10.2 I/O For Normal modes

The VIBRAN section supports it own I/O commands. Commands to read, write and print coordinates and internal coordinates are identical with those in the main program. This section can read and write the Normal Mode data structure and write out the second derivative matrix (for external use) and normal mode trajectories (for the movie programs). Also, useful information about normal modes may be printed using the PRINT NORM command.

Normal Mode vectors may only be read and written in binary (FILE) format. When writing, a unit must be specified, and a contiguous subset of modes may be specified using the mode-spec. When reading modes, all of the modes in the normal mode file will be read (assuming there is enough space). If the available space is exhausted, a warning is issued, and further reading stops. Existing modes will be deleted when the READ NORM command is executed unless the append option is used, in which case, the new modes are added sequentially at the end. No modification of modes is done upon reading (i.e. normalization, or orthogonalization).

When printing Normal Modes, a variety of options may be specified. A contiguous subset of modes may be specified (the default is all modes), and an appropriate magnitude may be specified (see Normal Modes). For each specified mode, the frequency, eigenvalue, force projection, percentage of translation-rotation, and magnitude information will be printed. In addition, internal derivatives (by finite differences of the internal coordinate data structure), displacements in coordinate space, and dotproducts with other modes can be printed.

Trajectory files may be written out for a set of modes with a given magnitude factor. The modes for all specified modes may be written out in one file, or in separate files for different modes where sequential unit numbers are used starting with the specified unit number. The SEQUENTIAL keyword will cause sequential files to be written.