Added 'timeout <value>' option to the adios reader, so that a rerun can...

       *format* values = format of dump file, must be last keyword if used

         *native* = native LAMMPS dump file

         *xyz* = XYZ file

         *adios* = dump file written by the :doc:`dump adios <dump_adios>` command

         *adios* [*timeout* value] = dump file written by the :doc:`dump adios <dump_adios>` command

           *timeout* = specify waiting time for the arrival of the timestep when running concurrently.

                     The value is a float number and is interpreted in seconds.

         *molfile* style path = VMD molfile plugin interface

           style = *dcd* or *xyz* or others supported by molfile plugins

           path = optional path for location of molfile plugins

   read_dump dump.dcd 0 x y z format molfile dcd

   read_dump dump.file 1000 x y z vx vy vz format molfile lammpstrj /usr/local/lib/vmd/plugins/LINUXAMD64/plugins/molfile

   read_dump dump.bp 5000 x y z vx vy vz format adios

   read_dump dump.bp 5000 x y z vx vy vz format adios timeout 60.0

Description

"""""""""""

the atoms evenly amongs the processes. The number of writers that

has written the dump file does not matter. Using the adios style for

dump and read_dump is a convenient way to dump all atoms from *N* 

writers and read it back by *M* readers.

writers and read it back by *M* readers. If one is running two 

LAMMPS instances concurrently where one dumps data and the other is 

reading it with the rerun command, the timeout option can be specified 

to wait on the reader side for the arrival of the requested step. 

Support for other dump format readers may be added in the future.

   rerun dump.vels dump x y z vx vy vz box yes format molfile lammpstrj

   rerun dump.dcd dump x y z box no format molfile dcd

   rerun ../run7/dump.file.gz skip 2 dump x y z box yes

   rerun dump.bp dump x y z box no format adios 

   rerun dump.bp dump x y z vx vy vz format adios timeout 10.0

Description

"""""""""""

    (10,31999,0)    31924 1 32.8007 32.8736 32.5882 -0.980419 -0.237448 -1.21369

Concurrent rerun use case

=========================

The ADIOS BP4 engine allows for reading from the dump file (completed steps) while the writer is still running (and dumping new steps). In two terminals one can run the in.first and in.rerun examples concurrently. The second simulation will blocking wait for the steps from the first.

$ mpirun -n 2 lmp -in in.first

$ mpirun -n 4 lmp -in in.rerun 

    <io name="read_dump">

        <engine type="BP4">

            <parameter key="OpenTimeoutSecs" value="10.0"/>

        </engine>

    </io>

thermo          100

rerun           lj_dump.bp first 200 last 800 every 200 &

                dump x y z vx vy vz format adios

                dump x y z vx vy vz format adios timeout 10.0