JSON Output Format

Metalquicha produces JSON output files containing calculation results. The output format is standardized using the json-fortran library with scientific notation (ES format) for all real numbers.

Overview
Common Fields
Unfragmented Calculations
- Schema
- Fields
MBE Detailed Breakdown
- Schema
- Fields
GMBE Output
- Schema
- Fields
GMBE PIE Output
- Schema
- Fields
Vibrational Analysis
- Schema
- Key Thermochemistry Fields
Number Format

Overview 

All JSON output files follow a common structure:

{
  "<basename>": {
    ...calculation results...
  }
}

Where <basename> is derived from the input filename (e.g., water.mqc produces output with key water).

Output files are named output_<basename>.json and placed in the working directory.

Common Fields 

Several fields appear across multiple output types:

Field	Type	Description
`total_energy`	float	Total electronic energy in Hartree
`gradient_norm`	float	Euclidean norm of the nuclear gradient (Hartree/Bohr)
`hessian_frobenius_norm`	float	Frobenius norm of the Hessian matrix
`dipole`	object	Dipole moment with `x`, `y`, `z` components (a.u.) and `magnitude_debye`

Unfragmented Calculations 

For single-point calculations without fragmentation (driver: Energy, Gradient, or Hessian).

Schema 

{
  "<basename>": {
    "total_energy": -76.123456789012,
    "dipole": {
      "x": 0.0,
      "y": 0.0,
      "z": 0.756123456789,
      "magnitude_debye": 1.923456789012
    },
    "gradient_norm": 0.012345678901,
    "hessian_frobenius_norm": 1.234567890123
  }
}

Fields 

All fields are optional depending on the calculation type:

total_energy: Present for Energy, Gradient, and Hessian calculations
dipole: Present when dipole moments are computed
gradient_norm: Present for Gradient and Hessian calculations
hessian_frobenius_norm: Present for Hessian calculations

MBE Detailed Breakdown 

For Many-Body Expansion (MBE) calculations, provides detailed fragment energies organized by n-mer level.

Schema 

{
  "<basename>": {
    "total_energy": -152.234567890123,
    "levels": [
      {
        "frag_level": 1,
        "name": "monomers",
        "count": 10,
        "total_energy": -150.123456789012,
        "fragments": [
          {
            "indices": [1],
            "energy": -15.012345678901,
            "distance": 0.0
          },
          {
            "indices": [2],
            "energy": -15.012345678901,
            "distance": 0.0
          }
        ]
      },
      {
        "frag_level": 2,
        "name": "dimers",
        "count": 45,
        "total_energy": -2.111111111111,
        "fragments": [
          {
            "indices": [1, 2],
            "energy": -30.034567890123,
            "distance": 3.456789012345,
            "delta_energy": -0.009876543210
          }
        ]
      }
    ],
    "dipole": { ... },
    "gradient_norm": 0.012345678901,
    "hessian_frobenius_norm": 1.234567890123
  }
}

Fields 

Field	Type	Description
`levels`	array	Array of n-mer levels (monomers, dimers, trimers, etc.)
`levels[].frag_level`	integer	The n-mer order (1 = monomer, 2 = dimer, etc.)
`levels[].name`	string	Human-readable name (monomers, dimers, …, decamers, or “N-mers”)
`levels[].count`	integer	Number of fragments at this level
`levels[].total_energy`	float	Sum of all fragment energies at this level
`levels[].fragments`	array	Individual fragment data
`fragments[].indices`	array[int]	Monomer indices that compose this fragment
`fragments[].energy`	float	Raw fragment energy (Hartree)
`fragments[].distance`	float	Characteristic distance for n-mers (n > 1)
`fragments[].delta_energy`	float	MBE correction energy for n-mers (n > 1)

GMBE Output 

For Generalized Many-Body Expansion with overlapping fragments.

Schema 

{
  "<basename>": {
    "total_energy": -152.234567890123,
    "monomers": {
      "count": 3,
      "fragments": [
        {
          "index": 1,
          "energy": -50.123456789012
        },
        {
          "index": 2,
          "energy": -50.123456789012
        }
      ]
    },
    "intersections": {
      "total_count": 3,
      "levels": [
        {
          "level": 2,
          "count": 3,
          "fragments": [
            {
              "indices": [1, 2],
              "energy": -25.012345678901
            }
          ]
        }
      ]
    }
  }
}

Fields 

Field	Type	Description
`monomers.count`	integer	Number of primary fragments
`monomers.fragments`	array	Array of monomer data with `index` and `energy`
`intersections`	object	Present only when fragments overlap
`intersections.total_count`	integer	Total number of intersection terms
`intersections.levels`	array	Intersections grouped by overlap level

GMBE PIE Output 

For Pairwise Interaction Energy decomposition within GMBE.

