| [ |
| { |
| "id": "1", |
| "category": "smiles_lookup", |
| "query": "Provide the SMILES string corresponding to this molecule: sulfur dioxide", |
| "answer": { |
| "tool_calls": [ |
| { |
| "molecule_name_to_smiles": { |
| "name": "sulfur dioxide" |
| } |
| } |
| ], |
| "result": { |
| "name": "sulfur dioxide", |
| "smiles": "O=S=O" |
| }, |
| "structured_output": { |
| "smiles": [ |
| "O=S=O" |
| ], |
| "scalar_answer": null, |
| "dipole": null, |
| "vibrational_answer": null, |
| "ir_spectrum": null, |
| "atoms_data": null |
| } |
| } |
| }, |
| { |
| "id": "2", |
| "category": "smiles_lookup", |
| "query": "Provide the SMILES string corresponding to this molecule: Nitrogen Dioxide", |
| "answer": { |
| "tool_calls": [ |
| { |
| "molecule_name_to_smiles": { |
| "name": "Nitrogen Dioxide" |
| } |
| } |
| ], |
| "result": { |
| "name": "Nitrogen Dioxide", |
| "smiles": "N(=O)[O]" |
| }, |
| "structured_output": { |
| "smiles": [ |
| "N(=O)[O]" |
| ], |
| "scalar_answer": null, |
| "dipole": null, |
| "vibrational_answer": null, |
| "ir_spectrum": null, |
| "atoms_data": null |
| } |
| } |
| }, |
| { |
| "id": "3", |
| "category": "smiles_lookup", |
| "query": "Provide the SMILES string corresponding to this molecule: water", |
| "answer": { |
| "tool_calls": [ |
| { |
| "molecule_name_to_smiles": { |
| "name": "water" |
| } |
| } |
| ], |
| "result": { |
| "name": "water", |
| "smiles": "O" |
| }, |
| "structured_output": { |
| "smiles": [ |
| "O" |
| ], |
| "scalar_answer": null, |
| "dipole": null, |
| "vibrational_answer": null, |
| "ir_spectrum": null, |
| "atoms_data": null |
| } |
| } |
| }, |
| { |
| "id": "4", |
| "category": "smiles_lookup", |
| "query": "Provide the SMILES string corresponding to this molecule: carbon dioxide", |
| "answer": { |
| "tool_calls": [ |
| { |
| "molecule_name_to_smiles": { |
| "name": "carbon dioxide" |
| } |
| } |
| ], |
| "result": { |
| "name": "carbon dioxide", |
| "smiles": "C(=O)=O" |
| }, |
| "structured_output": { |
| "smiles": [ |
| "C(=O)=O" |
| ], |
| "scalar_answer": null, |
| "dipole": null, |
| "vibrational_answer": null, |
| "ir_spectrum": null, |
| "atoms_data": null |
| } |
| } |
| }, |
| { |
| "id": "5", |
| "category": "optimization_from_name", |
| "query": "Run geometry optimization for sulfur dioxide using the mace_mp calculator with the medium-mpa-0 model. Report the optimized energy in eV.", |
| "answer": { |
| "tool_calls": [ |
| { |
| "molecule_name_to_smiles": { |
| "name": "sulfur dioxide" |
| } |
| }, |
| { |
| "smiles_to_coordinate_file": { |
| "smiles": "O=S=O" |
| } |
| }, |
| { |
| "run_ase": { |
| "params": { |
| "input_structure_file": "molecule.xyz", |
| "driver": "opt", |
| "calculator": { |
| "calculator_type": "mace_mp", |
| "model": "medium-mpa-0" |
| } |
| } |
| } |
| } |
| ], |
| "result": { |
| "status": "success", |
| "message": "Geometry optimization converged. Results saved to /var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_d4so2zji/entry_5/output.json", |
| "driver": "opt", |
| "potential_energy": -16.815808019299542, |
| "energy_unit": "eV", |
| "results_file": "/var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_d4so2zji/entry_5/output.json", |
| "converged": true, |
| "optimization_steps": 7, |
| "single_point_energy": -16.815808019299542, |
| "unit": "eV" |
| }, |
| "structured_output": { |
| "smiles": null, |
| "scalar_answer": { |
| "value": -16.815808019299542, |
| "property": "optimized energy", |
| "unit": "eV" |
| }, |
| "dipole": null, |
| "vibrational_answer": null, |
| "ir_spectrum": null, |
| "atoms_data": null |
| } |
| } |
| }, |
| { |
| "id": "6", |
| "category": "vibrations_from_name", |
| "query": "Report the vibrational frequencies of water using the mace_mp calculator with the medium-mpa-0 model. Report the frequencies in cm-1.", |
| "answer": { |
| "tool_calls": [ |
| { |
| "molecule_name_to_smiles": { |
| "name": "water" |
| } |
| }, |
| { |
| "smiles_to_coordinate_file": { |
| "smiles": "O" |
| } |
| }, |
| { |
| "run_ase": { |
| "params": { |
| "input_structure_file": "molecule.xyz", |
| "driver": "vib", |
| "calculator": { |
| "calculator_type": "mace_mp", |
| "model": "medium-mpa-0" |
| } |
| } |
| } |
| } |
| ], |
| "result": { |
| "status": "success", |
| "driver": "vib", |
| "potential_energy": -13.786081737592212, |
| "energy_unit": "eV", |
| "results_file": "/var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_d4so2zji/entry_6/output.json", |
| "converged": true, |
| "optimization_steps": 5, |
| "result": { |
| "vibrational_frequencies": { |
| "energies": [ |
| "207.53984955905088", |
| "461.69465375900324", |
| "484.0428021982815" |
| ], |
| "energy_unit": "meV", |
| "frequencies": [ |
| "1673.9217893672067", |
| "3723.81854667216", |
| "3904.0685213348656" |
| ], |
| "frequency_unit": "cm-1" |
| } |
| }, |
| "message": "Vibrational analysis completed; frequencies returned. Full results (structure, vibrations and metadata) saved to /var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_d4so2zji/entry_6/output.json." |
| }, |
| "structured_output": { |
| "smiles": null, |
| "scalar_answer": null, |
| "dipole": null, |
| "vibrational_answer": { |
| "frequency_cm1": [ |
| "1673.9217893672067", |
| "3723.81854667216", |
| "3904.0685213348656" |
| ] |
| }, |
| "ir_spectrum": null, |
| "atoms_data": null |
| } |
| } |
| }, |
| { |
| "id": "7", |
| "category": "thermochemistry_from_name", |
| "query": "Report the thermochemical properties (Gibbs free energy) of carbon dioxide at 800 K using GFN2-xTB. Report the Gibbs free energy in eV.", |
| "answer": { |
| "tool_calls": [ |
| { |
| "molecule_name_to_smiles": { |
| "name": "carbon dioxide" |
| } |
| }, |
| { |
| "smiles_to_coordinate_file": { |
| "smiles": "O=C=O" |
| } |
| }, |
| { |
| "run_ase": { |
| "params": { |
| "input_structure_file": "molecule.xyz", |
| "driver": "thermo", |
| "calculator": { |
| "calculator_type": "TBLite", |
| "method": "GFN2-xTB" |
| }, |
| "temperature": 800 |
| } |
| } |
| } |
| ], |
| "result": { |
| "status": "success", |
| "driver": "thermo", |
| "potential_energy": -280.5072746974306, |
| "energy_unit": "eV", |
| "results_file": "/var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_d4so2zji/entry_7/output.json", |
| "converged": true, |
| "optimization_steps": 4, |
| "result": { |
| "thermochemistry": { |
| "enthalpy": -279.8479687871831, |
| "entropy": 0.0026755327913969397, |
| "gibbs_free_energy": -281.9883950203007, |
| "unit": "eV" |
| } |
| }, |
| "message": "Thermochemistry computed and returned. Full results (structure, vibrations, thermochemistry and metadata) saved to /var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_d4so2zji/entry_7/output.json" |
| }, |
| "structured_output": { |
| "smiles": null, |
| "scalar_answer": { |
| "value": -281.9883950203007, |
| "property": "Gibbs free energy", |
| "unit": "eV" |
| }, |
| "dipole": null, |
| "vibrational_answer": null, |
| "ir_spectrum": null, |
| "atoms_data": null |
| } |
| } |
| }, |
| { |
| "id": "8", |
| "category": "dipole_from_name", |
| "query": "Report the dipole moment of carbon monoxide using GFN2-xTB. Report the unit in e * Angstrom.", |
| "answer": { |
| "tool_calls": [ |
| { |
| "molecule_name_to_smiles": { |
| "name": "carbon monoxide" |
| } |
| }, |
| { |
| "smiles_to_coordinate_file": { |
| "smiles": "[C-]#[O+]" |
| } |
| }, |
| { |
| "run_ase": { |
| "params": { |
| "input_structure_file": "molecule.xyz", |
| "driver": "dipole", |
| "calculator": { |
| "calculator_type": "TBLite", |
| "method": "GFN2-xTB" |
| } |
| } |
| } |
| } |
| ], |
| "result": { |
| "status": "success", |
| "message": "Dipole calculation completed. Results saved to /var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_d4so2zji/entry_8/output.json", |
| "driver": "dipole", |
| "potential_energy": -166.583990551454, |
| "energy_unit": "eV", |
| "results_file": "/var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_d4so2zji/entry_8/output.json", |
