toml index 07d7fecd..8b1cd05d 100644 --- a/pyproject.toml +++ b/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",