NanoDesign: FORTRAN index files

The FORTRAN file tube.f from the example in the paper will contain: 
      INTEGER*4 tube(2)
      tube(1) = 1
      tube(2) = 616
This case is so simple that the FORTRAN indices are not very useful, but a more complex FORTRAN file for two gears with teeth might look like: 
      INTEGER*4 gear1(2)
      INTEGER*4 tube1(2)
      INTEGER*4 teeth1(2)
      INTEGER*4 gear2(2)
      INTEGER*4 tube2(2)
      INTEGER*4 teeth2(2)
      gear1(1) = 1
      gear1(2) = 686
      tube1(1) = 1
      tube1(2) = 616
      teeth1(1) = 617
      teeth1(2) = 686
      gear2(1) = 687
      gear2(2) = 1372
      tube2(1) = 687
      tube2(2) = 1302
      teeth2(1) = 1303
      teeth2(2) = 1372
This information is necessary for the molecular dynamics to treat different parts of the system properly.

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