Schema 

{
  "<basename>": {
    "total_energy": -152.234567890123,
    "gradient_norm": 0.012345678901,
    "hessian_frobenius_norm": 1.234567890123,
    "pie_terms": {
      "count": 100,
      "terms": [
        {
          "atom_indices": [0, 1, 2],
          "coefficient": 1,
          "energy": -50.123456789012,
          "weighted_energy": -50.123456789012
        },
        {
          "atom_indices": [0, 1],
          "coefficient": -1,
          "energy": -30.012345678901,
          "weighted_energy": 30.012345678901
        }
      ]
    }
  }
}

Fields 

Field	Type	Description
`pie_terms.count`	integer	Number of non-zero PIE terms
`pie_terms.terms`	array	Array of PIE term data
`terms[].atom_indices`	array[int]	Atom indices in this term (0-indexed)
`terms[].coefficient`	integer	Inclusion-exclusion coefficient (+1 or -1)
`terms[].energy`	float	Raw subsystem energy (Hartree)
`terms[].weighted_energy`	float	`coefficient * energy` contribution to total

Vibrational Analysis 

For Hessian calculations with thermochemistry analysis.

Schema 

{
  "<basename>": {
    "total_energy": -76.123456789012,
    "dipole": { ... },
    "gradient_norm": 0.000012345678,
    "hessian_frobenius_norm": 1.234567890123,
    "vibrational_analysis": {
      "n_modes": 9,
      "frequencies_cm1": [1650.123, 3800.456, ...],
      "reduced_masses_amu": [1.023, 1.045, ...],
      "force_constants_mdyne_ang": [5.123, 8.456, ...],
      "ir_intensities_km_mol": [45.67, 89.01, ...]
    },
    "thermochemistry": {
      "temperature_K": 298.15,
      "pressure_atm": 1.0,
      "molecular_mass_amu": 18.015,
      "symmetry_number": 2,
      "spin_multiplicity": 1,
      "is_linear": false,
      "n_real_frequencies": 3,
      "n_imaginary_frequencies": 0,
      "moments_of_inertia_amu_ang2": {
        "Ia": 0.612,
        "Ib": 1.156,
        "Ic": 1.768
      },
      "rotational_constants_GHz": {
        "A": 825.234,
        "B": 437.123,
        "C": 285.789
      },
      "partition_functions": {
        "translational": 3.456e+06,
        "rotational": 34.567,
        "vibrational": 1.000
      },
      "contributions": {
        "translational": {
          "energy_hartree": 0.001416,
          "entropy_cal_mol_K": 34.608,
          "Cv_cal_mol_K": 2.981
        },
        "rotational": { ... },
        "vibrational": { ... },
        "electronic": { ... }
      },
      "contribution_table": {
        "VIB": {
          "H_cal_mol": 0.0,
          "Cp_cal_mol_K": 0.0,
          "S_cal_mol_K": 0.0,
          "S_J_mol_K": 0.0
        },
        "ROT": { ... },
        "INT": { ... },
        "TR": { ... },
        "TOT": { ... }
      },
      "zero_point_energy_hartree": 0.021234,
      "zero_point_energy_kcal_mol": 13.325,
      "thermal_corrections_hartree": {
        "to_energy": 0.024567,
        "to_enthalpy": 0.025511,
        "to_gibbs": 0.002345
      },
      "total_energies_hartree": {
        "electronic": -76.123456789012,
        "electronic_plus_zpe": -76.102222789012,
        "electronic_plus_thermal_E": -76.098889789012,
        "electronic_plus_thermal_H": -76.097945789012,
        "electronic_plus_thermal_G": -76.121111789012
      }
    }
  }
}

Key Thermochemistry Fields 

Field	Description
`zero_point_energy_hartree`	Zero-point vibrational energy (ZPE)
`thermal_corrections_hartree.to_gibbs`	Thermal correction to Gibbs free energy
`total_energies_hartree.electronic_plus_thermal_G`	Total Gibbs free energy (E + thermal G correction)

The contribution_table provides a summary matching common quantum chemistry output formats:

VIB: Vibrational contributions
ROT: Rotational contributions
INT: Internal (VIB + ROT)
TR: Translational contributions
TOT: Total thermodynamic properties

All real numbers are output in scientific notation (ES format) using json-fortran’s default machine precision. The format is controlled by the JSON_REAL_FORMAT parameter in mqc_program_limits.f90.