grafen 0.9.1

Create graphene and other substrates for use in molecular dynamics simulations.
Documentation 
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{
  "residue_definitions": [
    {
      "code": "GRA",
      "atoms": [
        {
          "code": "C",
          "position": {
            "x": 0.071,
            "y": 0.071,
            "z": 0.0
          }
        }
      ]
    },
    {
      "code": "SIO",
      "atoms": [
        {
          "code": "O1",
          "position": {
            "x": 0.1125,
            "y": 0.075,
            "z": 0.151
          }
        },
        {
          "code": "SI",
          "position": {
            "x": 0.1125,
            "y": 0.075,
            "z": 0.0
          }
        },
        {
          "code": "O2",
          "position": {
            "x": 0.1125,
            "y": 0.075,
            "z": -0.151
          }
        }
      ]
    },
    {
      "code": "SOL",
      "atoms": [
        {
          "code": "OW",
          "position": {
            "x": 0.0,
            "y": 0.0,
            "z": 0.0
          }
        },
        {
          "code": "HW2",
          "position": {
            "x": 0.0,
            "y": 0.0,
            "z": 0.1
          }
        },
        {
          "code": "HW1",
          "position": {
            "x": 0.0943,
            "y": 0.0,
            "z": -0.0333
          }
        }
      ]
    }
  ],
  "component_definitions": [
    {
      "SurfaceSheet": {
        "name": "Graphene",
        "residue": {
          "code": "GRA",
          "atoms": [
            {
              "code": "C",
              "position": {
                "x": 0.071,
                "y": 0.071,
                "z": 0.0
              }
            }
          ]
        },
        "lattice": {
          "Hexagonal": {
            "a": 0.142
          }
        },
        "std_z": null,
        "normal": "Z"
      }
    },
    {
      "SurfaceSheet": {
        "name": "Silica",
        "residue": {
          "code": "SIO",
          "atoms": [
            {
              "code": "O1",
              "position": {
                "x": 0.1125,
                "y": 0.075,
                "z": 0.151
              }
            },
            {
              "code": "SI",
              "position": {
                "x": 0.1125,
                "y": 0.075,
                "z": 0.0
              }
            },
            {
              "code": "O2",
              "position": {
                "x": 0.1125,
                "y": 0.075,
                "z": -0.151
              }
            }
          ]
        },
        "lattice": {
          "Triclinic": {
            "a": 0.45,
            "b": 0.45,
            "gamma": 60.0
          }
        },
        "std_z": null,
        "normal": "Z"
      }
    },
    {
      "SurfaceCylinder": {
        "name": "Graphene Nanotube",
        "residue": {
          "code": "GRA",
          "atoms": [
            {
              "code": "C",
              "position": {
                "x": 0.071,
                "y": 0.071,
                "z": 0.0
              }
            }
          ]
        },
        "lattice": {
          "Hexagonal": {
            "a": 0.142
          }
        },
        "alignment": "Z",
        "cap": "Bottom"
      }
    }
  ]
}