| "dipole_moment": [ |
| -0.1278, |
| -0.0, |
| -0.0 |
| ], |
| "dipole_unit": "e * Angstrom" |
| }, |
| "structured_output": { |
| "smiles": null, |
| "scalar_answer": null, |
| "dipole": { |
| "value": [ |
| -0.1278, |
| -0.0, |
| -0.0 |
| ], |
| "unit": "e * Angstrom" |
| }, |
| "vibrational_answer": null, |
| "ir_spectrum": null, |
| "atoms_data": null |
| } |
| } |
| }, |
| { |
| "id": "9", |
| "category": "energy_from_name", |
| "query": "Report the single-point energy of nitrogen using the mace_mp calculator with the medium-mpa-0 model. Report the energy in eV.", |
| "answer": { |
| "tool_calls": [ |
| { |
| "molecule_name_to_smiles": { |
| "name": "nitrogen" |
| } |
| }, |
| { |
| "smiles_to_coordinate_file": { |
| "smiles": "N#N" |
| } |
| }, |
| { |
| "run_ase": { |
| "params": { |
| "input_structure_file": "molecule.xyz", |
| "driver": "energy", |
| "calculator": { |
| "calculator_type": "mace_mp", |
| "model": "medium-mpa-0" |
| } |
| } |
| } |
| } |
| ], |
| "result": { |
| "status": "success", |
| "message": "Single-point energy calculation completed. Results saved to /var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_d4so2zji/entry_9/output.json", |
| "driver": "energy", |
| "potential_energy": -16.42796019351169, |
| "energy_unit": "eV", |
| "results_file": "/var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_d4so2zji/entry_9/output.json", |
| "single_point_energy": -16.42796019351169, |
| "unit": "eV" |
| }, |
| "structured_output": { |
| "smiles": null, |
| "scalar_answer": { |
| "value": -16.42796019351169, |
| "property": "single-point energy", |
| "unit": "eV" |
| }, |
| "dipole": null, |
| "vibrational_answer": null, |
| "ir_spectrum": null, |
| "atoms_data": null |
| } |
| } |
| }, |
| { |
| "id": "10", |
| "category": "optimization_from_name", |
| "query": "Run geometry optimization for ethene using GFN2-xTB. Report the optimized energy in eV.", |
| "answer": { |
| "tool_calls": [ |
| { |
| "molecule_name_to_smiles": { |
| "name": "ethene" |
| } |
| }, |
| { |
| "smiles_to_coordinate_file": { |
| "smiles": "C=C" |
| } |
| }, |
| { |
| "run_ase": { |
| "params": { |
| "input_structure_file": "molecule.xyz", |
| "driver": "opt", |
| "calculator": { |
| "calculator_type": "TBLite", |
| "method": "GFN2-xTB" |
| } |
| } |
| } |
| } |
| ], |
| "result": { |
| "status": "success", |
| "message": "Geometry optimization converged. Results saved to /var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_d4so2zji/entry_10/output.json", |
| "driver": "opt", |
| "potential_energy": -170.6496929174168, |
| "energy_unit": "eV", |
| "results_file": "/var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_d4so2zji/entry_10/output.json", |
| "converged": true, |
| "optimization_steps": 7, |
| "single_point_energy": -170.6496929174168, |
| "unit": "eV" |
| }, |
| "structured_output": { |
| "smiles": null, |
| "scalar_answer": { |
| "value": -170.6496929174168, |
| "property": "optimized energy", |
| "unit": "eV" |
| }, |
| "dipole": null, |
| "vibrational_answer": null, |
| "ir_spectrum": null, |
| "atoms_data": null |
| } |
| } |
| }, |
| { |
| "id": "11", |
| "category": "vibrations_from_name", |
| "query": "Report the vibrational frequencies of ethanol using GFN2-xTB. Report the frequencies in cm-1.", |
| "answer": { |
| "tool_calls": [ |
| { |
| "molecule_name_to_smiles": { |
| "name": "ethanol" |
| } |
| }, |
| { |
| "smiles_to_coordinate_file": { |
| "smiles": "CCO" |
| } |
| }, |
| { |
| "run_ase": { |
| "params": { |
| "input_structure_file": "molecule.xyz", |
| "driver": "vib", |
| "calculator": { |
| "calculator_type": "TBLite", |
| "method": "GFN2-xTB" |
| } |
| } |
| } |
| } |
| ], |
| "result": { |
| "status": "success", |
| "driver": "vib", |
| "potential_energy": -310.05574173057624, |
| "energy_unit": "eV", |
| "results_file": "/var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_d4so2zji/entry_11/output.json", |
| "converged": true, |
| "optimization_steps": 42, |
| "result": { |
| "vibrational_frequencies": { |
| "energies": [ |
| "27.79839738085244", |
| "42.20918825556391", |
| "52.10585749803795", |
| "103.03144226048957", |
| "115.54432766434203", |
| "129.5674349675032", |
| "135.1503825352714", |
| "140.1157651795237", |
| "153.1473372364309", |
| "162.92095441870595", |
| "167.31662813378034", |
| "174.18841138098236", |
| "183.86516633113928", |
| "184.71269264793014", |
| "185.6084932767352", |
| "355.6598375077792", |
| "369.8819486599839", |
| "374.1891849590782", |
| "377.5211675990512", |
| "377.96641454036194", |
| "439.2993477525251" |
| ], |
| "energy_unit": "meV", |
| "frequencies": [ |
| "224.20919733806318", |
| "340.44006528195706", |
| "420.26208655803964", |
| "831.0046314295472", |
| "931.9278592812851", |
| "1045.0318483189035", |
| "1090.0613576032051", |
| "1130.109869821071", |
| "1235.2165876977222", |
| "1314.046127167389", |
| "1349.4996269470455", |
| "1404.9242971187714", |
| "1482.9725899928867", |
| "1489.8083507961858", |
| "1497.0334701873367", |
| "2868.590070157485", |
| "2983.2991334966882", |
| "3018.039337406087", |
| "3044.913590012004", |
| "3048.504748810147", |
| "3543.1882205760453" |
| ], |
| "frequency_unit": "cm-1" |
| } |
| }, |
| "message": "Vibrational analysis completed; frequencies returned. Full results (structure, vibrations and metadata) saved to /var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_d4so2zji/entry_11/output.json." |
| }, |
| "structured_output": { |
| "smiles": null, |
| "scalar_answer": null, |
| "dipole": null, |
| "vibrational_answer": { |
| "frequency_cm1": [ |
| "224.20919733806318", |
| "340.44006528195706", |
| "420.26208655803964", |
| "831.0046314295472", |
| "931.9278592812851", |
| "1045.0318483189035", |
| "1090.0613576032051", |
| "1130.109869821071", |
| "1235.2165876977222", |
| "1314.046127167389", |
| "1349.4996269470455", |
| "1404.9242971187714", |
| "1482.9725899928867", |
| "1489.8083507961858", |
| "1497.0334701873367", |
| "2868.590070157485", |
| "2983.2991334966882", |
| "3018.039337406087", |
| "3044.913590012004", |
| "3048.504748810147", |
| "3543.1882205760453" |
| ] |
| }, |
| "ir_spectrum": null, |
| "atoms_data": null |
| } |
| } |
| }, |
| { |
| "id": "12", |
| "category": "thermochemistry_from_name", |
| "query": "Report the thermochemical properties (Gibbs free energy) of methane at 500 K using the mace_mp calculator with the medium-mpa-0 model. Report the Gibbs free energy in eV.", |
| "answer": { |
| "tool_calls": [ |
| { |
| "molecule_name_to_smiles": { |
| "name": "methane" |
| } |
| }, |
| { |
| "smiles_to_coordinate_file": { |
| "smiles": "C" |
| } |
| }, |
| { |
| "run_ase": { |
| "params": { |
| "input_structure_file": "molecule.xyz", |
| "driver": "thermo", |
| "calculator": { |
| "calculator_type": "mace_mp", |
| "model": "medium-mpa-0" |
| }, |
| "temperature": 500 |
| } |
| } |
| } |
| ], |
| "result": { |
| "status": "success", |
| "driver": "thermo", |
| "potential_energy": -23.166948941922847, |
| "energy_unit": "eV", |
| "results_file": "/var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_d4so2zji/entry_12/output.json", |
| "converged": true, |
| "optimization_steps": 3, |
| "result": { |
| "thermochemistry": { |
| "enthalpy": -21.793386183692945, |
| "entropy": 0.002150524757040044, |
| "gibbs_free_energy": -22.868648562212968, |
| "unit": "eV" |
| } |
| }, |
| "message": "Thermochemistry computed and returned. Full results (structure, vibrations, thermochemistry and metadata) saved to /var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_d4so2zji/entry_12/output.json" |
| }, |
| "structured_output": { |
| "smiles": null, |
| "scalar_answer": { |
| "value": -22.868648562212968, |
| "property": "Gibbs free energy", |
| "unit": "eV" |
| }, |
| "dipole": null, |
| "vibrational_answer": null, |
| "ir_spectrum": null, |
| "atoms_data": null |
| } |
| } |
| }, |
| { |
| "id": "13", |
| "category": "dipole_from_name", |
