[ { "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 and report its energy using the mace_mp calculator with the medium-mpa-0 model.", "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": "Simulation completed. Results saved to /var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_rfasv6kf/entry_5/output.json", "single_point_energy": -16.815808019358535, "unit": "eV" }, "structured_output": { "smiles": null, "scalar_answer": { "value": -16.815808019358535, "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.", "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", "result": { "vibrational_frequencies": { "energies": [ "5.278838012595982i", "0.04764407633090353i", "0.005321020506525112i", "0.06055744294822688", "4.520458491661813", "5.344478380954939", "207.53984955909357", "461.6946537572708", "484.0428021965612" ], "energy_unit": "meV", "frequencies": [ "42.57670028478123i", "0.38427539421474816i", "0.04291692504579866i", "0.48842872091682965", "36.4599568863508", "43.1061255642714", "1673.921789367551", "3723.818546658187", "3904.0685213209904" ], "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_rfasv6kf/entry_6/output.json." }, "structured_output": { "smiles": null, "scalar_answer": null, "dipole": null, "vibrational_answer": { "frequency_cm1": [ "42.57670028478123i", "0.38427539421474816i", "0.04291692504579866i", "0.48842872091682965", "36.4599568863508", "43.1061255642714", "1673.921789367551", "3723.818546658187", "3904.0685213209904" ] }, "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.", "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", "result": { "thermochemistry": { "enthalpy": -279.8479687871829, "entropy": 0.00267553279139694, "gibbs_free_energy": -281.98839502030046, "unit": "eV" } }, "message": "Thermochemistry computed and returned. Full results (structure, vibrations, thermochemistry and metadata) saved to /var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_rfasv6kf/entry_7/output.json" }, "structured_output": { "smiles": null, "scalar_answer": { "value": -281.98839502030046, "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.", "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": "Simulation completed. Results saved to /var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_rfasv6kf/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.", "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": "Simulation completed. Results saved to /var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_rfasv6kf/entry_9/output.json", "single_point_energy": -16.42796020021993, "unit": "eV" }, "structured_output": { "smiles": null, "scalar_answer": { "value": -16.42796020021993, "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 and report its energy using GFN2-xTB.", "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": "Simulation completed. Results saved to /var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_rfasv6kf/entry_10/output.json", "single_point_energy": -170.64969292571737, "unit": "eV" }, "structured_output": { "smiles": null, "scalar_answer": { "value": -170.64969292571737, "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.", "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", "result": { "vibrational_frequencies": { "energies": [ "2.848747767957554i", "1.3603132350582101i", "0.21983103137383805i", "0.008847338225235977i", "0.14881363941963582", "1.1251489861137578", "27.79839738088794", "42.209188255548554", "52.105857498041146", "103.03144226048241", "115.54432766433321", "129.5674349674995", "135.15038253526842", "140.1157651795348", "153.14733723642294", "162.9209544186943", "167.31662813377238", "174.18841138098614", "183.86516633114522", "184.7126926479384", "185.60849327672668", "355.65983750782635", "369.8819486600176", "374.18918495906934", "377.5211675990331", "377.96641454035523", "439.29934775255975" ], "energy_unit": "meV", "frequencies": [ "22.976700481025212i", "10.971666257668005i", "1.7730568571653174i", "0.07135859578095197i", "1.2002629572528742", "9.074938659451792", "224.20919733834953", "340.4400652818332", "420.26208655806545", "831.0046314294893", "931.927859281214", "1045.031848318874", "1090.0613576031812", "1130.1098698211606", "1235.216587697658", "1314.046127167295", "1349.4996269469812", "1404.9242971188019", "1482.9725899929344", "1489.8083507962524", "1497.033470187268", "2868.5900701578657", "2983.29913349696", "3018.039337406015", "3044.913590011858", "3048.5047488100927", "3543.1882205763245" ], "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_rfasv6kf/entry_11/output.json." }, "structured_output": { "smiles": null, "scalar_answer": null, "dipole": null, "vibrational_answer": { "frequency_cm1": [ "22.976700481025212i", "10.971666257668005i", "1.7730568571653174i", "0.07135859578095197i", "1.2002629572528742", "9.074938659451792", "224.20919733834953", "340.4400652818332", "420.26208655806545", "831.0046314294893", "931.927859281214", "1045.031848318874", "1090.0613576031812", "1130.1098698211606", "1235.216587697658", "1314.046127167295", "1349.4996269469812", "1404.9242971188019", "1482.9725899929344", "1489.8083507962524", "1497.033470187268", "2868.5900701578657", "2983.29913349696", "3018.039337406015", "3044.913590011858", "3048.5047488100927", "3543.1882205763245" ] }, "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.", "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", "result": { "thermochemistry": { "enthalpy": -21.793386183692945, "entropy": 0.0021505247570400435, "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_rfasv6kf/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.", "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": "Simulation completed. Results saved to /var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_rfasv6kf/entry_13/output.json", "dipole_moment": [ -0.0051, -0.002, -0.3835 ], "dipole_unit": "e * Angstrom" }, "structured_output": { "smiles": null, "scalar_answer": null, "dipole": { "value": [ -0.0051, -0.002, -0.3835 ], "unit": "e * Angstrom" }, "vibrational_answer": null, "ir_spectrum": null, "atoms_data": null } } }, { "id": "14", "category": "energy_from_name", "query": "Report the single-point energy of methane using GFN2-xTB.", "answer": { "tool_calls": [ { "molecule_name_to_smiles": { "name": "methane" } }, { "smiles_to_coordinate_file": { "smiles": "C" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "energy", "calculator": { "calculator_type": "TBLite", "method": "GFN2-xTB" } } } } ], "result": { "status": "success", "message": "Simulation completed. Results saved to /var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_rfasv6kf/entry_14/output.json", "single_point_energy": -113.5639578693412, "unit": "eV" }, "structured_output": { "smiles": null, "scalar_answer": { "value": -113.5639578693412, "property": "single-point energy", "unit": "eV" }, "dipole": null, "vibrational_answer": null, "ir_spectrum": null, "atoms_data": null } } }, { "id": "15", "category": "energy_from_name", "query": "Report the single-point energy of nitrogen using the mace_mp calculator with the medium-mpa-0 model.", "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" } } } }, { "extract_output_json": { "json_file": "output.json" } } ], "result": { "input_structure_file": "molecule.xyz", "converged": true, "final_structure": { "numbers": [ 7, 7 ], "positions": [ [ 0.56000414, 0.0, 0.0 ], [ -0.56000414, 0.0, 0.0 ] ], "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": "energy", "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 }, "single_point_energy": -16.42796020021993, "energy_unit": "eV", "dipole_value": [ null, null, null ], "dipole_unit": " e * angstrom", "vibrational_frequencies": {}, "ir_data": {}, "thermochemistry": {}, "success": true, "error": "", "wall_time": 0.09614682197570801 }, "structured_output": { "smiles": null, "scalar_answer": { "value": -16.42796020021993, "property": "single-point energy", "unit": "eV" }, "dipole": null, "vibrational_answer": null, "ir_spectrum": null, "atoms_data": null } } }, { "id": "16", "category": "optimization_from_name", "query": "Run geometry optimization for propane and report its energy using GFN2-xTB.", "answer": { "tool_calls": [ { "molecule_name_to_smiles": { "name": "propane" } }, { "smiles_to_coordinate_file": { "smiles": "CCC" } }, { "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, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1 ], "positions": [ [ 1.1836990220404628, -0.44581775611645036, -0.21608217898758894 ], [ 0.013755939163535435, 0.5231870496938726, -0.335027797060295 ], [ -1.1939989710707708, 0.05407615523023987, 0.4669374481125456 ], [ 1.4921405564582126, -0.5456000103085406, 0.8224939842948523 ], [ 2.0343314895638027, -0.092915128054742, -0.7950762275075878 ], [ 0.9022153167897161, -1.4304444860699346, -0.5835196058847643 ], [ -0.26707932569687615, 0.623247536938491, -1.3858926897307557 ], [ 0.32312914097944345, 1.508516255499464, 0.020798142197863335 ], [ -2.0168236556709367, 0.7588112197659456, 0.3686624037829177 ], [ -0.940722226408455, -0.03410841244112985, 1.5213603013613985 ], [ -1.5306472961481374, -0.9189524341372163, 0.11534622942141526 ] ], "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 }, "single_point_energy": -285.7420444910578, "energy_unit": "eV", "dipole_value": [ null, null, null ], "dipole_unit": " e * angstrom", "vibrational_frequencies": {}, "ir_data": {}, "thermochemistry": {}, "success": true, "error": "", "wall_time": 0.12388396263122559 }, "structured_output": { "smiles": null, "scalar_answer": { "value": -285.7420444910578, "property": "optimized energy", "unit": "eV" }, "dipole": null, "vibrational_answer": null, "ir_spectrum": null, "atoms_data": null } } }, { "id": "17", "category": "thermochemistry_from_name", "query": "Report the thermochemical properties (Gibbs free energy) of ammonia at 500 K using the mace_mp calculator with the medium-mpa-0 model.", "answer": { "tool_calls": [ { "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": "mace_mp", "model": "medium-mpa-0" }, "temperature": 500 } } }, { "extract_output_json": { "json_file": "output.json" } } ], "result": { "input_structure_file": "molecule.xyz", "converged": true, "final_structure": { "numbers": [ 7, 1, 1, 1 ], "positions": [ [ 0.003690286031697614, 0.0014517023245638478, 0.2782984081375093 ], [ -0.5243290899394131, -0.7867688603042043, -0.08172821051080162 ], [ -0.42060408841591523, 0.8457563471952523, -0.09161946537099143 ], [ 0.9412428923236309, -0.06043919921561174, -0.10495074225571631 ] ], "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": "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": 500.0, "pressure": 101325.0 }, "single_point_energy": -18.996991017234492, "energy_unit": "eV", "dipole_value": [ null, null, null ], "dipole_unit": " e * angstrom", "vibrational_frequencies": { "energies": [ "0.24294906810791458i", "0.1307692365477951i", "0.00405509797098614i", "2.3596437712477236", "3.781055210110371", "4.865268074396271", "114.75574227402079", "203.81605514250245", "203.87526854502778", "421.0187350418408", "432.0811779216365", "432.1695468268274" ], "energy_unit": "meV", "frequencies": [ "1.9595163997484952i", "1.054725031849781i", "0.03270657112874651i", "19.031810672640617", "30.496267181707292", "39.24103374917082", "925.5674891141101", "1643.8873616357228", "1644.3649499394644", "3395.745134323393", "3484.969754170924", "3485.682497464397" ], "frequency_unit": "cm-1" }, "ir_data": {}, "thermochemistry": { "enthalpy": -17.908497948341136, "entropy": 0.0022003386308278253, "gibbs_free_energy": -19.008667263755047, "unit": "eV" }, "success": true, "error": "", "wall_time": 0.6874349117279053 }, "structured_output": { "smiles": null, "scalar_answer": { "value": -19.008667263755047, "property": "Gibbs free energy", "unit": "eV" }, "dipole": null, "vibrational_answer": null, "ir_spectrum": null, "atoms_data": null } } }, { "id": "18", "category": "energy_from_name", "query": "Report the single-point energy of ethane using GFN2-xTB.", "answer": { "tool_calls": [ { "molecule_name_to_smiles": { "name": "ethane" } }, { "smiles_to_coordinate_file": { "smiles": "CC" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "energy", "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, 6, 1, 1, 1, 