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Workflows

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 second ORCA step is a frequency job. Gibbs free energy, enthalpy, frequencies, and related values are reported only when parsed from output.

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 "c1ccccc1" --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 benzene from SMILES c1ccccc1 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.

AGAPI Materials Query

cspilot graph-run "Find all Al2O3 materials" \
  --profile auto --agent-mode multi --html --workdir runs/al2o3

This uses the materials profile when routed successfully and records AGAPI response content in JSON. It does not run local DFT.

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.