Add Lammps function for backwards compatibility to pyiron_atomistics #262
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| import os | ||
| import subprocess | ||
| from typing import Optional | ||
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| from ase.atoms import Atoms | ||
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| from pyiron_lammps.compatibility.calculate import ( | ||
| calc_md, | ||
| calc_minimize, | ||
| calc_static, | ||
| ) | ||
| from pyiron_lammps.output import parse_lammps_output | ||
| from pyiron_lammps.potential import get_potential_by_name | ||
| from pyiron_lammps.structure import write_lammps_datafile | ||
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| def lammps_file_interface_function( | ||
| working_directory: str, | ||
| structure: Atoms, | ||
| potential: str, | ||
| calc_mode: str = "static", | ||
| calc_kwargs: Optional[dict] = None, | ||
| units: str = "metal", | ||
| lmp_command: str = "mpiexec -n 1 --oversubscribe lmp_mpi -in lmp.in", | ||
| resource_path: Optional[str] = None, | ||
| ): | ||
| """ | ||
| A single function to execute a LAMMPS calculation based on the LAMMPS job implemented in pyiron | ||
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| Examples: | ||
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| >>> import os | ||
| >>> from ase.build import bulk | ||
| >>> from pyiron_atomistics.lammps.lammps import lammps_function | ||
| >>> | ||
| >>> shell_output, parsed_output, job_crashed = lammps_function( | ||
| ... working_directory=os.path.abspath("lmp_working_directory"), | ||
| ... structure=bulk("Al", cubic=True), | ||
| ... potential='2009--Mendelev-M-I--Al-Mg--LAMMPS--ipr1', | ||
| ... calc_mode="md", | ||
| ... calc_kwargs={"temperature": 500.0, "pressure": 0.0, "n_ionic_steps": 1000, "n_print": 100}, | ||
| ... cutoff_radius=None, | ||
| ... units="metal", | ||
| ... bonds_kwargs={}, | ||
| ... enable_h5md=False, | ||
| ... ) | ||
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| Args: | ||
| working_directory (str): directory in which the LAMMPS calculation is executed | ||
| structure (Atoms): ase.atoms.Atoms - atomistic structure | ||
| potential (str): Name of the LAMMPS potential based on the NIST database and the OpenKIM database | ||
| calc_mode (str): select mode of calculation ["static", "md", "minimize", "vcsgc"] | ||
| calc_kwargs (dict): key-word arguments for the calculate function, the input parameters depend on the calc_mode: | ||
| "static": No parameters | ||
| "md": "temperature", "pressure", "n_ionic_steps", "time_step", "n_print", "temperature_damping_timescale", | ||
| "pressure_damping_timescale", "seed", "tloop", "initial_temperature", "langevin", "delta_temp", | ||
| "delta_press", job_name", "rotation_matrix" | ||
| "minimize": "ionic_energy_tolerance", "ionic_force_tolerance", "max_iter", "pressure", "n_print", "style", | ||
| "rotation_matrix" | ||
| "vcsgc": "mu", "ordered_element_list", "target_concentration", "kappa", "mc_step_interval", "swap_fraction", | ||
| "temperature_mc", "window_size", "window_moves", "temperature", "pressure", "n_ionic_steps", | ||
| "time_step", "n_print", "temperature_damping_timescale", "pressure_damping_timescale", "seed", | ||
| "initial_temperature", "langevin", "job_name", "rotation_matrix" | ||
| cutoff_radius (float): cut-off radius for the interatomic potential | ||
| units (str): Units for LAMMPS | ||
| bonds_kwargs (dict): key-word arguments to create atomistic bonds: | ||
| "species", "element_list", "cutoff_list", "max_bond_list", "bond_type_list", "angle_type_list", | ||
| server_kwargs (dict): key-word arguments to create server object - the available parameters are: | ||
| "user", "host", "run_mode", "queue", "qid", "cores", "threads", "new_h5", "structure_id", "run_time", | ||
| "memory_limit", "accept_crash", "additional_arguments", "gpus", "conda_environment_name", | ||
| "conda_environment_path" | ||
| enable_h5md (bool): activate h5md mode for LAMMPS | ||
| write_restart_file (bool): enable writing the LAMMPS restart file | ||
| read_restart_file (bool): enable loading the LAMMPS restart file | ||
| restart_file (str): file name of the LAMMPS restart file to copy | ||
| executable_version (str): LAMMPS version to for the execution | ||
| executable_path (str): path to the LAMMPS executable | ||
| input_control_file (str|list|dict): Option to modify the LAMMPS input file directly | ||
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There was a problem hiding this comment. 🧩 Analysis chainFunction docstring is out of sync with the actual signature and supported modes
Currently, only: (working_directory, structure, potential, calc_mode, calc_kwargs, units, lmp_command, resource_path)are accepted, and To avoid confusion for users of this new entry point:
Similarly, remove or clarify Also applies to: 87-105, 107-121 🏁 Script executed: #!/bin/bash
# Extract the function definition, docstring, and implementation
cat pyiron_lammps/compatibility/file.py | head -150 | tail -110Length of output: 5353 🏁 Script executed: #!/bin/bash
# Search for calc_mode validation and ValueError handling
rg -n -A5 -B5 'calc_mode' pyiron_lammps/compatibility/file.pyLength of output: 2890 🏁 Script executed: #!/bin/bash