1, 1, 1 ], "positions": [ [ 0.75817634, -0.00414207, 0.04613654 ], [ -0.75817615, 0.00414192, -0.04613682 ], [ 1.08728759, -0.78406587, 0.76471975 ], [ 1.1947984, -0.22109989, -0.95148439 ], [ 1.11953509, 0.986582, 0.3937618 ], [ -1.1195354, -0.98658189, -0.39376044 ], [ -1.1947983, 0.22110085, 0.95148386 ], [ -1.08728755, 0.78406493, -0.76472029 ] ], "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": "energy", "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 }, "single_point_energy": -199.5763243283149, "energy_unit": "eV", "dipole_value": [ null, null, null ], "dipole_unit": " e * angstrom", "vibrational_frequencies": {}, "ir_data": {}, "thermochemistry": {}, "success": true, "error": "", "wall_time": 0.021041154861450195 }, "structured_output": { "smiles": null, "scalar_answer": { "value": -199.5763243283149, "property": "single-point energy", "unit": "eV" }, "dipole": null, "vibrational_answer": null, "ir_spectrum": null, "atoms_data": null } } }, { "id": "19", "category": "optimization_from_name", "query": "Run geometry optimization for ethanol and report its energy using the mace_mp calculator with the medium-mpa-0 model.", "answer": { "tool_calls": [ { "molecule_name_to_smiles": { "name": "ethanol" } }, { "smiles_to_coordinate_file": { "smiles": "CCO" } }, { "run_ase": { "params": { "input_structure_file": "molecule.xyz", "driver": "opt", "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": [ 6, 6, 8, 1, 1, 1, 1, 1, 1 ], "positions": [ [ -0.8794906755245444, -0.12517653079525462, 0.13049741585746044 ], [ 0.5213304505800801, 0.48341392630125873, -0.007283766986061524 ], [ 1.4108996978379476, -0.4187880795329846, -0.7019155658145357 ], [ -1.2985557068327698, -0.35485212462745636, -0.8592997997501077 ], [ -1.529212856302033, 0.5967248507727829, 0.6403442234257548 ], [ -0.8515944623695518, -1.0522427941799235, 0.7242420708541866 ], [ 0.4903838833697194, 1.4242401579727364, -0.576471284495241 ], [ 0.9344039971315186, 0.7411951613000017, 0.9872610025235883 ], [ 1.2018356621096296, -1.2945145472112138, -0.33737429561505033 ] ], "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": "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 }, "single_point_energy": -46.24649506270806, "energy_unit": "eV", "dipole_value": [ null, null, null ], "dipole_unit": " e * angstrom", "vibrational_frequencies": {}, "ir_data": {}, "thermochemistry": {}, "success": true, "error": "", "wall_time": 1.8350181579589844 }, "structured_output": { "smiles": null, "scalar_answer": { "value": -46.24649506270806, "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.", "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": [ [ 1.183699022040464, -0.44581775611645047, -0.21608217898758905 ], [ 0.013755939163535395, 0.523187049693873, -0.33502779706029573 ], [ -1.1939989710707715, 0.05407615523023984, 0.4669374481125455 ], [ 1.492140556458212, -0.5456000103085396, 0.8224939842948531 ], [ 2.0343314895638054, -0.09291512805474277, -0.7950762275075873 ], [ 0.9022153167897168, -1.4304444860699344, -0.5835196058847639 ], [ -0.2670793256968766, 0.6232475369384921, -1.385892689730757 ], [ 0.32312914097944384, 1.508516255499465, 0.020798142197862877 ], [ -2.016823655670938, 0.7588112197659446, 0.36866240378291915 ], [ -0.9407222264084557, -0.034108412441129755, 1.5213603013613985 ], [ -1.5306472961481372, -0.9189524341372167, 0.1153462294214151 ] ], "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 }, "single_point_energy": -285.7420444910579, "energy_unit": "eV", "dipole_value": [ null, null, null ], "dipole_unit": " e * angstrom", "vibrational_frequencies": { "energies": [ "1.9310675484852602i", "0.40143578160534193i", "0.025482006114124035i", "0.025567899657861468", "0.07130391144313077", "0.9938585405125054", "25.672748385895904", "31.767145002935948", "46.299719001106844", "98.28573698682733", "115.08128382694085", "115.92647077262204", "118.10590256733721", "138.50928706464967", "144.78589979833484", "149.67230610087714", "157.82018744745346", "166.8055180592063", "175.16494251935572", "176.13314007841973", "185.77408646726914", "185.92993424467087", "186.5205580971103", "187.1044413494621", "187.34686647797224", "368.0068186375104", "369.763497311251", "375.3253945728285", "375.3839656494207", "375.9583635959352", "376.21105767327913", "376.539097351378", "376.66719154014993" ], "energy_unit": "meV", "frequencies": [ "15.575110288540841i", "3.237797961637446i", "0.2055262416439408i", "0.20621901980068288", "0.5751048354586277", "8.016009793045654", "207.06468183049148", "256.2193059279061", "373.4324210131034", "792.7279367110332", "928.1931588345764", "935.0100513372469", "952.5883543829731", "1117.1527498928133", "1167.777046097412", "1207.1885711558782", "1272.9056667025436", "1345.377246149274", "1412.8005519873748", "1420.6095920053415", "1498.3690693524827", "1499.626066459166", "1504.389769131298", "1509.0991051968047", "1511.0543957386717", "2968.1751897857143", "2982.3437589310556", "3027.2034860444614", "3027.6758936401243", "3032.3087255540013", "3034.3468407545697", "3036.9926592135957", "3038.025808529894" ], "frequency_unit": "cm-1" }, "ir_data": {}, "thermochemistry": { "enthalpy": -282.7983244265669, "entropy": 0.002789863332123275, "gibbs_free_energy": -283.6352834262039, "unit": "eV" }, "success": true, "error": "", "wall_time": 0.844555139541626 }, "structured_output": { "smiles": null, "scalar_answer": { "value": -283.6352834262039, "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 and report its energy.", "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": "Simulation completed. Results saved to /var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_rfasv6kf/entry_21/output.json", "single_point_energy": -16.815808019358535, "unit": "eV" }, "structured_output": { "smiles": null, "scalar_answer": { "value": -16.815808019358535, "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.", "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", "result": { "vibrational_frequencies": { "energies": [ "5.278838012595982i", "0.04764407633090353i", "0.005321020506525112i", "0.06055744294822688", "4.520458491661813", "5.344478380954939", "207.53984955909357", "461.6946537572708", "484.0428021965612" ], "energy_unit": "meV", "frequencies": [ "42.57670028478123i", "0.38427539421474816i", "0.04291692504579866i", "0.48842872091682965", "36.4599568863508", "43.1061255642714", "1673.921789367551", "3723.818546658187", "3904.0685213209904" ], "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_rfasv6kf/entry_22/output.json." }, "structured_output": { "smiles": null, "scalar_answer": null, "dipole": null, "vibrational_answer": { "frequency_cm1": [ "42.57670028478123i", "0.38427539421474816i", "0.04291692504579866i", "0.48842872091682965", "36.4599568863508", "43.1061255642714", "1673.921789367551", "3723.818546658187", "3904.0685213209904" ] }, "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.", "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", "result": { "thermochemistry": { "enthalpy": -279.8479687871829, "entropy": 0.002675532791396945, "gibbs_free_energy": -281.98839502030046, "unit": "eV" } }, "message": "Thermochemistry computed and returned. Full results (structure, vibrations, thermochemistry and metadata) saved to /var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_rfasv6kf/entry_23/output.json" }, "structured_output": { "smiles": null, "scalar_answer": { "value": -281.98839502030046, "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+].", "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": "Simulation completed. Results saved to /var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_rfasv6kf/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.", "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": "Simulation completed. Results saved to /var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_rfasv6kf/entry_25/output.json", "single_point_energy": -16.42796020021993, "unit": "eV" }, "structured_output": { "smiles": null, "scalar_answer": { "value": -16.42796020021993, "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.", "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": "Simulation