| "query": "Report the dipole moment of ammonia using GFN2-xTB. Report the unit in e * Angstrom.", |
| "answer": { |
| "tool_calls": [ |
| { |
| "molecule_name_to_smiles": { |
| "name": "ammonia" |
| } |
| }, |
| { |
| "smiles_to_coordinate_file": { |
| "smiles": "N" |
| } |
| }, |
| { |
| "run_ase": { |
| "params": { |
| "input_structure_file": "molecule.xyz", |
| "driver": "dipole", |
| "calculator": { |
| "calculator_type": "TBLite", |
| "method": "GFN2-xTB" |
| } |
| } |
| } |
| } |
| ], |
| "result": { |
| "status": "success", |
| "message": "Dipole calculation completed. Results saved to /var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_d4so2zji/entry_13/output.json", |
| "driver": "dipole", |
| "potential_energy": -120.3884877975335, |
| "energy_unit": "eV", |
| "results_file": "/var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_d4so2zji/entry_13/output.json", |
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| "model": "medium-mpa-0", |
| "device": "cpu", |
| "default_dtype": "float64", |
| "dispersion": false, |
| "damping": "bj", |
| "dispersion_xc": "pbe", |
| "dispersion_cutoff": 21.167088422553647 |
| }, |
| "fmax": 0.01, |
| "steps": 1000, |
| "temperature": null, |
| "pressure": 101325.0 |
| }, |
| "potential_energy": -46.24649506270807, |
| "single_point_energy": -46.24649506270807, |
| "energy_unit": "eV", |
| "dipole_value": [ |
| null, |
| null, |
| null |
| ], |
| "dipole_unit": " e * angstrom", |
| "vibrational_frequencies": {}, |
| "ir_data": {}, |
| "thermochemistry": {}, |
| "success": true, |
| "error": "", |
| "wall_time": 1.2704977989196777 |
| }, |
| "structured_output": { |
| "smiles": null, |
| "scalar_answer": { |
| "value": -46.24649506270807, |
| "property": "optimized energy", |
| "unit": "eV" |
| }, |
| "dipole": null, |
| "vibrational_answer": null, |
| "ir_spectrum": null, |
| "atoms_data": null |
| } |
| } |
| }, |
| { |
| "id": "20", |
| "category": "thermochemistry_from_name", |
| "query": "Report the thermochemical properties (Gibbs free energy) of propane at 300 K using GFN2-xTB. Report the Gibbs free energy in eV.", |
| "answer": { |
| "tool_calls": [ |
| { |
| "molecule_name_to_smiles": { |
| "name": "propane" |
| } |
| }, |
| { |
| "smiles_to_coordinate_file": { |
| "smiles": "CCC" |
| } |
| }, |
| { |
| "run_ase": { |
| "params": { |
| "input_structure_file": "molecule.xyz", |
| "driver": "thermo", |
| "calculator": { |
| "calculator_type": "TBLite", |
| "method": "GFN2-xTB" |
| }, |
| "temperature": 300 |
| } |
| } |
| }, |
| { |
| "extract_output_json": { |
| "json_file": "output.json" |
| } |
| } |
| ], |
| "result": { |
| "input_structure_file": "molecule.xyz", |
| "converged": true, |
| "final_structure": { |
| "numbers": [ |
| 6, |
| 6, |
| 6, |
| 1, |
| 1, |
| 1, |
| 1, |
| 1, |
| 1, |
| 1, |
| 1 |
| ], |
| "positions": [ |
| [ |
| 1.1836990220404633, |
| -0.44581775611645064, |
| -0.21608217898758916 |
| ], |
| [ |
| 0.013755939163534655, |
| 0.523187049693874, |
| -0.3350277970602955 |
| ], |
| [ |
| -1.193998971070771, |
| 0.054076155230239294, |
| 0.4669374481125455 |
| ], |
| [ |
| 1.4921405564582126, |
| -0.5456000103085404, |
| 0.822493984294852 |
| ], |
| [ |
| 2.034331489563804, |
| -0.09291512805474317, |
| -0.7950762275075877 |
| ], |
| [ |
| 0.9022153167897164, |
| -1.4304444860699346, |
| -0.5835196058847643 |
| ], |
| [ |
| -0.2670793256968761, |
| 0.6232475369384919, |
| -1.3858926897307557 |
| ], |
| [ |
| 0.3231291409794435, |
| 1.5085162554994642, |
| 0.020798142197863034 |
| ], |
| [ |
| -2.0168236556709362, |
| 0.7588112197659449, |
| 0.36866240378291865 |
| ], |
| [ |
| -0.9407222264084554, |
| -0.03410841244112987, |
| 1.5213603013613988 |
| ], |
| [ |
| -1.530647296148136, |
| -0.9189524341372167, |
| 0.1153462294214153 |
| ] |
| ], |
| "cell": [ |
| [ |
| 0.0, |
| 0.0, |
| 0.0 |
| ], |
| [ |
| 0.0, |
| 0.0, |
| 0.0 |
| ], |
| [ |
| 0.0, |
| 0.0, |
| 0.0 |
| ] |
| ], |
| "pbc": [ |
| false, |
| false, |
| false |
| ] |
| }, |
| "simulation_input": { |
| "input_structure_file": "molecule.xyz", |
| "output_results_file": "output.json", |
| "driver": "thermo", |
| "optimizer": "bfgs", |
| "calculator": { |
| "calculator_type": "TBLite", |
| "method": "GFN2-xTB", |
| "charge": null, |
| "multiplicity": null, |
| "accuracy": 1.0, |
| "electronic_temperature": 300.0, |
| "max_iterations": 250, |
| "initial_guess": "sad", |
| "mixer_damping": 0.4, |
| "electric_field": null, |
| "spin_polarization": null, |
| "cache_api": true, |
| "verbosity": 0 |
| }, |
| "fmax": 0.01, |
| "steps": 1000, |
| "temperature": 300.0, |
| "pressure": 101325.0 |
| }, |
| "potential_energy": -285.74204449105764, |
| "single_point_energy": -285.74204449105764, |
| "energy_unit": "eV", |
| "dipole_value": [ |
| null, |
| null, |
| null |
| ], |
| "dipole_unit": " e * angstrom", |
| "vibrational_frequencies": { |
| "energies": [ |
| "25.672748385887864", |
| "31.767145002963083", |
| "46.29971900110429", |
| "98.28573698682752", |
| "115.0812838269321", |
| "115.92647077262373", |
| "118.10590256733789", |
| "138.50928706464754", |
| "144.7858997983338", |
| "149.67230610087833", |
| "157.82018744745008", |
| "166.80551805921144", |
| "175.16494251935248", |
| "176.13314007842217", |
| "185.77408646726374", |
| "185.9299342446661", |
| "186.5205580971136", |
| "187.104441349465", |
| "187.34686647797358", |
| "368.00681863751487", |
| "369.7634973112615", |
| "375.3253945728226", |
| "375.38396564942155", |
| "375.9583635959367", |
| "376.2110576732755", |
| "376.53909735137614", |
| "376.66719154015556" |
| ], |
| "energy_unit": "meV", |
| "frequencies": [ |
| "207.06468183042665", |
| "256.2193059281249", |
| "373.4324210130828", |
| "792.7279367110348", |
| "928.1931588345058", |
| "935.0100513372606", |
| "952.5883543829785", |
| "1117.1527498927962", |
| "1167.7770460974036", |
| "1207.1885711558878", |
| "1272.9056667025163", |
| "1345.3772461493154", |
| "1412.8005519873486", |
| "1420.6095920053613", |
| "1498.369069352439", |
| "1499.6260664591275", |
| "1504.3897691313248", |
| "1509.099105196828", |
| "1511.0543957386824", |
| "2968.1751897857507", |
| "2982.34375893114", |
| "3027.203486044414", |
| "3027.675893640131", |
| "3032.3087255540136", |
| "3034.3468407545406", |
| "3036.9926592135803", |
| "3038.0258085299392" |
| ], |
| "frequency_unit": "cm-1" |
| }, |
| "ir_data": {}, |
| "thermochemistry": { |
| "enthalpy": -282.7983244265667, |
| "entropy": 0.00278986333212324, |
| "gibbs_free_energy": -283.63528342620367, |
| "unit": "eV" |
| }, |
| "success": true, |
| "error": "", |
| "wall_time": 0.7957310676574707 |
| }, |
| "structured_output": { |
| "smiles": null, |
| "scalar_answer": { |
| "value": -283.63528342620367, |
| "property": "Gibbs free energy", |
| "unit": "eV" |
| }, |
| "dipole": null, |
| "vibrational_answer": null, |
| "ir_spectrum": null, |
| "atoms_data": null |
| } |
| } |
| }, |
| { |
| "id": "21", |
| "category": "optimization_from_smiles", |
| "query": "Run geometry optimization using the mace_mp calculator with the medium-mpa-0 model for the molecule with SMILES: O=S=O. Report the optimized energy in eV.", |
| "answer": { |
| "tool_calls": [ |
| { |
| "smiles_to_coordinate_file": { |
| "smiles": "O=S=O" |
| } |
| }, |
| { |
| "run_ase": { |
| "params": { |
| "input_structure_file": "molecule.xyz", |
| "driver": "opt", |
| "calculator": { |
| "calculator_type": "mace_mp", |
| "model": "medium-mpa-0" |
| } |
| } |
| } |
| } |
| ], |
| "result": { |
| "status": "success", |
| "message": "Geometry optimization converged. Results saved to /var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_d4so2zji/entry_21/output.json", |
| "driver": "opt", |
| "potential_energy": -16.815808019299542, |
| "energy_unit": "eV", |
| "results_file": "/var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_d4so2zji/entry_21/output.json", |
| "converged": true, |
| "optimization_steps": 7, |
| "single_point_energy": -16.815808019299542, |
| "unit": "eV" |
| }, |
| "structured_output": { |