# Look for parameter handling in the file (cutoff_radius, bonds_kwargs, etc.)
rg -n 'cutoff_radius|bonds_kwargs|server_kwargs|enable_h5md|restart_file|executable' pyiron_lammps/compatibility/file.pyLength of output: 793 Update docstring to match actual function signature and supported calc_modes
Similarly, the docstring lists Users following the docstring will encounter immediate errors. Either:
Also remove |
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| Returns: | ||
| str, dict, bool: Tuple consisting of the shell output (str), the parsed output (dict) and a boolean flag if | ||
| the execution raised an accepted error. | ||
| """ | ||
| if calc_kwargs is None: | ||
| calc_kwargs = {} | ||
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| os.makedirs(working_directory, exist_ok=True) | ||
| potential_dataframe = get_potential_by_name( | ||
| potential_name=potential, resource_path=resource_path | ||
| ) | ||
| lmp_str_lst = lammps_file_initialization(structure=structure) | ||
| lmp_str_lst += potential_dataframe["Config"] | ||
| lmp_str_lst += ["variable dumptime equal {} ".format(calc_kwargs.get("n_print", 1))] | ||
| lmp_str_lst += [ | ||
| "dump 1 all custom ${dumptime} dump.out id type xsu ysu zsu fx fy fz vx vy vz", | ||
| 'dump_modify 1 sort id format line "%d %d %20.15g %20.15g %20.15g %20.15g %20.15g %20.15g %20.15g %20.15g %20.15g"', | ||
| ] | ||
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There was a problem hiding this comment.
You accept
but you call: lmp_str_lst = lammps_file_initialization(structure=structure)
even if the caller requested a different unit system. This desynchronises the simulation units from the datafile/output parsing. You probably want: - lmp_str_lst = lammps_file_initialization(structure=structure)
+ lmp_str_lst = lammps_file_initialization(structure=structure, units=units)so all components (input, datafile, parsing) agree on the unit system. Also applies to: 123-124 🤖 Prompt for AI Agents |
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| if calc_mode == "static": | ||
| lmp_str_lst += calc_static() | ||
| elif calc_mode == "md": | ||
| if "n_ionic_steps" in calc_kwargs.keys(): | ||
| n_ionic_steps = int(calc_kwargs.pop("n_ionic_steps")) | ||
| else: | ||
| n_ionic_steps = 1 | ||
| calc_kwargs["units"] = units | ||
| lmp_str_lst += calc_md(**calc_kwargs) | ||
| lmp_str_lst += ["run {} ".format(n_ionic_steps)] | ||
| elif calc_mode == "minimize": | ||
| calc_kwargs["units"] = units | ||
| lmp_str_tmp_lst, structure = calc_minimize(structure=structure, **calc_kwargs) | ||
| lmp_str_lst += lmp_str_tmp_lst | ||
| else: | ||
| raise ValueError( | ||
| f"calc_mode must be one of: static, md or minimize, not {calc_mode}" | ||
| ) | ||
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| with open(os.path.join(working_directory, "lmp.in"), "w") as f: | ||
| f.writelines([l + "\n" for l in lmp_str_lst]) | ||
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| write_lammps_datafile( | ||
| structure=structure, | ||
| potential_elements=potential_dataframe["Species"], | ||
| bond_dict=None, | ||
| units=units, | ||
| file_name="lammps.data", | ||
| working_directory=working_directory, | ||
| ) | ||
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| shell = subprocess.check_output( | ||
| lmp_command, | ||
| cwd=working_directory, | ||
| shell=True, | ||
| universal_newlines=True, | ||
| env=os.environ.copy(), | ||
| ) | ||
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Comment on lines
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There was a problem hiding this comment. 🧩 Analysis chain
The function executes: shell = subprocess.check_output(
lmp_command,
cwd=working_directory,
shell=True,
universal_newlines=True,
env=os.environ.copy(),
)Using If
Given this is a low‑level interface, tightening it or documenting the expectation would be enough. I'll verify this security concern by examining the code context to determine if 🏁 Script executed: #!/bin/bash
# Examine the full function context around the subprocess call
cat pyiron_lammps/compatibility/file.py | head -150 | tail -50Length of output: 1799 🏁 Script executed: #!/bin/bash
# Get broader context of the file to understand function signature and parameters
grep -n "def " pyiron_lammps/compatibility/file.pyLength of output: 113 🏁 Script executed: #!/bin/bash
# Search for lmp_command usage and origin in the file
rg -n "lmp_command" pyiron_lammps/compatibility/file.py -B 5 -A 5Length of output: 748 🏁 Script executed: #!/bin/bash
# Check for any imports and the overall structure of this module
head -50 pyiron_lammps/compatibility/file.pyLength of output: 1609 I need to examine where this function is called to understand the actual risk profile. Length of output: 624 🏁 Script executed: #!/bin/bash
# Check if the function is exported or documented as public API
grep -r "lammps_file_interface_function" --include="*.py" --include="*.md" . 2>/dev/null | head -20Length of output: 137 🏁 Script executed: #!/bin/bash
# Look for __init__.py or __all__ exports to see if function is in public API
find . -name "__init__.py" -type f -exec grep -l "lammps_file_interface_function" {} \;Length of output: 27 Tighten The security concern is valid. Recommended fixes:
🧰 Tools🪛 Ruff (0.14.5)126-126: (S602) |
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| output = parse_lammps_output( | ||
| working_directory=working_directory, | ||
| structure=structure, | ||
| potential_elements=potential_dataframe["Species"], | ||
| units=units, | ||
| prism=None, | ||
| dump_h5_file_name="dump.h5", | ||
| dump_out_file_name="dump.out", | ||
| log_lammps_file_name="log.lammps", | ||
| ) | ||
| return shell, output, False | ||
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| def lammps_file_initialization(structure, dimension=3, units="metal"): | ||
| boundary = " ".join(["p" if coord else "f" for coord in structure.pbc]) | ||
| init_commands = [ | ||
| "units " + units, | ||
| "dimension " + str(dimension), | ||
| "boundary " + boundary + "", | ||
| "atom_style atomic", | ||
| "read_data lammps.data", | ||
| ] | ||
| return init_commands | ||
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