Examples

Examples assume CSPilot is installed and .env.cspilot is configured for any external programs being used.

Inspect XYZ

cspilot inspect tests/examples/input.xyz

LangGraph equivalent:

cspilot graph-run "inspect examples/water.xyz" --workdir runs/water

If examples/water.xyz is not present, use tests/examples/input.xyz.

Molecule Name to XYZ

Direct agent:

cspilot agent "Create an XYZ file for water at runs/water_agent/water.xyz" \
  --workdir runs/water_agent --agent-profile chem

Python deterministic call:

python -c "from cspilot.tools.mol_tools import molecule_name_to_xyz; print(molecule_name_to_xyz('water', 'runs/water.xyz'))"

xTB Optimization

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

ORCA Single Point

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

xTB to ORCA

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

Frequency workflow:

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

stk Build and xTB

cspilot stk-build-smiles "c1ccccc1" --workdir runs/stk_benzene

cspilot stk-xtb "c1ccccc1" --workdir runs/stk_xtb

Graph request:

cspilot graph-run "use stk to build benzene from SMILES c1ccccc1 and optimize with xTB" \
  --workdir runs/stk_benzene

stk to xTB to ORCA

cspilot graph-run "use stk to build benzene from SMILES c1ccccc1 then run xTB and ORCA single point" \
  --workdir runs/stk_orca

This is a planned/executed agent workflow path, not a fixed deterministic workflow subcommand.

AGAPI Materials Query

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

Result JSON Property Extraction

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

NWPESSe

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

Quiet and HTML Reports

cspilot graph-run "inspect tests/examples/input.xyz" --workdir runs/water --quiet
cspilot graph-run "Find all Al2O3 materials" --workdir runs/al2o3 --profile auto --agent-mode multi --html