| "smiles": null, |
| "scalar_answer": { |
| "value": -16.815808019299542, |
| "property": "optimized energy", |
| "unit": "eV" |
| }, |
| "dipole": null, |
| "vibrational_answer": null, |
| "ir_spectrum": null, |
| "atoms_data": null |
| } |
| } |
| }, |
| { |
| "id": "22", |
| "category": "vibrations_from_smiles", |
| "query": "Report the vibrational frequencies using the mace_mp calculator with the medium-mpa-0 model for the molecule with SMILES: O. Report the frequencies in cm-1.", |
| "answer": { |
| "tool_calls": [ |
| { |
| "smiles_to_coordinate_file": { |
| "smiles": "O" |
| } |
| }, |
| { |
| "run_ase": { |
| "params": { |
| "input_structure_file": "molecule.xyz", |
| "driver": "vib", |
| "calculator": { |
| "calculator_type": "mace_mp", |
| "model": "medium-mpa-0" |
| } |
| } |
| } |
| } |
| ], |
| "result": { |
| "status": "success", |
| "driver": "vib", |
| "potential_energy": -13.786081737592212, |
| "energy_unit": "eV", |
| "results_file": "/var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_d4so2zji/entry_22/output.json", |
| "converged": true, |
| "optimization_steps": 5, |
| "result": { |
| "vibrational_frequencies": { |
| "energies": [ |
| "207.53984955905088", |
| "461.69465375900324", |
| "484.0428021982815" |
| ], |
| "energy_unit": "meV", |
| "frequencies": [ |
| "1673.9217893672067", |
| "3723.81854667216", |
| "3904.0685213348656" |
| ], |
| "frequency_unit": "cm-1" |
| } |
| }, |
| "message": "Vibrational analysis completed; frequencies returned. Full results (structure, vibrations and metadata) saved to /var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_d4so2zji/entry_22/output.json." |
| }, |
| "structured_output": { |
| "smiles": null, |
| "scalar_answer": null, |
| "dipole": null, |
| "vibrational_answer": { |
| "frequency_cm1": [ |
| "1673.9217893672067", |
| "3723.81854667216", |
| "3904.0685213348656" |
| ] |
| }, |
| "ir_spectrum": null, |
| "atoms_data": null |
| } |
| } |
| }, |
| { |
| "id": "23", |
| "category": "thermochemistry_from_smiles", |
| "query": "Report the thermochemical properties (Gibbs free energy) at 800 K using GFN2-xTB for the molecule with SMILES: O=C=O. Report the Gibbs free energy in eV.", |
| "answer": { |
| "tool_calls": [ |
| { |
| "smiles_to_coordinate_file": { |
| "smiles": "O=C=O" |
| } |
| }, |
| { |
| "run_ase": { |
| "params": { |
| "input_structure_file": "molecule.xyz", |
| "driver": "thermo", |
| "calculator": { |
| "calculator_type": "TBLite", |
| "method": "GFN2-xTB" |
| }, |
| "temperature": 800 |
| } |
| } |
| } |
| ], |
| "result": { |
| "status": "success", |
| "driver": "thermo", |
| "potential_energy": -280.5072746974304, |
| "energy_unit": "eV", |
| "results_file": "/var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_d4so2zji/entry_23/output.json", |
| "converged": true, |
| "optimization_steps": 4, |
| "result": { |
| "thermochemistry": { |
| "enthalpy": -279.8479687871829, |
| "entropy": 0.002675532791396939, |
| "gibbs_free_energy": -281.9883950203004, |
| "unit": "eV" |
| } |
| }, |
| "message": "Thermochemistry computed and returned. Full results (structure, vibrations, thermochemistry and metadata) saved to /var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_d4so2zji/entry_23/output.json" |
| }, |
| "structured_output": { |
| "smiles": null, |
| "scalar_answer": { |
| "value": -281.9883950203004, |
| "property": "Gibbs free energy", |
| "unit": "eV" |
| }, |
| "dipole": null, |
| "vibrational_answer": null, |
| "ir_spectrum": null, |
| "atoms_data": null |
| } |
| } |
| }, |
| { |
| "id": "24", |
| "category": "dipole_from_smiles", |
| "query": "Report the dipole moment using GFN2-xTB for the molecule with SMILES: [C-]#[O+]. Report the unit in e * Angstrom.", |
| "answer": { |
| "tool_calls": [ |
| { |
| "smiles_to_coordinate_file": { |
| "smiles": "[C-]#[O+]" |
| } |
| }, |
| { |
| "run_ase": { |
| "params": { |
| "input_structure_file": "molecule.xyz", |
| "driver": "dipole", |
| "calculator": { |
| "calculator_type": "TBLite", |
| "method": "GFN2-xTB" |
| } |
| } |
| } |
| } |
| ], |
| "result": { |
| "status": "success", |
| "message": "Dipole calculation completed. Results saved to /var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_d4so2zji/entry_24/output.json", |
| "driver": "dipole", |
| "potential_energy": -166.58399055145404, |
| "energy_unit": "eV", |
| "results_file": "/var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_d4so2zji/entry_24/output.json", |
| "dipole_moment": [ |
| -0.1278, |
| -0.0, |
| -0.0 |
| ], |
| "dipole_unit": "e * Angstrom" |
| }, |
| "structured_output": { |
| "smiles": null, |
| "scalar_answer": null, |
| "dipole": { |
| "value": [ |
| -0.1278, |
| -0.0, |
| -0.0 |
| ], |
| "unit": "e * Angstrom" |
| }, |
| "vibrational_answer": null, |
| "ir_spectrum": null, |
| "atoms_data": null |
| } |
| } |
| }, |
| { |
| "id": "25", |
| "category": "energy_from_smiles", |
| "query": "Report the single-point energy using the mace_mp calculator with the medium-mpa-0 model for the molecule with SMILES: N#N. Report the energy in eV.", |
| "answer": { |
| "tool_calls": [ |
| { |
| "smiles_to_coordinate_file": { |
| "smiles": "N#N" |
| } |
| }, |
| { |
| "run_ase": { |
| "params": { |
| "input_structure_file": "molecule.xyz", |
| "driver": "energy", |
| "calculator": { |
| "calculator_type": "mace_mp", |
| "model": "medium-mpa-0" |
| } |
| } |
| } |
| } |
| ], |
| "result": { |
| "status": "success", |
| "message": "Single-point energy calculation completed. Results saved to /var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_d4so2zji/entry_25/output.json", |
| "driver": "energy", |
| "potential_energy": -16.42796019351169, |
| "energy_unit": "eV", |
| "results_file": "/var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_d4so2zji/entry_25/output.json", |
| "single_point_energy": -16.42796019351169, |
| "unit": "eV" |
| }, |
| "structured_output": { |
| "smiles": null, |
| "scalar_answer": { |
| "value": -16.42796019351169, |
| "property": "single-point energy", |
| "unit": "eV" |
| }, |
| "dipole": null, |
| "vibrational_answer": null, |
| "ir_spectrum": null, |
| "atoms_data": null |
| } |
| } |
| }, |
| { |
| "id": "26", |
| "category": "energy_from_smiles", |
| "query": "Report the single-point energy using GFN2-xTB for the molecule with SMILES: CC. Report the energy in eV.", |
| "answer": { |
| "tool_calls": [ |
| { |
| "smiles_to_coordinate_file": { |
| "smiles": "CC" |
| } |
| }, |
| { |
| "run_ase": { |
| "params": { |
| "input_structure_file": "molecule.xyz", |
| "driver": "energy", |
| "calculator": { |
| "calculator_type": "TBLite", |
| "method": "GFN2-xTB" |
| } |
| } |
| } |
| } |
| ], |
| "result": { |
| "status": "success", |
| "message": "Single-point energy calculation completed. Results saved to /var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_d4so2zji/entry_26/output.json", |
| "driver": "energy", |
| "potential_energy": -199.57632432831494, |
| "energy_unit": "eV", |
| "results_file": "/var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_d4so2zji/entry_26/output.json", |
| "single_point_energy": -199.57632432831494, |
| "unit": "eV" |
| }, |
| "structured_output": { |
| "smiles": null, |
| "scalar_answer": { |
| "value": -199.57632432831494, |
| "property": "single-point energy", |
| "unit": "eV" |
| }, |
| "dipole": null, |
| "vibrational_answer": null, |
| "ir_spectrum": null, |
| "atoms_data": null |
| } |
| } |
| }, |
| { |
| "id": "27", |
| "category": "dipole_from_smiles", |
| "query": "Report the dipole moment using GFN2-xTB for the molecule with SMILES: O=CO. Report the unit in e * Angstrom.", |
| "answer": { |
| "tool_calls": [ |
| { |
| "smiles_to_coordinate_file": { |
| "smiles": "O=CO" |
| } |
| }, |
| { |
| "run_ase": { |
| "params": { |
| "input_structure_file": "molecule.xyz", |
| "driver": "dipole", |
| "calculator": { |
| "calculator_type": "TBLite", |
| "method": "GFN2-xTB" |
| } |
| } |
| } |
| } |
| ], |
| "result": { |
| "status": "success", |