completed. Results saved to /var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_rfasv6kf/entry_26/output.json", "single_point_energy": -199.57632432831485, "unit": "eV" }, "structured_output": { "smiles": null, "scalar_answer": { "value": -199.57632432831485, "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.", "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": "Simulation completed. Results saved to /var/folders/5b/vkn1l5ys6pz8nyp5rbcprw800000gp/T/chemgraph_gt_rfasv6kf/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+] and report its energy.", "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, 1.1833012223432164e-17, 7.385689453225058e-17 ], [ -0.5636640099849506, -1.1655577734965483e-17, -7.366045646342532e-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 }, "single_point_energy": -166.58403031419738, "energy_unit": "eV", "dipole_value": [ null, null, null ], "dipole_unit": " e * angstrom", "vibrational_frequencies": {}, "ir_data": {}, "thermochemistry": {}, "success": true, "error": "", "wall_time": 0.02695608139038086 }, "structured_output": { "smiles": null, "scalar_answer": { "value": -166.58403031419738, "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.", "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": [ [ 0.7173313648954498, -0.3035068172317547, 0.14914178551688717 ], [ -0.7100699595038744, -0.30792042922766866, -0.17294367023482538 ], [ 1.0401875068657742, 0.3386440627911562, -0.5155796228581969 ], [ -1.0474489122573503, 0.2727831936682675, 0.5393814975761353 ] ], "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 }, "single_point_energy": -17.680770798599116, "energy_unit": "eV", "dipole_value": [ null, null, null ], "dipole_unit": " e * angstrom", "vibrational_frequencies": { "energies": [ "5.839866667656922i", "1.4593731001068235i", "0.12933134375735306i", "0.021255179803343262i", "0.006931986696477268", "1.2933954804428005", "3.035423994928984", "139.88888051204034", "158.52951837598707", "166.69219033890974", "458.14470997922837", "461.2410654321238" ], "energy_unit": "meV", "frequencies": [ "47.1017015901266i", "11.770637958326722i", "1.0431276442742923i", "0.17143458803371012i", "0.05591024374109585", "10.431938163115298", "24.482345804312516", "1128.2799215514706", "1278.6268065205938", "1344.463196434259", "3695.186318901835", "3720.160110061652" ], "frequency_unit": "cm-1" }, "ir_data": {}, "thermochemistry": {}, "success": true, "error": "", "wall_time": 0.679455041885376 }, "structured_output": { "smiles": null, "scalar_answer": null, "dipole": null, "vibrational_answer": { "frequency_cm1": [ "47.1017015901266i", "11.770637958326722i", "1.0431276442742923i", "0.17143458803371012i", "0.05591024374109585", "10.431938163115298", "24.482345804312516", "1128.2799215514706", "1278.6268065205938", "1344.463196434259", "3695.186318901835", "3720.160110061652" ] }, "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.", "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": [ [ -1.056197052819566, -0.29427917323260794, -0.10865006030204143 ], [ 0.1512076227736271, 0.44754407566422616, 0.4237022099931135 ], [ 0.09946629579008992, 1.310898555116528, 1.2673611991673122 ], [ 1.3218771277009667, 0.06376164005303547, -0.14325991602950278 ], [ -0.866447598753617, -1.3639862268532053, -0.14187689925170255 ], [ -1.2781731740170452, 0.054741661454084954, -1.1152321135384529 ], [ -1.9126973076975242, -0.09409818431064684, 0.527643252942449 ], [ 2.1717530614148526, 0.5195445728223173, 0.1434203178519501 ], [ 1.3692110256082148, -0.6441269107137283, -0.853107980833123 ] ], "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 }, "single_point_energy": -376.0460382004621, "energy_unit": "eV", "dipole_value": [ null, null, null ], "dipole_unit": " e * angstrom", "vibrational_frequencies": { "energies": [ "1.8374182752358763i", "0.7827634084393327i", "0.10481322122202405i", "0.01592822135793458i", "0.03390964592509584", "0.4575280523269729", "7.960397334365384", "33.50703137753274", "50.06796322792542", "63.01681220574577", "64.70915396876732", "74.29366203655023", "108.15210519403244", "121.21165106695727", "124.3923258513069", "131.93424204093992", "160.02346532294237", "170.05844663467596", "180.0113069945711", "181.35416218304664", "182.1723306657071", "219.95760938838774", "375.2095295064486", "376.736145779706", "380.75676140736596", "431.0057289928986", "440.29519369252546" ], "energy_unit": "meV", "frequencies": [ "14.819777954130798i", "6.3134127161113165i", "0.8453756480506226i", "0.12846977028054826i", "0.2734997413959021", "3.6902126394716745", "64.20493499598248", "270.25243604556096", "403.82536064532593", "508.26487188739003", "521.9145288481939", "599.2188004332164", "872.3055636537634", "977.6379055744869", "1003.2917780126029", "1064.1214349205693", "1290.6763013620923", "1371.613884719182", "1451.8891179255031", "1462.719975540221", "1469.3189494404558", "1774.0777777117075", "3026.268971252956", "3038.581961983351", "3071.0104142546115", "3476.295673511278", "3551.220259827115" ], "frequency_unit": "cm-1" }, "ir_data": {}, "thermochemistry": { "enthalpy": -373.9391099584522, "entropy": 0.003089780455417055, "gibbs_free_energy": -374.8660440950773, "unit": "eV" }, "success": true, "error": "", "wall_time": 1.0072641372680664 }, "structured_output": { "smiles": null, "scalar_answer": { "value": -374.8660440950773, "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*(-22.794740964867238) + 2*(-13.693940906998133)) - (1*(-22.459430469602392) + 2*(-9.806576011384493))" } } ], "result": "-8.110040286492122", "structured_output": { "smiles": null, "scalar_answer": { "value": -8.110040286492122, "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*(-120.23055652416777)) - (1*(-157.40205733828975) + 3*(-26.96535305958073))" } } ], "result": "-2.1629965313036053", "structured_output": { "smiles": null, "scalar_answer": { "value": -2.1629965313036053, "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*(-23.2591982904147) + 1*(-6.8498115746834465)) - (1*(-15.11017325836859) + 1*(-14.10531608852551))" } } ], "result": "-0.8935205182040455", "structured_output": { "smiles": null, "scalar_answer": { "value": -0.8935205182040455, "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*(-198.20004456643932)) - (1*(-169.86383043609294) + 1*(-26.82484537010822))" } } ], "result": "-1.511368760238156", "structured_output": { "smiles": null, "scalar_answer": { "value": -1.511368760238156, "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*(-23.021725044406743) + 3*(-13.895177604585536)) - (1*(-45.20633988290186) + 3*(-10.014758620390138))" } } ], "result": "-12.478367158497832", "structured_output": { "smiles": null, "scalar_answer": { "value": -12.478367158497832, "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*(-309.2281660435372)) - (1*(-170.34623039985354) + 1*(-138.32288268386057))" } } ], "result": "-0.5590529598230773", "structured_output": { "smiles": null, "scalar_answer": { "value": -0.5590529598230773, "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*(-13.693940906998133) + 1*(-9.806576011384493)) - (2*(-17.63331235114692))" } } ], "result": "-1.92783312308692", "structured_output": { "smiles": null, "scalar_answer": { "value": -1.92783312308692, "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*(-418.4893834047747)) - (1*(-280.9793530752564) + 1*(-138.1130516753148))" } } ], "result": "0.6030213457965488", "structured_output": { "smiles": null, "scalar_answer": { "value": 0.6030213457965488, "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*(-23.2591982904147) + 4*(-14.10531608852551)) - (1*(-54.76195168042118) + 5*(-10.230824769847466))" } } ], "result": "-20.28278369568764", "structured_output": { "smiles": null, "scalar_answer": { "value": -20.28278369568764, "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*(-280.75091473772545) + 1*(-26.82484537010822)) - (1*(-306.8161777456496))" } } ], "result": "-0.7595823621840623", "structured_output": { "smiles": null, "scalar_answer": { "value": -0.7595823621840623, "property": "Gibbs free energy of reaction", "unit": "eV" }, "dipole": null, "vibrational_answer": null, "ir_spectrum": null, "atoms_data": null } } } ]