topologies

The “topologies” object in the json is an array of “topology” objects. Each “topology” contains the key aspects of the molecule or molecules you wish to study. Inside a “topology” the following fields are specified

topology

Molecular Data keywords
Keyword	Brief
geometry	An array that contains the xyz coordinates of the molecular system
symbols	An array that contains the atomic symbols of each atom specified
fragment_formal_charges	An array of charges for each fragment, for a single molecule, this is a one element array [0]
fragment_multiplicities	Similar to fragment_formal_charges, an array of multiplicities, or a one element array for non-fragmented calculation
fragments	An array of arrays, each containing the indices of atoms belonging to a fragment. These indices are ZERO-INDEXED
connectivity	An array of three element arrays that specify the connectivity of the molecule.
xyz	A string that points to a standard format xyz file to use in place of the geometry and symbols structures. It is compatible with the fragmentation keywords.

geometry

An array that contains the xyz coordinates of the topology. The coordinates are arranged per atom, for example:

"geometry": [
  -4.3997, 1.0764, 7.7009,   // atom 0 -> (x0,y0,z0)
  -3.9597, 0.2664, 7.3109,  // atom 1 -> (x1,y1,z1)
  -4.4297, 0.9964, 8.7009  // atom 2 -> (x2,y2,z2)
],

symbols

An array that contains the atomic symbols of each atom specified. For example:

"symbols": ["O", "H", "H"]

fragment_formal_charges

An array of charges for each fragment, for a single molecule, this is a one element array. This field is not required by default. If not specified, the calculation will default to a charge of 0.

{
  "topologies": [
    {
      "geometry": [
        -4.3997, 1.0764, 7.7009,
        -3.9597, 0.2664, 7.3109,
        -4.4297, 0.9964, 8.7009
      ],
      "symbols": ["O", "H", "H"],
      "fragment_formal_charges": [0]
    }
  ]
}

fragment_multiplicities

Similar to fragment_formal_charges, an array of multiplicities, or a one element array for non-fragmented calculation similar to the fragment_formal_charges. This field is not required by default. If not specified, the calculation will assume a singlet.

{
  "topologies": [
    {
      "geometry": [
        -4.3997, 1.0764, 7.7009,
        -3.9597, 0.2664, 7.3109,
        -4.4297, 0.9964, 8.7009
      ],
      "symbols": ["O", "H", "H"],
      "fragment_formal_charges": [0],
      "fragment_multiplicities": [1]
    }
  ]
}

fragments

An array of arrays, each containing the indices of atoms belonging to a fragment. These indices are ZERO-INDEXED. For example, if we had five water molecules, with one water molecule per fragment:

"fragments": [
  [ 0, 1, 2 ], [ 3,4,5 ],[ 6,7,8 ], [9,10,11 ], [12,13,14]
],

connectivity

An array of three element arrays that specify the connectivity of the molecule. The array represents:

[atom_index_1, atom_index_2, bond_order]

The bond orders can be:

Single bond (1)

Double bond (2)

Triple bond (3)

The connectivity is not needed unless the calculation contains fragments that are connected via a covalent bond. For example:

{
"topologies": [
  {
          "geometry": [
      1.1851, -0.0039, 0.9875,
      0.7516, -0.0225, -0.0209,
      1.1669, 0.833, -0.5693,
      1.1155, -0.9329, -0.5145,
      -0.7516, 0.0225, 0.0209,
      -1.1669, -0.8334, 0.5687,
      -1.1157, 0.9326, 0.5151,
      -1.185, 0.0044, -0.9875,
      1.1851, 1.9961, 1.9875,
      0.7516, 1.9775, 0.9791,
      1.1669, 2.833, 0.4307,
      1.1155, 1.0671, 0.4855,
      -0.7516, 2.0225, 1.0209,
      -1.1669, 1.1666, 1.5687,
      -1.1157, 2.9326, 1.5151,
      -1.185, 2.0044, 0.0125
    ],
    "symbols": [
      "H",
      "C",
      "H",
      "H",
      "C",
      "H",
      "H",
      "H",
      "H",
      "C",
      "H",
      "H",
      "C",
      "H",
      "H",
      "H"
    ]
    "fragments": [
      [0, 1, 2, 3],
      [4, 5, 6, 7],
      [8, 9, 10, 11],
      [12, 13, 14, 15]
    ],
    "connectivity": [
      [1, 4, 1],
      [9, 12, 1]
    ],
    "fragment_formal_charges": [0, 0, 0, 0]
  }
]
}

This system has two ethanes which are fragmented across the C-C bond. The “connectivity” signals that there’s a single bond between atom indices 1 and 4, hence [1,4,1].

The fragmentation algorithm will iterate across the fragment list and check with the connectivity, if there’s a bond being broken between two fragments, it will cap each empty valence with a hydrogen. At the end of the fragmentation calculation this Hydrogen caps are automatically subtracted out.

xyz

A string that points to a standard format xyz file to use in place of the geometry and symbols structures. It is compatible with the fragmentation keywords.