| "message": "Dipole calculation completed. Results saved to /var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_d4so2zji/entry_27/output.json", |
| "driver": "dipole", |
| "potential_energy": -306.5615867600617, |
| "energy_unit": "eV", |
| "results_file": "/var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_d4so2zji/entry_27/output.json", |
| "dipole_moment": [ |
| 0.2982, |
| -0.3036, |
| -0.0806 |
| ], |
| "dipole_unit": "e * Angstrom" |
| }, |
| "structured_output": { |
| "smiles": null, |
| "scalar_answer": null, |
| "dipole": { |
| "value": [ |
| 0.2982, |
| -0.3036, |
| -0.0806 |
| ], |
| "unit": "e * Angstrom" |
| }, |
| "vibrational_answer": null, |
| "ir_spectrum": null, |
| "atoms_data": null |
| } |
| } |
| }, |
| { |
| "id": "28", |
| "category": "optimization_from_smiles", |
| "query": "Run geometry optimization using GFN2-xTB for the molecule with SMILES: [C-]#[O+]. Report the optimized energy in eV.", |
| "answer": { |
| "tool_calls": [ |
| { |
| "smiles_to_coordinate_file": { |
| "smiles": "[C-]#[O+]" |
| } |
| }, |
| { |
| "run_ase": { |
| "params": { |
| "input_structure_file": "molecule.xyz", |
| "driver": "opt", |
| "calculator": { |
| "calculator_type": "TBLite", |
| "method": "GFN2-xTB" |
| } |
| } |
| } |
| }, |
| { |
| "extract_output_json": { |
| "json_file": "output.json" |
| } |
| } |
| ], |
| "result": { |
| "input_structure_file": "molecule.xyz", |
| "converged": true, |
| "final_structure": { |
| "numbers": [ |
| 6, |
| 8 |
| ], |
| "positions": [ |
| [ |
| 0.5636640099849505, |
| 1.1808251099592349e-17, |
| 7.38756240636133e-17 |
| ], |
| [ |
| -0.5636640099849506, |
| -1.1655577734965465e-17, |
| -7.36604564634253e-17 |
| ] |
| ], |
| "cell": [ |
| [ |
| 0.0, |
| 0.0, |
| 0.0 |
| ], |
| [ |
| 0.0, |
| 0.0, |
| 0.0 |
| ], |
| [ |
| 0.0, |
| 0.0, |
| 0.0 |
| ] |
| ], |
| "pbc": [ |
| false, |
| false, |
| false |
| ] |
| }, |
| "simulation_input": { |
| "input_structure_file": "molecule.xyz", |
| "output_results_file": "output.json", |
| "driver": "opt", |
| "optimizer": "bfgs", |
| "calculator": { |
| "calculator_type": "TBLite", |
| "method": "GFN2-xTB", |
| "charge": null, |
| "multiplicity": null, |
| "accuracy": 1.0, |
| "electronic_temperature": 300.0, |
| "max_iterations": 250, |
| "initial_guess": "sad", |
| "mixer_damping": 0.4, |
| "electric_field": null, |
| "spin_polarization": null, |
| "cache_api": true, |
| "verbosity": 0 |
| }, |
| "fmax": 0.01, |
| "steps": 1000, |
| "temperature": null, |
| "pressure": 101325.0 |
| }, |
| "potential_energy": -166.58403031419724, |
| "single_point_energy": -166.58403031419724, |
| "energy_unit": "eV", |
| "dipole_value": [ |
| null, |
| null, |
| null |
| ], |
| "dipole_unit": " e * angstrom", |
| "vibrational_frequencies": {}, |
| "ir_data": {}, |
| "thermochemistry": {}, |
| "success": true, |
| "error": "", |
| "wall_time": 0.024730205535888672 |
| }, |
| "structured_output": { |
| "smiles": null, |
| "scalar_answer": { |
| "value": -166.58403031419724, |
| "property": "optimized energy", |
| "unit": "eV" |
| }, |
| "dipole": null, |
| "vibrational_answer": null, |
| "ir_spectrum": null, |
| "atoms_data": null |
| } |
| } |
| }, |
| { |
| "id": "29", |
| "category": "vibrations_from_smiles", |
| "query": "Report the vibrational frequencies using the mace_mp calculator with the medium-mpa-0 model for the molecule with SMILES: OO. Report the frequencies in cm-1.", |
| "answer": { |
| "tool_calls": [ |
| { |
| "smiles_to_coordinate_file": { |
| "smiles": "OO" |
| } |
| }, |
| { |
| "run_ase": { |
| "params": { |
| "input_structure_file": "molecule.xyz", |
| "driver": "vib", |
| "calculator": { |
| "calculator_type": "mace_mp", |
| "model": "medium-mpa-0" |
| } |
| } |
| } |
| }, |
| { |
| "extract_output_json": { |
| "json_file": "output.json" |
| } |
| } |
| ], |
| "result": { |
| "input_structure_file": "molecule.xyz", |
| "converged": true, |
| "final_structure": { |
| "numbers": [ |
| 8, |
| 8, |
| 1, |
| 1 |
| ], |
| "positions": [ |
| [ |
| 0.7173313648954506, |
| -0.30350681723175466, |
| 0.1491417855168849 |
| ], |
| [ |
| -0.7100699595038746, |
| -0.3079204292276688, |
| -0.172943670234823 |
| ], |
| [ |
| 1.0401875068657729, |
| 0.3386440627911561, |
| -0.5155796228581963 |
| ], |
| [ |
| -1.0474489122573492, |
| 0.2727831936682675, |
| 0.5393814975761345 |
| ] |
| ], |
| "cell": [ |
| [ |
| 0.0, |
| 0.0, |
| 0.0 |
| ], |
| [ |
| 0.0, |
| 0.0, |
| 0.0 |
| ], |
| [ |
| 0.0, |
| 0.0, |
| 0.0 |
| ] |
| ], |
| "pbc": [ |
| false, |
| false, |
| false |
| ] |
| }, |
| "simulation_input": { |
| "input_structure_file": "molecule.xyz", |
| "output_results_file": "output.json", |
| "driver": "vib", |
| "optimizer": "bfgs", |
| "calculator": { |
| "calculator_type": "mace_mp", |
| "model": "medium-mpa-0", |
| "device": "cpu", |
| "default_dtype": "float64", |
| "dispersion": false, |
| "damping": "bj", |
| "dispersion_xc": "pbe", |
| "dispersion_cutoff": 21.167088422553647 |
| }, |
| "fmax": 0.01, |
| "steps": 1000, |
| "temperature": null, |
| "pressure": 101325.0 |
| }, |
| "potential_energy": -17.680770798599116, |
| "single_point_energy": -17.680770798599116, |
| "energy_unit": "eV", |
| "dipole_value": [ |
| null, |
| null, |
| null |
| ], |
| "dipole_unit": " e * angstrom", |
| "vibrational_frequencies": { |
| "energies": [ |
| "3.0354239948576773", |
| "139.888880512038", |
| "158.52951837598616", |
| "166.69219033890997", |
| "458.14470997922865", |
| "461.2410654321233" |
| ], |
| "energy_unit": "meV", |
| "frequencies": [ |
| "24.482345803737388", |
| "1128.2799215514517", |
| "1278.6268065205868", |
| "1344.463196434261", |
| "3695.1863189018372", |
| "3720.1601100616485" |
| ], |
| "frequency_unit": "cm-1" |
| }, |
| "ir_data": {}, |
| "thermochemistry": {}, |
| "success": true, |
| "error": "", |
| "wall_time": 0.4964940547943115 |
| }, |
| "structured_output": { |
| "smiles": null, |
| "scalar_answer": null, |
| "dipole": null, |
| "vibrational_answer": { |
| "frequency_cm1": [ |
| "24.482345803737388", |
| "1128.2799215514517", |
| "1278.6268065205868", |
| "1344.463196434261", |
| "3695.1863189018372", |
| "3720.1601100616485" |
| ] |
| }, |
| "ir_spectrum": null, |
| "atoms_data": null |
| } |
| } |
| }, |
| { |
| "id": "30", |
| "category": "thermochemistry_from_smiles", |
| "query": "Report the thermochemical properties (Gibbs free energy) at 300 K using GFN2-xTB for the molecule with SMILES: CC(=O)N. Report the Gibbs free energy in eV.", |
| "answer": { |
| "tool_calls": [ |
| { |
| "smiles_to_coordinate_file": { |
| "smiles": "CC(=O)N" |
| } |
| }, |
| { |
| "run_ase": { |
| "params": { |
| "input_structure_file": "molecule.xyz", |
| "driver": "thermo", |
| "calculator": { |
| "calculator_type": "TBLite", |
| "method": "GFN2-xTB" |
| }, |
| "temperature": 300 |
| } |
| } |
| }, |
| { |
| "extract_output_json": { |
| "json_file": "output.json" |
| } |
| } |
| ], |
| "result": { |
| "input_structure_file": "molecule.xyz", |
| "converged": true, |
| "final_structure": { |
| "numbers": [ |
| 6, |
| 6, |
| 8, |
| 7, |
| 1, |
| 1, |
| 1, |
| 1, |
| 1 |
| ], |
| "positions": [ |
| [ |
| -1.0561970528195654, |
| -0.2942791732326082, |
| -0.10865006030204082 |
| ], |
| [ |
| 0.15120762277362695, |
| 0.44754407566422527, |
| 0.42370220999311276 |
| ], |
| [ |
| 0.09946629579008696, |
| 1.3108985551165295, |
| 1.2673611991673097 |
| ], |
| [ |
| 1.321877127700965, |
| 0.06376164005303514, |
| -0.14325991602950267 |
| ], |
| [ |
| -0.8664475987536161, |
| -1.363986226853206, |
| -0.14187689925170305 |
| ], |
| [ |
| -1.2781731740170457, |
| 0.05474166145408574, |
| -1.1152321135384529 |
| ], |
| [ |
| -1.912697307697526, |
| -0.09409818431064794, |
| 0.527643252942447 |
| ], |
| [ |
| 2.171753061414852, |
| 0.5195445728223171, |
| 0.14342031785194903 |
| ], |
| [ |
| 1.3692110256082155, |
| -0.6441269107137323, |
| -0.8531079808331195 |
| ] |
| ], |
| "cell": [ |
| [ |
| 0.0, |
| 0.0, |
| 0.0 |
| ], |
| [ |
| 0.0, |
| 0.0, |
| 0.0 |
