"""Deprecated legacy VASP ASE interface.
This module is kept for compatibility with older imports. New ALF workflows
should use ``alframework.qm_interfaces.ase_calculator_interface`` instead,
especially ``VASP_ase_calculator_task`` for VASP calculations through ASE.
"""
import os
import pickle as pkl
import shutil
import warnings
from contextlib import contextmanager
import numpy as np
from ase import Atoms
from ase.calculators.vasp import Vasp
[docs]
class SCFConvergenceFailure(Exception):
"""Raised when a VASP calculation finishes without SCF convergence."""
@contextmanager
def _temporary_environment(updates):
old_values = {}
for key, value in updates.items():
old_values[key] = os.environ.get(key)
if value is None:
os.environ.pop(key, None)
else:
os.environ[key] = str(value)
try:
yield
finally:
for key, value in old_values.items():
if value is None:
os.environ.pop(key, None)
else:
os.environ[key] = value
def _atoms_from_input(molecule):
if isinstance(molecule, Atoms):
return molecule.copy()
if hasattr(molecule, "get_atoms"):
return molecule.get_atoms().copy()
if hasattr(molecule, "S") and hasattr(molecule, "X"):
cell = getattr(molecule, "C", None)
pbc = cell is not None
return Atoms(molecule.S, positions=molecule.X, cell=cell, pbc=pbc)
raise TypeError("molecule must be an ase.Atoms, MoleculesObject, or legacy object with S/X attributes")
def _molecule_id(molecule):
if hasattr(molecule, "get_moleculeid"):
return molecule.get_moleculeid()
return getattr(molecule, "ids", "vasp")
[docs]
class VASPGenerator:
"""Deprecated VASP single-point helper.
Parameters are intentionally site-neutral. Provide the VASP launch command,
pseudopotential path, and any module/environment setup from the caller or
Parsl worker initialization. This class no longer constructs LANL-specific
commands or relies on MPI/GPU globals.
The legacy helper applies ALF-specific defaults before merging user
``vasp_options``: ``xc='pbe'``, ``prec='Accurate'``, ``ncore=1``,
``lreal='Auto'``, ``nelm=120``, and ``ivdw=0``. These are compatibility
defaults, not recommended settings for every VASP workflow. In particular,
review ``lreal`` when migrating old calculations or comparing forces.
"""
def __init__(
self,
vasp_options,
vasp_command=None,
scratch="./",
output_store=None,
rm_scratch=False,
vasp_pp_path=None,
environment=None,
omp_num_threads=None,
):
warnings.warn(
"VASPGenerator is deprecated. Use "
"alframework.qm_interfaces.ase_calculator_interface.VASP_ase_calculator_task "
"or ase_calculator_task for new ALF workflows.",
DeprecationWarning,
stacklevel=2,
)
self.vasp_options = vasp_options.copy()
self.vasp_command = vasp_command or self.vasp_options.pop("command", None)
self.working_dir = scratch
self.output_store = output_store
self.rm_scratch = rm_scratch
self.environment = {} if environment is None else environment.copy()
if self.vasp_command is not None:
self.environment["VASP_COMMAND"] = self.vasp_command
if vasp_pp_path is not None:
self.environment["VASP_PP_PATH"] = vasp_pp_path
if omp_num_threads is not None:
self.environment["OMP_NUM_THREADS"] = omp_num_threads
os.makedirs(self.working_dir, exist_ok=True)
if self.output_store is not None:
os.makedirs(self.output_store, exist_ok=True)
self.settings = {
"xc": "pbe",
"prec": "Accurate",
"ncore": self.vasp_options.get("ncore", 1),
"lreal": "Auto",
"nelm": self.vasp_options.get("nelm", 120),
"ivdw": self.vasp_options.get("ivdw", 0),
}
for key, val in self.vasp_options.items():
if key == "kpoints":
self.settings["kpts"] = val
elif key != "command":
self.settings[key] = val
[docs]
def get_magmom(self, atomic_no):
"""Return configured magnetic moments or a simple atomic-number default."""
if "magmom" in self.vasp_options:
return self.vasp_options["magmom"]
return np.array(atomic_no).copy()
[docs]
def single_point(self, molecule, force_calculation=False, output_file=None):
"""Run one VASP calculation through ASE.
:param molecule: ``ase.Atoms``, ``MoleculesObject``, or legacy object
with ``S`` and ``X`` attributes.
:param force_calculation: If True, include forces in the returned
properties.
:param output_file: Kept for legacy call compatibility. It is not used.
:returns: ``(atoms, properties)`` where ``atoms`` is the final
``ase.Atoms`` object and ``properties`` contains ASE-unit results.
"""
del output_file
atoms = _atoms_from_input(molecule)
molecule_id = _molecule_id(molecule)
run_dir = os.path.join(self.working_dir, str(molecule_id))
os.makedirs(run_dir, exist_ok=True)
calc = Vasp(directory=run_dir, command=self.vasp_command, **self.settings)
atoms.calc = calc
properties = {}
with _temporary_environment(self.environment):
properties["energy"] = atoms.get_potential_energy()
properties["stress"] = atoms.get_stress(voigt=False)
if force_calculation:
properties["forces"] = atoms.get_forces()
if not getattr(calc, "converged", False):
raise SCFConvergenceFailure("VASP calculation did not converge")
if self.output_store is not None:
self._copy_outputs(run_dir, molecule_id)
pkl.dump(
{"atoms": atoms.copy(), "props": properties},
open(os.path.join(self.output_store, "data-" + str(molecule_id) + ".p"), "wb"),
)
atoms.calc = None
if self.rm_scratch:
shutil.rmtree(run_dir, ignore_errors=True)
return atoms, properties
def _copy_outputs(self, run_dir, molecule_id):
for filename in ("OUTCAR", "POSCAR", "CONTCAR"):
src = os.path.join(run_dir, filename)
if os.path.exists(src):
dst = os.path.join(self.output_store, "data-" + str(molecule_id) + "." + filename)
shutil.copyfile(src, dst)