qcopt

Minimizations, transition-state searches, and IRCs for the qc* stack. Inputs and outputs are qcdata objects; gradients and Hessians come from axtb in-process or from any program qccompute runs.

import qcopt
from qcdata import Structure

# accuracy 0.01: at axtb's default SCF accuracy, g-xTB gradients carry ~1e-5 Eh/bohr
# of noise, the size of qcopt's convergence threshold (12% more time per gradient).
gxtb = {"program": "axtb", "model": {"method": "gxtb-v2.0.1"}, "keywords": {"accuracy": 0.01}}
guess = Structure.open("ts_guess.xyz")

ts = qcopt.find_ts(guess, gxtb, hessian=True, frequencies=True)  # ProgramOutput
ts.results.extras["n_imaginary"]                                   # 1
path = qcopt.irc(ts.results.final_structure, gxtb, hessian=True)   # ProgramOutput (PathData)

hessian names the program computing Hessians: True for the gradient program, or another one, often a cheaper method. Frames keep the gradient program's energies and gradients:

gfn2 = {"program": "axtb", "model": {"method": "gfn2"}, "keywords": {"accuracy": 0.01}}
ts = qcopt.find_ts(guess, gxtb, hessian=gfn2)   # g-xTB saddle from a GFN2 starting Hessian

Keyword arguments are qcopt's keywords (qcopt.keywords), such as maxiter, initial_hessian ("model", "exact", ...) or hessian_every.

Or as a qcdata input, alone or many at once (they advance together, and each round's gradients from all of them are computed in one call):

from qcdata import ProgramInput, ProgramSpec

inp = ProgramInput(
    program="qcopt",
    calctype="transition_state",
    structure=guess,
    keywords={"maxiter": 300},
    subprograms=[
        ProgramSpec(program="axtb", calctype="gradient", model={"method": "gxtb-v2.0.1"},
                    keywords={"accuracy": 0.01}),
        ProgramSpec(program="axtb", calctype="hessian", model={"method": "gxtb-v2.0.1"},
                    keywords={"accuracy": 0.01}),
    ],
)
out = qcopt.run(inp)            # or qcopt.run([inp1, inp2, ...])

What it does

Distances, angles and dihedrals can be held at target values (constraints), atoms frozen (frozen_atoms). Every frame is a qcdata Frame with the energy and gradient computed there.

With qccompute installed, qcopt is also a program it runs:

from qccompute import compute
out = compute(inp)   # the ProgramInput above

Benchmarks

benchmarks/ compares qcopt with Sella, geomeTRIC and OptKing on the same axtb gradients; results are summarized in AFH's findings.

Install

pip install qcopt               # or: pip install "qcopt[qccompute]" for any program qccompute runs

axtb (in-process g-xTB and GFN2-xTB with analytic Hessians) is installed from its repository until it is on PyPI.

Status

0.1: the API may still change between minor versions.

License

MIT.