| ], |
| [ |
| 0.0, |
| 0.0, |
| 0.0 |
| ] |
| ], |
| "pbc": [ |
| false, |
| false, |
| false |
| ] |
| }, |
| "simulation_input": { |
| "input_structure_file": "molecule.xyz", |
| "output_results_file": "output.json", |
| "driver": "thermo", |
| "optimizer": "bfgs", |
| "calculator": { |
| "calculator_type": "TBLite", |
| "method": "GFN2-xTB", |
| "charge": null, |
| "multiplicity": null, |
| "accuracy": 1.0, |
| "electronic_temperature": 300.0, |
| "max_iterations": 250, |
| "initial_guess": "sad", |
| "mixer_damping": 0.4, |
| "electric_field": null, |
| "spin_polarization": null, |
| "cache_api": true, |
| "verbosity": 0 |
| }, |
| "fmax": 0.01, |
| "steps": 1000, |
| "temperature": 300.0, |
| "pressure": 101325.0 |
| }, |
| "potential_energy": -376.04603820046225, |
| "single_point_energy": -376.04603820046225, |
| "energy_unit": "eV", |
| "dipole_value": [ |
| null, |
| null, |
| null |
| ], |
| "dipole_unit": " e * angstrom", |
| "vibrational_frequencies": { |
| "energies": [ |
| "7.96039733434048", |
| "33.507031377538226", |
| "50.06796322791752", |
| "63.01681220574526", |
| "64.70915396876808", |
| "74.29366203654509", |
| "108.15210519403792", |
| "121.21165106695638", |
| "124.3923258513124", |
| "131.9342420409418", |
| "160.0234653229489", |
| "170.05844663467028", |
| "180.0113069945646", |
| "181.35416218304755", |
| "182.1723306657076", |
| "219.9576093883842", |
| "375.20952950644755", |
| "376.7361457797097", |
| "380.7567614073652", |
| "431.0057289929032", |
| "440.2951936925229" |
| ], |
| "energy_unit": "meV", |
| "frequencies": [ |
| "64.20493499578161", |
| "270.25243604560524", |
| "403.82536064526226", |
| "508.2648718873859", |
| "521.9145288481999", |
| "599.2188004331749", |
| "872.3055636538076", |
| "977.6379055744796", |
| "1003.2917780126473", |
| "1064.1214349205843", |
| "1290.676301362145", |
| "1371.6138847191362", |
| "1451.8891179254506", |
| "1462.7199755402282", |
| "1469.3189494404598", |
| "1774.0777777116791", |
| "3026.2689712529473", |
| "3038.5819619833806", |
| "3071.010414254605", |
| "3476.2956735113153", |
| "3551.2202598270947" |
| ], |
| "frequency_unit": "cm-1" |
| }, |
| "ir_data": {}, |
| "thermochemistry": { |
| "enthalpy": -373.9391099584523, |
| "entropy": 0.003089780455417321, |
| "gibbs_free_energy": -374.86604409507754, |
| "unit": "eV" |
| }, |
| "success": true, |
| "error": "", |
| "wall_time": 0.9351739883422852 |
| }, |
| "structured_output": { |
| "smiles": null, |
| "scalar_answer": { |
| "value": -374.86604409507754, |
| "property": "Gibbs free energy", |
| "unit": "eV" |
| }, |
| "dipole": null, |
| "vibrational_answer": null, |
| "ir_spectrum": null, |
| "atoms_data": null |
| } |
| } |
| }, |
| { |
| "id": "31", |
| "category": "reaction_energy", |
| "query": "Report the Gibbs free energy of reaction for Methane Combustion at 300 K using the mace_mp calculator with the medium-mpa-0 model. Report the energy in eV. The balanced reaction is: Methane + 2 Oxygen -> Carbon dioxide + 2 Water", |
| "answer": { |
| "tool_calls": [ |
| { |
| "molecule_name_to_smiles": { |
| "name": "Methane" |
| } |
| }, |
| { |
| "smiles_to_coordinate_file": { |
| "smiles": "C" |
| } |
| }, |
| { |
| "run_ase": { |
| "params": { |
| "input_structure_file": "molecule.xyz", |
| "driver": "thermo", |
| "calculator": { |
| "calculator_type": "mace_mp", |
| "model": "medium-mpa-0" |
| }, |
| "temperature": 300.0 |
| } |
| } |
| }, |
| { |
| "molecule_name_to_smiles": { |
| "name": "Oxygen" |
| } |
| }, |
| { |
| "smiles_to_coordinate_file": { |
| "smiles": "O=O" |
| } |
| }, |
| { |
| "run_ase": { |
| "params": { |
| "input_structure_file": "molecule.xyz", |
| "driver": "thermo", |
| "calculator": { |
| "calculator_type": "mace_mp", |
| "model": "medium-mpa-0" |
| }, |
| "temperature": 300.0 |
| } |
| } |
| }, |
| { |
| "molecule_name_to_smiles": { |
| "name": "Carbon dioxide" |
| } |
| }, |
| { |
| "smiles_to_coordinate_file": { |
| "smiles": "O=C=O" |
| } |
| }, |
| { |
| "run_ase": { |
| "params": { |
| "input_structure_file": "molecule.xyz", |
| "driver": "thermo", |
| "calculator": { |
| "calculator_type": "mace_mp", |
| "model": "medium-mpa-0" |
| }, |
| "temperature": 300.0 |
| } |
| } |
| }, |
| { |
| "molecule_name_to_smiles": { |
| "name": "Water" |
| } |
| }, |
| { |
| "smiles_to_coordinate_file": { |
| "smiles": "O" |
| } |
| }, |
| { |
| "run_ase": { |
| "params": { |
| "input_structure_file": "molecule.xyz", |
| "driver": "thermo", |
| "calculator": { |
| "calculator_type": "mace_mp", |
| "model": "medium-mpa-0" |
| }, |
| "temperature": 300.0 |
| } |
| } |
| }, |
| { |
| "calculator": { |
| "expression": "(1*(-22.79474096690007) + 2*(-13.693940906996428)) - (1*(-22.459430469602392) + 2*(-9.806576011375233))" |
| } |
| } |
| ], |
| "result": "-8.11004028854007", |
| "structured_output": { |
| "smiles": null, |
| "scalar_answer": { |
| "value": -8.11004028854007, |
| "property": "Gibbs free energy of reaction", |
| "unit": "eV" |
| }, |
| "dipole": null, |
| "vibrational_answer": null, |
| "ir_spectrum": null, |
| "atoms_data": null |
| } |
| } |
| }, |
| { |
| "id": "32", |
| "category": "reaction_energy", |
| "query": "Report the Gibbs free energy of reaction for Ammonia Synthesis at 400 K using GFN2-xTB. Report the energy in eV. The balanced reaction is: Nitrogen gas + 3 Hydrogen gas -> 2 Ammonia", |
| "answer": { |
| "tool_calls": [ |
| { |
| "molecule_name_to_smiles": { |
| "name": "Nitrogen gas" |
| } |
| }, |
| { |
| "smiles_to_coordinate_file": { |
| "smiles": "N#N" |
| } |
| }, |
| { |
| "run_ase": { |
| "params": { |
| "input_structure_file": "molecule.xyz", |
| "driver": "thermo", |
| "calculator": { |
| "calculator_type": "TBLite", |
| "method": "GFN2-xTB" |
| }, |
| "temperature": 400.0 |
| } |
| } |
| }, |
| { |
| "molecule_name_to_smiles": { |
| "name": "Hydrogen gas" |
| } |
| }, |
| { |
| "smiles_to_coordinate_file": { |
| "smiles": "[H][H]" |
| } |
| }, |
| { |
| "run_ase": { |
| "params": { |
| "input_structure_file": "molecule.xyz", |
| "driver": "thermo", |
| "calculator": { |
| "calculator_type": "TBLite", |
| "method": "GFN2-xTB" |
| }, |
| "temperature": 400.0 |
| } |
| } |
| }, |
| { |
| "molecule_name_to_smiles": { |
| "name": "Ammonia" |
| } |
| }, |
| { |
| "smiles_to_coordinate_file": { |
| "smiles": "N" |
| } |
| }, |
| { |
| "run_ase": { |
| "params": { |
| "input_structure_file": "molecule.xyz", |
| "driver": "thermo", |
| "calculator": { |
| "calculator_type": "TBLite", |
| "method": "GFN2-xTB" |
| }, |
| "temperature": 400.0 |
| } |
| } |
| }, |
| { |
| "calculator": { |
| "expression": "(2*(-120.23055652416788)) - (1*(-157.40205733754945) + 3*(-26.96535305958073))" |
| } |
| } |
| ], |
| "result": "-2.162996532044133", |
| "structured_output": { |
| "smiles": null, |
| "scalar_answer": { |
| "value": -2.162996532044133, |
| "property": "Gibbs free energy of reaction", |
| "unit": "eV" |
| }, |
| "dipole": null, |
| "vibrational_answer": null, |
| "ir_spectrum": null, |
| "atoms_data": null |
| } |
| } |
| }, |
| { |
| "id": "33", |
| "category": "reaction_energy", |
| "query": "Report the Gibbs free energy of reaction for Water Gas Shift Reaction at 500 K using the mace_mp calculator with the medium-mpa-0 model. Report the energy in eV. The balanced reaction is: Carbon monoxide + Water -> Carbon dioxide + Hydrogen gas", |
| "answer": { |
| "tool_calls": [ |
| { |
| "molecule_name_to_smiles": { |
| "name": "Carbon monoxide" |
| } |
| }, |
| { |
| "smiles_to_coordinate_file": { |
| "smiles": "[C-]#[O+]" |
| } |
| }, |
| { |
| "run_ase": { |
| "params": { |
| "input_structure_file": "molecule.xyz", |
| "driver": "thermo", |
| "calculator": { |
| "calculator_type": "mace_mp", |
| "model": "medium-mpa-0" |
| }, |
| "temperature": 500.0 |
| } |
| } |
| }, |
| { |
| "molecule_name_to_smiles": { |
| "name": "Water" |
| } |
| }, |
| { |
| "smiles_to_coordinate_file": { |
| "smiles": "O" |
| } |
| }, |
| { |
| "run_ase": { |
| "params": { |
