Quantum alchemy data - Atoms

All PySCF calculation logs and JSON files for the atom study of quantum alchemy. A cumulative JSON file is provided with all files organized by atom and state (i.e., charge and multiplicity).

Data generation

A generator Python script is used with dictionary of all desired calculations. For more information, visit the keithgroup/qa-atoms-dimers repository.

JSON data

JSONs contain the following information.

• "schema_name": Name of the JSON format.
• "provenance": Origin of the JSON data.
  • "creator": Name of the originating software.
  • "version": Version of the originating software.
• "molecule": Information about the atoms making up the system.
  • "geometry": Cartesian coordinates of all atoms in the system.
  • "symbols": All chemical symbols in the system in the same order as in the "geometry".
• "molecular_charge": Total system charge.
• "molecular_multiplicity": Multiplicity of the system, 2S + 1.
• "name": Unique name specifying the calculation.
• "atomic_numbers": List of atomic numbers of all atoms in the system in the same order as "geometry".
• "n_electrons": Total number of electrons in the system.
• "model": Methods used to calculation system properties.
  • "method": Overall quantum chemical method used.
  • "basis": Employed basis set.
  • "scf_conv_tol": Change in electronic energy SCF convergence criteria.
  • "scf_conv_tol_grad": Norm of the gradient convergence criteria.
  • "cc_conv_tol": Change in coupled cluster electronic energy convergence criteria.
  • "cc_conv_tol_normt": Norm of the coupled cluster amplitude vectors convergence criteria.
• "broken_symmetry": If start with an excited state guess.
• "finite_diff_delta": h used for central finite differences.
• "finite_diff_acc": General accuracy for central finite difference.
• "qa_lambdas": List of all calculations and their change in nuclear charge.
• "electronic_energies": Total electronic energies of the systems.
• "qats_energies": Predicted total electron energies with a Taylor series of nth order.
• "qats_poly_coeffs": Taylor series polynomial coefficients (derivatives are from finite differences).
• "hf_energies": Hartree–Fock energy contributions (if we are using coupled cluster).
• "triples_corrections": Perturbative triple corrections (if selected).
• "scf_converged": If the SCF iterations have converged.
• "cc_converged": If the coupled cluster iterations have converged.
• "scf_spin_squared": Spin squared expectation value of the last SCF iteration, S(S + 1).
• "cc_spin_squared": Spin squared expectation value of the last coupled cluster iteration, S(S + 1).
• "t1_diagnostic": T1 diagnostic for coupled cluster calculations.

Note: Atom property predictions involving three-electron systems might slightly differ (± 0.001 eV) from values presented in the respective manuscript. Data here uses CCSD(T) calculations for three-electron ground state systems; whereas the manuscript does not include the perturbative triples corrections.

Here is an example of a typical JSON file for a unrestricted CCSD(T) calculation.

