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Search and verify a transition state

Submit a TS search strategy, run strict Hessian/IRC verification and publish the result.

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Before you start

A reaction proposal UUID and a published `ts-search@1` Program.

A `search → verify → save` chain with strict transition-state verification.

Submit a transition-state (TS) search strategy for a proposed reaction. Each submission runs a 3-stage pipeline—search (ts-search@1), verify (ts-verify@1), and save (ts-save@1)—so candidate saddle points are independently checked by Hessian and IRC calculations before being saved.

1. Check prerequisites

Before submitting a TS search, make sure you have:

  1. A saved reaction proposal UUID in your project with balanced atoms, charge, and a single elementary step.
  2. Published TS Programs in your project. Check that ts-search@1 is registered:
bash
ct-cli program listct-cli program show ts-search@1

2. Submit a TS search from the CLI or Python

From the CLI, pass a reaction proposal UUID, your strategy script (see compute/ts/examples/strategy.py) and the spin multiplicity:

bash
ct-cli ts submit PROPOSAL_UUID \  --strategy compute/ts/examples/strategy.py \  --multiplicity 1 \  --wait

Or submit directly from Python for a reaction proposal UUID:

python
from pathlib import Pathfrom uuid import UUIDfrom chemistry_compute import Clientfrom chemistry_ts.submission import submit
client = Client.from_login()assert client.project_id is not None, "Run ct-cli login --project PROJECT_UUID first"
run = submit(    client,    client.project_id,    proposal_id=UUID("00000000-0000-7000-8000-000000000001"),    source=Path("compute/ts/examples/strategy.py").read_text(),    multiplicity=1,)print(run.id, run.search.id, run.verify.id, run.save.id)saved = run.result(timeout=3600)print(saved)

Key parameters:

  • proposal_id — UUID of the stored elementary reaction proposal.
  • source — Python source code of your search strategy, which defines find_ts(reactant_smiles, product_smiles, charge, multiplicity, calculator).
  • multiplicity — Spin multiplicity (1 = singlet, 2 = doublet, 3 = triplet).

3. Understand how verification works

Optimizer convergence alone never marks a transition state as verified. The 3-stage pipeline separates proposing a geometry from proving it:

StageWhat it runsOutput
1. ts-search@1Runs your strategy.py to propose a candidate TS geometryresults/candidate.json
2. ts-verify@1Computes the Hessian (1 imaginary frequency) and forward/reverse IRC endpointsresults/result.json with Hessian and IRC
3. ts-save@1Publishes the verified TS and IRC endpoints to your projectSaved calculation record

Note: If a reaction step is barrierless or the IRC connects to different species, ts-verify@1 records a scientific negative. That is a valid scientific result, not an infrastructure crash.

4. Check status and retry failed stages

Inspect all three stages of a TS run with ct-cli ts status:

bash
ct-cli ts status RUN_UUID

If verify or save fails due to a transient worker error, retry from the failed stage without re-running the upstream search:

bash
ct-cli ts retry RUN_UUID

ct-cli ts retry reuses the completed upstream artifacts and prints the new RUN_UUID for the retried chain. See Inspect and recover a run for details, Test parsers and TS strategies to benchmark a new search strategy, or Evaluate DFT energies to compute single-point DFT barriers on verified geometries.