| [ |
| { |
| "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", |
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| "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 |
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| "positions": [ |
| [ |
| 1.183699022040464, |
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| [ |
| 0.013755939163535395, |
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| [ |
| -1.1939989710707715, |
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| [ |
| 1.492140556458212, |
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| [ |
| 2.0343314895638054, |
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| [ |
| 0.9022153167897168, |
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| [ |
| -0.2670793256968766, |
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| 0.32312914097944384, |
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| [ |
| -2.016823655670938, |
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| [ |
| -0.9407222264084557, |
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| [ |
| -1.5306472961481372, |
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| "cell": [ |
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| [ |
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| "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, |
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| "electronic_temperature": 300.0, |
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| "initial_guess": "sad", |
| "mixer_damping": 0.4, |
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| "spin_polarization": null, |
| "cache_api": true, |
| "verbosity": 0 |
| }, |
| "fmax": 0.01, |
| "steps": 1000, |
| "temperature": 300.0, |
| "pressure": 101325.0 |
| }, |
| "single_point_energy": -285.7420444910579, |
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| "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", |
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| "1499.626066459166", |
| "1504.389769131298", |
| "1509.0991051968047", |
| "1511.0543957386717", |
| "2968.1751897857143", |
| "2982.3437589310556", |
| "3027.2034860444614", |
| "3027.6758936401243", |
| "3032.3087255540013", |
| "3034.3468407545697", |
| "3036.9926592135957", |
| "3038.025808529894" |
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| "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 |
| } |
| } |
| } |
| ] |
