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7.8 Manipulating Trajectories

The trajectories produced from a dynamics calculation generally require some sort of additional processing to make them easier to analyze. Currently, two such commands are provided, MERGE and ROTATE. MERGE is described below, and ROTATE is described under the COMPARE command, see Reorienting a Coordinate Trajectory.

Frequently, one generates a trajectory into small files to minimize the CPU time of one job. However, so many files are usually hard to manage so it is desirable to merge said files into larger units. This command provides that capacity. In addition, it is possible to break up the trajectory into smaller pieces and to sample the trajectory less frequently than originally generated.

7.8.1 Merge Trajectory Syntax

          MERGE DYN [ COOR ] [FIRSTU unit-number] [NUNIT integer] [SKIP integer]
                    [ VEL  ]       [OUTPUTU unit-number] [NFILE integer]

7.8.2 Merge Trajectory Options

     Option  Default  Purpose
     [COOR]    COOR   Specification of the type of trajectory file. COOR is
     [VEL ]           coordinates; VEL is velocities.
     FIRSTU     51    The first unit of the trajectory to be read.
     NUNIT      1     The number of units to be read starting with FIRSTU
     SKIP       1     Only those coordinate whose dynamics step number
                      modulo SKIP will be reoriented and written out.
     OUTPUTU    61    The first unit number of the output trajectory
     NFILE            The number of coordinates written to each output file.
                      If left out, this will be set to the number of
                      coordinates in the first input file times the number of
                      input files. WARNING: This default will generate a bad
                      trajectory file if SKIP is not set to the interval
                      actually present in the trajectories. Further, if you
                      set its value to be larger than the number of
                      coordinates that are actually written in any output
                      file, you will have problems. The error that is
                      generated results from the control array in the
                      beginning specifying that there are more coordinates
                      than actually exist in the file. EOF errors will result
                      when the trajectory is read.

The title of the output trajectory will be copied from the input trajectory.