{
    "schema_name": "pyscf_qa_output",
    "provenance": {
        "creator": "PySCF",
        "version": "1.7.6"
    },
    "molecule": {
        "geometry": [[0.0, 0.0, 0.0]],
        "symbols": [ "C" ]
    },
    "molecular_charge": 0,
    "molecular_multiplicity": 3,
    "name": "c.chrg0.mult3-pyscf-uccsdt.augccpv5z",
    "atomic_numbers": [ 6 ],
    "n_electrons": 6,
    "model": {
        "method": "UCCSD(T)",
        "basis": "aug-cc-pV5Z",
        "scf_conv_tol": 1e-09,
        "scf_conv_tol_grad": 1e-06,
        "cc_conv_tol": 1e-07,
        "cc_conv_tol_normt": 1e-05
    },
    "broken_symmetry": false,
    "finite_diff_delta": 0.01,
    "finite_diff_acc": 2,
    "qa_lambdas": [-2.0, -1.75, -1.5, -1.25, -1.0, -0.75, -0.5, -0.25, -0.02, -0.01, 0.0, 0.01, 0.02, 0.25, 0.5, 0.75, 1.0, 1.25, 1.5, 1.75, 2.0],
    "electronic_energies": [-14.484563521780775, -16.755012804999193, -19.20134196738246, -21.829474788173297, -24.64514044379976, -27.652478081221968, -30.851525517344523, -34.24087642997402, -37.52628463028216, -37.67275331139264, -37.81952364527374, -37.966595580511424, -38.11396906538776, -41.586662183011946, -45.5413920989799, -49.682572272882716, -54.00871704426481, -58.51791734854164, -63.207784803991316, -68.07542508517481, -73.11743600087422],
    "qats_energies": {
        "0": [-37.819523645273655, -37.819523645273655, -37.819523645273655, -37.819523645273655, -37.819523645273655, -37.819523645273655, -37.819523645273655, -37.819523645273655, -37.819523645273655, -37.819523645273655, -37.819523645273655, -37.819523645273655, -37.819523645273655, -37.819523645273655, -37.819523645273655, -37.819523645273655, -37.819523645273655, -37.819523645273655, -37.819523645273655, -37.819523645273655, -37.819523645273655],
        "1": [-8.435296733395269, -12.108325097380067, -15.781353461364866, -19.454381825349664, -23.127410189334462, -26.80043855331926, -30.47346691730406, -34.14649528128886, -37.52568137615487, -37.67260251071426, -37.819523645273655, -37.96644477983305, -38.11336591439244, -41.49255200925845, -45.16558037324325, -48.83860873722805, -52.51163710121285, -56.18466546519765, -59.857693829182445, -63.53072219316724, -67.20375055715203],
        "2": [-14.467323868458614, -16.72659587266294, -19.174368724837997, -21.810642424983783, -24.6354169731003, -27.648692369187543, -30.850468613245518, -34.24074570527422, -37.52628457886838, -37.67275331139264, -37.819523645273655, -37.966595580511424, -38.113969117105945, -41.58680243324382, -45.54258206918471, -49.68686255309633, -54.019643884978684, -58.540926064831766, -63.250709092655576, -68.14899296845012, -73.23577769221538],
        "3": [-14.53607851783985, -16.77265611629139, -19.203374592545707, -21.827428228055375, -24.64401130427295, -27.65231810265101, -30.8515429046421, -34.2408799916988, -37.52628464762303, -37.672753319986974, -37.819523645273655, -37.96659557191709, -38.113969048351294, -41.58666814681924, -45.54150777778813, -49.68323681963287, -54.01104955380603, -58.524140261760174, -63.221703224947866, -68.10293272482167, -73.16702304283415],
        "4": [-14.515783522525915, -16.760759562641784, -19.196953129184656, -21.824331457530178, -24.642742867065834, -27.65191676119094, -30.851463627316654, -34.24087503686595, -37.52628464742008, -37.672753319974284, -37.819523645273655, -37.966595571904406, -38.11396904814835, -41.5866631919864, -45.541428500462686, -49.682835478172805, -54.00978111659891, -58.52104349123498, -63.215281761586816, -68.09103617117208, -73.14672804752021]
    },
    "qats_poly_coeffs": [ -37.819523645273655, -14.692113455939193, -1.5080067837658362, 0.008594331172654771, 0.0012684372071210721 ],
    "hf_energies": [-14.384823062111412, -16.647391126113256, -19.08535962305732, -21.70762057554105, -24.52125552494976, -27.5280856336613, -30.726637565820834, -34.11546870729174, -37.4004800625491, -37.54693406161179, -37.693689950201474, -37.840747679181504, -37.98810719906119, -41.46055017353023, -45.41517698101154, -49.55644085249811, -53.88285636322785, -58.39250513343741, -63.08298400581805, -67.95137966032644, -72.99426752670709],
    "triples_corrections": [-0.003248126337486383, -0.00384691242808078, -0.004469037687967998, -0.004689170827925569, -0.004317286665632256, -0.003769377962233152, -0.0033525629716953925, -0.0030439965566141608, -0.0028170135950197836, -0.0028080630428685177, -0.002799179540999761, -0.002790362106286786, -0.0027816097744297716, -0.002596297149072977, -0.00242277885871379, -0.0022705761743076667, -0.002134486042245201, -0.00201115065069897, -0.0018981962500425552, -0.0017937696788774779, -0.001696304466383435],
    "scf_converged": [true, true, true, true, true, true, true, true, true, true, true, true, true, true, true, true, true, true, true, true, true],
    "cc_converged": [true, true, true, true, true, true, true, true, true, true, true, true, true, true, true, true, true, true, true, true, true],
    "scf_spin_squared": [2.030856731445663, 2.0182217759905625, 2.01144093646185, 2.0085838643013045, 2.0096626884968813, 2.011575572466355, 2.011940729805693, 2.0113555286046205, 2.010524756576609, 2.0104862468622113, 2.0104476404428686, 2.010408947144103, 2.0103701764832262, 2.0094751678454514, 2.0085479565856925, 2.007710249183533, 2.0069706506543104, 2.006321923108402, 2.0057530502989445, 2.005254214523824, 2.0048172984622736],
    "cc_spin_squared": [2.001160511292121, 2.0011728549991665, 2.0011077595680957, 2.000919589919363, 2.0006422376453354, 2.0004397807384544, 2.00031851416144, 2.000239145809311, 2.0001879595925254, 2.000186078459877, 2.0001842219748083, 2.0001823897211564, 2.0001805812920628, 2.000144745857075, 2.0001156265238293, 2.00009374700278, 2.0000770512451864, 2.0000641080590222, 2.0000539049215202, 2.0000457362431963, 2.000039107285555]
}

Naming convention

Each file is named following this convention: <structure>-<calculation>-<options>. Information within each <> block is generally separated by a period; this minimizes the width of the file name. Lowercase is always used to speed up navigation with a terminal.

• <structure>: A human-readable, unique label for the structure involved. It should also specify refinements (i.e., optimizations) to represent a breadcrumb trail.
  
  Example

  The excited state for a Nitrogen atom with a charge of -1 would be labeled as n.chrg-1.mult1, whereas the ground state would be n.chrg-1.mult3. Neutral systems are still explicitly defined; for example, the ground state of a neutral Argon atom would be ar.chrg0.mult1.

• <calculation>: Specification of the program and calculation type for output files. Restarts should be specified by appending a r.
  
  Example

  Every calculation is labeled as a pyscf.qa calculation as the driver Python script performs several PySCF calculations and calculates data for quantum alchemy.

• <options>: Calculation specifications or parameters.
  
  Example

  Only the quantum chemical method and basis set are specified. Non-alphanumeric are dropped; for example, a CCSD(T)/aug-cc-pV5Z calculation would be ccsdt.augccpv5z. In these data, all coupled cluster triples corrections are perturbative. In the directory names, the u (for unrestricted) is typically dropped, but included in the file names.

Citation

If you use this dataset, please cite the corresponding manuscript in addition to this repository as specified in CITATION.cff.

License

This work is licensed under a Creative Commons Attribution 4.0 International License.