Orca Freq

catgo_view(action: "get_state")

curl -s http://localhost:8000/api/hpc/connections

catgo_workflow(action: "create", name: "Water frequencies B3LYP")

catgo_workflow(action: "batch", workflow_id: "<wf_id>", operations: [
  {"op": "add_node", "node_type": "freq", "label": "freq1",
   "params": {
     "software": "orca",
     "method": "B3LYP",
     "basis": "def2-SVP",
     "charge": 0,
     "multiplicity": 1,
     "extra_blocks": "%output jsongbwfile True jsonpropfile True end"
   }},
  {"op": "connect", "from_id": "<structure_input_id>", "to_id": "freq1",
   "from_handle": "structure", "to_handle": "structure"}
])

catgo_workflow(action: "batch", workflow_id: "<wf_id>", operations: [
  {"op": "add_node", "node_type": "geo_opt", "label": "opt1",
   "params": {
     "software": "orca",
     "method": "B3LYP",
     "basis": "def2-TZVP",
     "opt_convergence": "TightOpt",
     "dispersion": "D3BJ",
     "charge": 0,
     "multiplicity": 1
   }},
  {"op": "add_node", "node_type": "freq", "label": "freq1",
   "params": {
     "software": "orca",
     "method": "B3LYP",
     "basis": "def2-TZVP",
     "dispersion": "D3BJ",
     "charge": 0,
     "multiplicity": 1
   }},
  {"op": "connect", "from_id": "<structure_input_id>", "to_id": "opt1",
   "from_handle": "structure", "to_handle": "structure"},
  {"op": "connect", "from_id": "opt1", "to_id": "freq1",
   "from_handle": "structure", "to_handle": "structure"}
])

{"op": "add_node", "node_type": "gibbs_energy", "label": "gibbs1",
 "params": {"temperature": 373.15, "phase": "gas"}},
{"op": "connect", "from_id": "freq1", "to_id": "gibbs1",
 "from_handle": "frequencies", "to_handle": "frequencies"}

catgo_workflow(action: "run", workflow_id: "<wf_id>", run_config: {
  "execution_mode": "hpc",
  "default_session_id": "<expanse_session_id>",
  "base_work_dir": "/expanse/lustre/projects/sdp126/jyang25/ORCA/catgo",
  "default_job_params": {
    "nodes": 1, "ntasks": 4, "cpus_per_task": 1,
    "walltime": "00:30:00", "partition": "debug"
  },
  "cluster_configs": {
    "<expanse_session_id>": {
      "account": "sdp126",
      "partition": "debug",
      "module_loads": "module load cpu/0.17.3b\nmodule load gcc/10.2.0/npcyll4\nexport PATH=$HOME/openmpi-4.1.8/bin:$PATH\nexport LD_LIBRARY_PATH=$HOME/openmpi-4.1.8/lib:$LD_LIBRARY_PATH",
      "orca_dir": "/home/jyang25/orca_6_1_1_RRP8",
      "default_template": "<contents of server/templates/orca_generic.sh>",
      "default_job_params": {
        "nodes": 1, "ntasks": 4, "cpus_per_task": 1,
        "walltime": "00:30:00", "partition": "debug"
      }
    }
  }
})

catgo_workflow(action: "status", workflow_id: "<wf_id>")

mkdir -p ./local_run
for f in ORCA.out ORCA.hess ORCA.property.json ORCA.json; do
  curl -s -X POST http://localhost:8000/api/hpc/files/read-content \
    -H 'Content-Type: application/json' \
    -d "{\"session_id\":\"<expanse_session_id>\",\"file_path\":\"<work_dir>/$f\"}" \
    > ./local_run/$f
done

import sys
sys.path.insert(0, ".claude/skills")  # for the _shared helper
from _shared.orca_opi import parse_local

out = parse_local("./local_run")

# IR table — replaces frequencies + intensities + is_imaginary trio
ir = out.get_ir()  # dict[int, IrMode]
for mode_idx, mode in ir.items():
    print(mode_idx, mode.wavenumber, mode.intensity, mode.dipole)

# Thermochemistry (units: hartree, hartree/K)
thermo = {
    "zpe_eh":           out.get_zpe(),
    "inner_energy_eh":  out.get_inner_energy(),
    "enthalpy_eh":      out.get_enthalpy(),
    "entropy_eh_per_K": out.get_entropy(),
    "free_energy_eh":   out.get_free_energy(),
    "G_minus_Eel_eh":   out.get_free_energy_delta(),
}

# Imaginary check from the raw frequency list (negatives = imaginary)
freqs = out.results_properties.geometries[0].thermochemistry_energies[0].freq
n_imag = sum(1 for f in freqs if f < 0)
print(f"Imaginary modes: {n_imag}")

from _shared.orca_opi import quick_plot_ir, show_png
png = quick_plot_ir(out)             # writes ./local_run/ir_spectrum.png
show_png(png, "IR spectrum")         # prints `![IR spectrum](local_run/ir_spectrum.png)`