ase_qsm

QSM-style chain-of-states path optimizer for ASE.

ase_qsm optimizes discrete chain-of-states paths between two molecular configurations.

Installation

pip install ase_qsm

From a source checkout:

git clone https://github.com/ss0832/ase_qsm
cd ase_qsm
pip install -e ".[dev]"
pytest

Requires Python 3.10+, NumPy 1.24+, SciPy 1.10+, ASE 3.23+.

Basic example

Prepare endpoint geometries as external structure files, for example reactant.xyz and product.xyz. The two endpoint files must use the same atom count and the same atom ordering; use auto_match_atoms=True only when you intentionally want ase_qsm to reorder atoms before path construction.

from ase.io import read
from ase.calculators.emt import EMT
from ase_qsm import QSM, finalize_path

reactant = read("reactant.xyz")
product = read("product.xyz")

# Replace EMT() with the calculator appropriate for the endpoint files.
calc = EMT()

# QSM with 11 images and explicit run/report settings.
# The run-level controls mirror the examples/08 suite invocation:
#   --steps 32 --output-dir lst_reaction_suite_results --full-hessian-for none
qsm = QSM(
    images=[reactant, product],
    calculator=calc,
    n_images=11,
    fmax=0.05,
    max_iter=32,
    blend_ratio=0.5,            # 50/50 FIRE/RFO
    hessian_mode="model",       # Fischer model Hessian per node
    redistribute_interval=1,    # redistribute nodes every 1 eligible steps
    trajectory="qsm.traj",
)
qsm.run()

report = finalize_path(
    qsm,
    "results",
    refine_ts=False,
    full_hessian_for="none",
)
print("TS candidates:", report.ts_candidates)

for k, atoms in enumerate(qsm.images):
    print(f"image {k}: E = {atoms.get_potential_energy():.6f} eV")

Additional usage patterns

Endpoint-only input can omit n_images. In that case the constructor infers the initial image count from the configured pre-climb target chord and minimum image count. Replace EMT() with the calculator appropriate for the system.

from ase.io import read
from ase.calculators.emt import EMT
from ase_qsm import QSM

reactant = read("reactant.xyz")
product = read("product.xyz")

qsm = QSM([reactant, product], calculator=EMT(), fmax=0.05)
converged = qsm.run()
print("converged:", converged)
print("images:", len(qsm.images))

For a pre-built image stack, pass all images directly. The constructor then ignores n_images and interpolation.

from ase.io import read
from ase.calculators.emt import EMT
from ase_qsm import QSM

images = read("initial_path.xyz", index=":")
qsm = QSM(images, calculator=EMT(), fix_endpoints="both")
qsm.run(steps=100)

Use QSMConfig when several controls should be recorded as one object. The example below enables climbing-image selection and monitor redistribution, while keeping final reporting limited by skipping post-run Hessian and TS-refinement work.

from ase.io import read
from ase.calculators.emt import EMT
from ase_qsm import QSM, QSMConfig, finalize_path

reactant = read("reactant.xyz")
product = read("product.xyz")
calc = EMT()

cfg = QSMConfig(
    climb=True,
    climb_use_rsirfo=True,
    max_climbers=3,
    redistribute_method="monitor",
    adaptive_image_insertion=True,
    adaptive_max_images=40,
)

qsm = QSM([reactant, product], calculator=calc, config=cfg)
qsm.run()
report = finalize_path(
    qsm,
    "qsm_results",
    refine_ts=False,
    full_hessian_for="none",
)
print(report.ts_candidates)

By default, QSM.run() writes monitoring files under qsm_path_history/. Set path_history_dir=None and path_metrics_enabled=False for an in-memory-only run. If path_history_dir=None but path metrics remain enabled, the metric CSVs are written in the current working directory as qsm_path_metrics*.csv.

Three or more input structures are treated as waypoints by default. The constructor uses the waypoint polyline as a guide and resamples it to the requested or inferred total image count. This can increase or decrease the number of supplied structures.

from ase.io import read
from ase.calculators.emt import EMT
from ase_qsm import QSM

waypoints = read("waypoints.xyz", index=":")
qsm = QSM(
    waypoints,
    calculator=EMT(),
    n_images=17,                 # total images after waypoint resampling
    interpolation="lst",
    fix_endpoints="both",
)
qsm.run(steps=32)

For a pre-built image stack that should be preserved exactly, opt into image-stack mode. In this mode the constructor ignores n_images and interpolation.

from ase.io import read
from ase.calculators.emt import EMT
from ase_qsm import QSM

images = read("initial_path.xyz", index=":")
qsm = QSM(
    images,
    calculator=EMT(),
    initial_path_input_mode="images",
    fix_endpoints="both",
)
qsm.run(steps=32)

Reaction-path preset

For ordinary reaction-path searches, use the reaction_path preset rather than specifying the full set of QSM controls manually. This preset mirrors the settings used by examples/08_lst_reaction_suite.py and is intended as the main practical entry point for molecular reaction paths.

from ase.io import read
from ase.calculators.emt import EMT
from ase_qsm import QSM, QSMConfig, finalize_path

reactant = read("reactant.xyz")
product = read("product.xyz")
calc = EMT()

cfg = QSMConfig.reaction_path(
    steps=32,       # QSM iteration limit used by the reaction-suite example
    max_images=40,  # optional upper bound for adaptive image insertion
)

qsm = QSM(
    [reactant, product],
    calculator=calc,
    config=cfg,
)

qsm.run()

report = finalize_path(
    qsm,
    "results",
    refine_ts=False,
    full_hessian_for="none",
)

print("TS candidates:", report.ts_candidates)

References

• ASE: Hjorth Larsen et al., The atomic simulation environment—A Python library for working with atoms. Journal of Physics: Condensed Matter 29, 273002 (2017). DOI: 10.1088/1361-648X/aa680e

• ASE early interface paper: Bahn and Jacobsen, An object-oriented scripting interface to a legacy electronic structure code. Computing in Science & Engineering 4(3), 56–66 (2002). DOI: 10.1109/5992.998641

• Quadratic String Method: Burger and Yang, Quadratic string method for determining the minimum-energy path based on multiobjective optimization. The Journal of Chemical Physics 124(5), 054109 (2006). DOI: 10.1063/1.2163875

License

GPL-3.0-or-later. See LICENSE and NOTICE.md for details.

Copyright (C) 2026 ss0832.