MDIO (molecular dynamics input/output) library

Need to design a library interface to be used by all MD-related codes
for file I/O.

Proposal:  A three-level C-interface architecture.

  Level 3 (top) -- routines that allow you to read into or write from
      MDAPI type arrays; more specifically, this level facilitates data
      manipulation with the highest level data structures, so there might
      be several level 3 modules that are plug compatible into the
      architecture hierarchy, each designed to work with a particular
      set of high-level data structures; there must also be a file-type
      structure defined in which the name and type of file is specified.

  Level 2 (middle) -- routines for reading from or writing to specific
      types of files using data structures native to that file-type;
      this level is called by level 3 and uses low-level routines from
      level 1; this middle layer can be designed as a single module
      with several sets of functions and data structures, one for each
      type of supported file.

  Level 1 (bottom) -- low-level routines for performing the raw data
      reads and writes to the files; might be best to create a nice
      file I/O abstraction that can take advantage of the underlying
      facilities of the particular file system; for example, depending
      on the size or other qualities of the file, the actual I/O
      mechanism might be the standard C library, the UNIX I/O library,
      mmap, or POSIX asynchronous I/O; support could even be provided
      for other low-level aspects such as file compression or remote
      file access via FTP.

  Graceful error handling needs to be built into the design so that
  any errors would propagate up the hierarchy to the initial call.
  Appropriate diagnostic messages should be returned, e.g. syntax
  error in (text) file on line (number).

  An application should be able to use the library at whatever level
  best suits its needs.  Level 3 modules should be straightforward to
  create in support of additional high-level data structures.  There
  should also be a method for introducing level 2 support for new file
  types, and for providing additional low-level reading and writing
  facilities for level 1.

Diagram:

         +------------+  +------------+  +------------+
Level 3  | MDAPI data |  | VMD data   |  | QM/MM data |  ...
         | interface  |  | interface  |  | interface  |
         +------------+  +------------+  +------------+
                |               |               |
                +---------------+---------------+
                                |
         +----------------------+--------------------------+
         |                                                 |
         |  +----------+  +----------+  +----------+       |
Level 2  |  | DCD file |  | PDB file |  | PSF file |  ...  |
         |  +----------+  +----------+  +----------+       |
         |                                                 |
         +----------------------+--------------------------+
                                |
         +----------------------+--------------------------+
         |                                                 |
         |  +---------------+  +------+                    |
Level 1  |  | C I/O library |  | mmap |  ...               |
         |  +---------------+  +------+                    |
         |                                                 |
         +-------------------------------------------------+