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Workflows

run and graph-run now choose tools iteratively from observed outputs. The fixed workflows below remain independently callable and may be selected as one action by the agent. Decisions and observations are saved alongside results.

--multiagent adds independent child loops and deterministic reaction/conformer aggregation without changing these tools. See multi-agent and Multiwfn for supported conditions, per-child artifacts, GBW handoffs and menu maps.

xTB Optimization

cspilot xtb-opt tests/examples/input.xyz --charge 0 --uhf 0

Inputs: XYZ file, charge, UHF count.

Outputs: timestamped run directory, copied input, result.json, and xTB output files such as xtbopt.xyz when xTB succeeds.

ORCA Single Point

cspilot orca-sp tests/examples/input.xyz \
  --method r2scan-3c --basis def2-SVP --charge 0 --mult 1

Inputs: XYZ file, method, basis, charge, multiplicity.

Outputs: timestamped run directory, result.json, ORCA input/output files, and parsed properties when present in ORCA output.

xTB to ORCA Single Point

cspilot workflow xtb-orca-sp tests/examples/input.xyz \
  --charge 0 --mult 1 --method r2scan-3c --basis def2-SVP

Steps:

  1. Copy input XYZ.
  2. Run xTB optimization in 01_xtb_opt/.
  3. Use optimized XYZ for ORCA SP in 02_orca_sp/.
  4. Write workflow_result.json.

xTB to ORCA Frequency

cspilot workflow xtb-orca-freq tests/examples/input.xyz \
  --charge 0 --mult 1 --method r2scan-3c --basis def2-SVP

The ORCA stage runs Opt Freq after xTB preoptimization, so frequencies are computed at the geometry optimized with the requested ORCA method. For r2SCAN-3c the method-defined basis is used; an extra def2-SVP keyword is not added. Gibbs free energy, enthalpy, frequencies, temperature, and pressure are reported only when parsed. Verification checks optimization convergence, required thermochemistry, and significant imaginary modes (below -20 cm^-1). See the ORCA optimization/frequency example.

MACE to ORCA

cspilot workflow mace-orca tests/examples/input.xyz \
  --model /path/to/model.model --charge 0 --mult 1

Requires mace-torch and a valid MACE model. If --model is omitted, the workflow uses MACE_MODEL.

stk to xTB

cspilot stk-xtb "O" --workdir runs/stk_xtb --charge 0 --uhf 0

Steps:

  1. Build a molecule from SMILES.
  2. Export XYZ.
  3. Run xTB optimization.
  4. Save workflow_result.json.

stk to xTB to ORCA

There is no fixed deterministic stk-to-xtb-orca CLI command yet. Use the planner/graph path:

cspilot graph-run "use stk to build water from SMILES O then run xTB and ORCA single point" \
  --workdir runs/stk_orca --profile chem --agent-mode single

The planner should create an stk build step producing an XYZ, then pass that same XYZ into the xTB to ORCA workflow tool.

Result JSON Extraction

cspilot run "extract Gibbs free energy from the latest result JSON in runs/water" \
  --workdir runs/query --profile analysis

The result tools search stored JSON and return matching properties by alias. If a property is absent, reports say it was not found in parsed results.

cspilot nwpesse-search "(h2o)4Mg" \
  --workdir runs/h2o4mg --max-calculations 10 --box-size 3.0

Outputs include mol.cluster, mol.inp, external run logs, workflow_result.json, candidate XYZ files, and lowest_energy.xyz when a valid lowest-energy structure is parsed.