| "input_structure_file": "molecule.xyz", |
| "driver": "thermo", |
| "calculator": { |
| "calculator_type": "mace_mp", |
| "model": "medium-mpa-0" |
| }, |
| "temperature": 500.0 |
| } |
| } |
| }, |
| { |
| "molecule_name_to_smiles": { |
| "name": "Carbon dioxide" |
| } |
| }, |
| { |
| "smiles_to_coordinate_file": { |
| "smiles": "O=C=O" |
| } |
| }, |
| { |
| "run_ase": { |
| "params": { |
| "input_structure_file": "molecule.xyz", |
| "driver": "thermo", |
| "calculator": { |
| "calculator_type": "mace_mp", |
| "model": "medium-mpa-0" |
| }, |
| "temperature": 500.0 |
| } |
| } |
| }, |
| { |
| "molecule_name_to_smiles": { |
| "name": "Hydrogen gas" |
| } |
| }, |
| { |
| "smiles_to_coordinate_file": { |
| "smiles": "[H][H]" |
| } |
| }, |
| { |
| "run_ase": { |
| "params": { |
| "input_structure_file": "molecule.xyz", |
| "driver": "thermo", |
| "calculator": { |
| "calculator_type": "mace_mp", |
| "model": "medium-mpa-0" |
| }, |
| "temperature": 500.0 |
| } |
| } |
| }, |
| { |
| "calculator": { |
| "expression": "(1*(-23.259198292438935) + 1*(-6.8498115746834465)) - (1*(-15.110173260039074) + 1*(-14.105316088523805))" |
| } |
| } |
| ], |
| "result": "-0.8935205185595017", |
| "structured_output": { |
| "smiles": null, |
| "scalar_answer": { |
| "value": -0.8935205185595017, |
| "property": "Gibbs free energy of reaction", |
| "unit": "eV" |
| }, |
| "dipole": null, |
| "vibrational_answer": null, |
| "ir_spectrum": null, |
| "atoms_data": null |
| } |
| } |
| }, |
| { |
| "id": "34", |
| "category": "reaction_energy", |
| "query": "Report the Gibbs free energy of reaction for Ethene Hydrogenation at 300 K using GFN2-xTB. Report the energy in eV. The balanced reaction is: Ethene + Hydrogen gas -> Ethane", |
| "answer": { |
| "tool_calls": [ |
| { |
| "molecule_name_to_smiles": { |
| "name": "Ethene" |
| } |
| }, |
| { |
| "smiles_to_coordinate_file": { |
| "smiles": "C=C" |
| } |
| }, |
| { |
| "run_ase": { |
| "params": { |
| "input_structure_file": "molecule.xyz", |
| "driver": "thermo", |
| "calculator": { |
| "calculator_type": "TBLite", |
| "method": "GFN2-xTB" |
| }, |
| "temperature": 300.0 |
| } |
| } |
| }, |
| { |
| "molecule_name_to_smiles": { |
| "name": "Hydrogen gas" |
| } |
| }, |
| { |
| "smiles_to_coordinate_file": { |
| "smiles": "[H][H]" |
| } |
| }, |
| { |
| "run_ase": { |
| "params": { |
| "input_structure_file": "molecule.xyz", |
| "driver": "thermo", |
| "calculator": { |
| "calculator_type": "TBLite", |
| "method": "GFN2-xTB" |
| }, |
| "temperature": 300.0 |
| } |
| } |
| }, |
| { |
| "molecule_name_to_smiles": { |
| "name": "Ethane" |
| } |
| }, |
| { |
| "smiles_to_coordinate_file": { |
| "smiles": "CC" |
| } |
| }, |
| { |
| "run_ase": { |
| "params": { |
| "input_structure_file": "molecule.xyz", |
| "driver": "thermo", |
| "calculator": { |
| "calculator_type": "TBLite", |
| "method": "GFN2-xTB" |
| }, |
| "temperature": 300.0 |
| } |
| } |
| }, |
| { |
| "calculator": { |
| "expression": "(1*(-198.20004456643926)) - (1*(-169.86383082086292) + 1*(-26.82484537010822))" |
| } |
| } |
| ], |
| "result": "-1.5113683754681233", |
| "structured_output": { |
| "smiles": null, |
| "scalar_answer": { |
| "value": -1.5113683754681233, |
| "property": "Gibbs free energy of reaction", |
| "unit": "eV" |
| }, |
| "dipole": null, |
| "vibrational_answer": null, |
| "ir_spectrum": null, |
| "atoms_data": null |
| } |
| } |
| }, |
| { |
| "id": "35", |
| "category": "reaction_energy", |
| "query": "Report the Gibbs free energy of reaction for Ethanol Combustion at 400 K using the mace_mp calculator with the medium-mpa-0 model. Report the energy in eV. The balanced reaction is: Ethanol + 3 Oxygen -> 2 Carbon dioxide + 3 Water", |
| "answer": { |
| "tool_calls": [ |
| { |
| "molecule_name_to_smiles": { |
| "name": "Ethanol" |
| } |
| }, |
| { |
| "smiles_to_coordinate_file": { |
| "smiles": "CCO" |
| } |
| }, |
| { |
| "run_ase": { |
| "params": { |
| "input_structure_file": "molecule.xyz", |
| "driver": "thermo", |
| "calculator": { |
| "calculator_type": "mace_mp", |
| "model": "medium-mpa-0" |
| }, |
| "temperature": 400.0 |
| } |
| } |
| }, |
| { |
| "molecule_name_to_smiles": { |
| "name": "Oxygen" |
| } |
| }, |
| { |
| "smiles_to_coordinate_file": { |
| "smiles": "O=O" |
| } |
| }, |
| { |
| "run_ase": { |
| "params": { |
| "input_structure_file": "molecule.xyz", |
| "driver": "thermo", |
| "calculator": { |
| "calculator_type": "mace_mp", |
| "model": "medium-mpa-0" |
| }, |
| "temperature": 400.0 |
| } |
| } |
| }, |
| { |
| "molecule_name_to_smiles": { |
| "name": "Carbon dioxide" |
| } |
| }, |
| { |
| "smiles_to_coordinate_file": { |
| "smiles": "O=C=O" |
| } |
| }, |
| { |
| "run_ase": { |
| "params": { |
| "input_structure_file": "molecule.xyz", |
| "driver": "thermo", |
| "calculator": { |
| "calculator_type": "mace_mp", |
| "model": "medium-mpa-0" |
| }, |
| "temperature": 400.0 |
| } |
| } |
| }, |
| { |
| "molecule_name_to_smiles": { |
| "name": "Water" |
| } |
| }, |
| { |
| "smiles_to_coordinate_file": { |
| "smiles": "O" |
| } |
| }, |
| { |
| "run_ase": { |
| "params": { |
| "input_structure_file": "molecule.xyz", |
| "driver": "thermo", |
| "calculator": { |
| "calculator_type": "mace_mp", |
| "model": "medium-mpa-0" |
| }, |
| "temperature": 400.0 |
| } |
| } |
| }, |
| { |
| "calculator": { |
| "expression": "(2*(-23.02172504643544) + 3*(-13.89517760458383)) - (1*(-45.206339882899954) + 3*(-10.014758620380904))" |
| } |
| } |
| ], |
| "result": "-12.478367162579701", |
| "structured_output": { |
| "smiles": null, |
| "scalar_answer": { |
| "value": -12.478367162579701, |
| "property": "Gibbs free energy of reaction", |
| "unit": "eV" |
| }, |
| "dipole": null, |
| "vibrational_answer": null, |
| "ir_spectrum": null, |
| "atoms_data": null |
| } |
| } |
| }, |
| { |
| "id": "36", |
| "category": "reaction_energy", |
| "query": "Report the Gibbs free energy of reaction for Hydration of Alkene at 500 K using GFN2-xTB. Report the energy in eV. The balanced reaction is: Ethene + Water -> Ethanol", |
| "answer": { |
| "tool_calls": [ |
| { |
| "molecule_name_to_smiles": { |
| "name": "Ethene" |
| } |
| }, |
| { |
| "smiles_to_coordinate_file": { |
| "smiles": "C=C" |
| } |
| }, |
| { |
| "run_ase": { |
| "params": { |
| "input_structure_file": "molecule.xyz", |
| "driver": "thermo", |
| "calculator": { |
| "calculator_type": "TBLite", |
| "method": "GFN2-xTB" |
| }, |
| "temperature": 500.0 |
| } |
| } |
| }, |
| { |
| "molecule_name_to_smiles": { |
| "name": "Water" |
| } |
| }, |
| { |
| "smiles_to_coordinate_file": { |
| "smiles": "O" |
| } |
| }, |
| { |
| "run_ase": { |
| "params": { |
| "input_structure_file": "molecule.xyz", |
| "driver": "thermo", |
| "calculator": { |
| "calculator_type": "TBLite", |
| "method": "GFN2-xTB" |
| }, |
| "temperature": 500.0 |
| } |
| } |
| }, |
| { |
| "molecule_name_to_smiles": { |
| "name": "Ethanol" |
| } |
| }, |
| { |
| "smiles_to_coordinate_file": { |
| "smiles": "CCO" |
| } |
| }, |
| { |
| "run_ase": { |
| "params": { |
| "input_structure_file": "molecule.xyz", |
| "driver": "thermo", |
| "calculator": { |
| "calculator_type": "TBLite", |
| "method": "GFN2-xTB" |
| }, |
| "temperature": 500.0 |
| } |
| } |
| }, |
| { |
| "calculator": { |
| "expression": "(1*(-309.22816604353767)) - (1*(-170.34623079585663) + 1*(-138.32288268386057))" |
| } |
| } |
| ], |
| "result": "-0.559052563820444", |
| "structured_output": { |
| "smiles": null, |
| "scalar_answer": { |
| "value": -0.559052563820444, |
| "property": "Gibbs free energy of reaction", |
| "unit": "eV" |
| }, |
| "dipole": null, |
| "vibrational_answer": null, |
| "ir_spectrum": null, |
| "atoms_data": null |
| } |
| } |
| }, |
| { |
| "id": "37", |
| "category": "reaction_energy", |
| "query": "Report the Gibbs free energy of reaction for Hydrogen Peroxide Decomposition at 300 K using the mace_mp calculator with the medium-mpa-0 model. Report the energy in eV. The balanced reaction is: 2 Hydrogen peroxide -> 2 Water + Oxygen", |
| "answer": { |
| "tool_calls": [ |
| { |
| "molecule_name_to_smiles": { |
| "name": "Hydrogen peroxide" |
| } |
| }, |
| { |
| "smiles_to_coordinate_file": { |
| "smiles": "OO" |
| } |
| }, |
| { |
| "run_ase": { |
| "params": { |
| "input_structure_file": "molecule.xyz", |
| "driver": "thermo", |
| "calculator": { |
| "calculator_type": "mace_mp", |
| "model": "medium-mpa-0" |
| }, |
| "temperature": 300.0 |
| } |
| } |
| }, |
| { |
| "molecule_name_to_smiles": { |
| "name": "Water" |
| } |
| }, |
| { |
| "smiles_to_coordinate_file": { |
| "smiles": "O" |
| } |
| }, |
| { |
| "run_ase": { |
| "params": { |
| "input_structure_file": "molecule.xyz", |
| "driver": "thermo", |
| "calculator": { |
| "calculator_type": "mace_mp", |
| "model": "medium-mpa-0" |
| }, |
| "temperature": 300.0 |
| } |
| } |
| }, |
| { |
| "molecule_name_to_smiles": { |
| "name": "Oxygen" |
| } |
| }, |
| { |
| "smiles_to_coordinate_file": { |
| "smiles": "O=O" |
| } |
| }, |
| { |
| "run_ase": { |
| "params": { |
| "input_structure_file": "molecule.xyz", |
| "driver": "thermo", |
| "calculator": { |
| "calculator_type": "mace_mp", |
| "model": "medium-mpa-0" |
| }, |
| "temperature": 300.0 |
| } |
| } |
| }, |
| { |
| "calculator": { |
| "expression": "(2*(-13.693940906996428) + 1*(-9.806576011375233)) - (2*(-17.633312351147527))" |
| } |
| } |
| ], |
| "result": "-1.927833123073036", |
| "structured_output": { |
| "smiles": null, |
| "scalar_answer": { |
| "value": -1.927833123073036, |
| "property": "Gibbs free energy of reaction", |
| "unit": "eV" |
| }, |
| "dipole": null, |
| "vibrational_answer": null, |
| "ir_spectrum": null, |
| "atoms_data": null |
| } |
| } |
| }, |
| { |
| "id": "38", |
| "category": "reaction_energy", |
| "query": "Report the Gibbs free energy of reaction for Carbonic Acid Formation at 400 K using GFN2-xTB. Report the energy in eV. The balanced reaction is: Carbon dioxide + Water -> Carbonic acid", |
| "answer": { |
| "tool_calls": [ |
| { |
| "molecule_name_to_smiles": { |
| "name": "Carbon dioxide" |
| } |
| }, |
| { |
| "smiles_to_coordinate_file": { |
| "smiles": "O=C=O" |
| } |
| }, |
| { |
| "run_ase": { |
| "params": { |
| "input_structure_file": "molecule.xyz", |
| "driver": "thermo", |
| "calculator": { |
| "calculator_type": "TBLite", |
| "method": "GFN2-xTB" |
| }, |
| "temperature": 400.0 |
| } |
| } |
| }, |
| { |
| "molecule_name_to_smiles": { |
| "name": "Water" |
| } |
| }, |
| { |
| "smiles_to_coordinate_file": { |
| "smiles": "O" |
| } |
| }, |
| { |
| "run_ase": { |
| "params": { |
| "input_structure_file": "molecule.xyz", |
| "driver": "thermo", |
| "calculator": { |
| "calculator_type": "TBLite", |
| "method": "GFN2-xTB" |
| }, |
| "temperature": 400.0 |
| } |
| } |
| }, |
| { |
| "molecule_name_to_smiles": { |
| "name": "Carbonic acid" |
| } |
| }, |
| { |
| "smiles_to_coordinate_file": { |
| "smiles": "OC(=O)O" |
| } |
| }, |
| { |
| "run_ase": { |
| "params": { |
| "input_structure_file": "molecule.xyz", |
| "driver": "thermo", |
| "calculator": { |
| "calculator_type": "TBLite", |
| "method": "GFN2-xTB" |
| }, |
| "temperature": 400.0 |
| } |
| } |
| }, |
| { |
| "calculator": { |
| "expression": "(1*(-418.4893834047748)) - (1*(-280.9793530752564) + 1*(-138.11305167531467))" |
| } |
| } |
| ], |
| "result": "0.6030213457962645", |
| "structured_output": { |
| "smiles": null, |
| "scalar_answer": { |
| "value": 0.6030213457962645, |
| "property": "Gibbs free energy of reaction", |
| "unit": "eV" |
| }, |
| "dipole": null, |
| "vibrational_answer": null, |
| "ir_spectrum": null, |
| "atoms_data": null |
| } |
| } |
| }, |
| { |
| "id": "39", |
| "category": "reaction_energy", |
| "query": "Report the Gibbs free energy of reaction for Propane Combustion at 500 K using the mace_mp calculator with the medium-mpa-0 model. Report the energy in eV. The balanced reaction is: Propane + 5 Oxygen -> 3 Carbon dioxide + 4 Water", |
| "answer": { |
| "tool_calls": [ |
| { |
| "molecule_name_to_smiles": { |
| "name": "Propane" |
| } |
| }, |
| { |
| "smiles_to_coordinate_file": { |
| "smiles": "CCC" |
| } |
| }, |
| { |
| "run_ase": { |
| "params": { |
| "input_structure_file": "molecule.xyz", |
| "driver": "thermo", |
| "calculator": { |
| "calculator_type": "mace_mp", |
| "model": "medium-mpa-0" |
| }, |
| "temperature": 500.0 |
| } |
| } |
| }, |
| { |
| "molecule_name_to_smiles": { |
| "name": "Oxygen" |
| } |
| }, |
| { |
| "smiles_to_coordinate_file": { |
| "smiles": "O=O" |
| } |
| }, |
| { |
| "run_ase": { |
| "params": { |
| "input_structure_file": "molecule.xyz", |
| "driver": "thermo", |
| "calculator": { |
| "calculator_type": "mace_mp", |
| "model": "medium-mpa-0" |
| }, |
| "temperature": 500.0 |
| } |
| } |
| }, |
| { |
| "molecule_name_to_smiles": { |
| "name": "Carbon dioxide" |
| } |
| }, |
| { |
| "smiles_to_coordinate_file": { |
| "smiles": "O=C=O" |
| } |
| }, |
| { |
| "run_ase": { |
| "params": { |
| "input_structure_file": "molecule.xyz", |
| "driver": "thermo", |
| "calculator": { |
| "calculator_type": "mace_mp", |
| "model": "medium-mpa-0" |
| }, |
| "temperature": 500.0 |
| } |
| } |
| }, |
| { |
| "molecule_name_to_smiles": { |
| "name": "Water" |
| } |
| }, |
| { |
| "smiles_to_coordinate_file": { |
| "smiles": "O" |
| } |
| }, |
| { |
| "run_ase": { |
| "params": { |
| "input_structure_file": "molecule.xyz", |
| "driver": "thermo", |
| "calculator": { |
| "calculator_type": "mace_mp", |
| "model": "medium-mpa-0" |
| }, |
| "temperature": 500.0 |
| } |
| } |
| }, |
| { |
| "calculator": { |
| "expression": "(3*(-23.259198292438935) + 4*(-14.105316088523805)) - (1*(-54.761951680421184) + 5*(-10.230824769838229))" |
| } |
| } |
| ], |
| "result": "-20.2827837017997", |
| "structured_output": { |
| "smiles": null, |
| "scalar_answer": { |
| "value": -20.2827837017997, |
| "property": "Gibbs free energy of reaction", |
| "unit": "eV" |
| }, |
| "dipole": null, |
| "vibrational_answer": null, |
| "ir_spectrum": null, |
| "atoms_data": null |
| } |
| } |
| }, |
| { |
| "id": "40", |
| "category": "reaction_energy", |
| "query": "Report the Gibbs free energy of reaction for Formic Acid Decomposition at 300 K using GFN2-xTB. Report the energy in eV. The balanced reaction is: Formic acid -> Carbon dioxide + Hydrogen gas", |
| "answer": { |
| "tool_calls": [ |
| { |
| "molecule_name_to_smiles": { |
| "name": "Formic acid" |
| } |
| }, |
| { |
| "smiles_to_coordinate_file": { |
| "smiles": "O=CO" |
| } |
| }, |
| { |
| "run_ase": { |
| "params": { |
| "input_structure_file": "molecule.xyz", |
| "driver": "thermo", |
| "calculator": { |
| "calculator_type": "TBLite", |
| "method": "GFN2-xTB" |
| }, |
| "temperature": 300.0 |
| } |
| } |
| }, |
| { |
| "molecule_name_to_smiles": { |
| "name": "Carbon dioxide" |
| } |
| }, |
| { |
| "smiles_to_coordinate_file": { |
| "smiles": "O=C=O" |
| } |
| }, |
| { |
| "run_ase": { |
| "params": { |
| "input_structure_file": "molecule.xyz", |
| "driver": "thermo", |
| "calculator": { |
| "calculator_type": "TBLite", |
| "method": "GFN2-xTB" |
| }, |
| "temperature": 300.0 |
| } |
| } |
| }, |
| { |
| "molecule_name_to_smiles": { |
| "name": "Hydrogen gas" |
| } |
| }, |
| { |
| "smiles_to_coordinate_file": { |
| "smiles": "[H][H]" |
| } |
| }, |
| { |
| "run_ase": { |
| "params": { |
| "input_structure_file": "molecule.xyz", |
| "driver": "thermo", |
| "calculator": { |
| "calculator_type": "TBLite", |
| "method": "GFN2-xTB" |
| }, |
| "temperature": 300.0 |
| } |
| } |
| }, |
| { |
| "calculator": { |
| "expression": "(1*(-280.75091473772534) + 1*(-26.82484537010822)) - (1*(-306.8161777456493))" |
| } |
| } |
| ], |
| "result": "-0.7595823621842328", |
| "structured_output": { |
| "smiles": null, |
| "scalar_answer": { |
| "value": -0.7595823621842328, |
| "property": "Gibbs free energy of reaction", |
| "unit": "eV" |
| }, |
| "dipole": null, |
| "vibrational_answer": null, |
| "ir_spectrum": null, |
| "atoms_data": null |
| } |
| } |
| } |
| ] |
