question regarding restart2data tool

Hello Lammps users:

I just found out that the restart2data tool will generate data file containing type 0 bonds if the MD process prior to the restart file is associated with bond breakage (like for quartic bonds, broken bond is set to type zero). Using the generated data file will cause error but directly using the restart file seems to be fine. Now I need to use the data file, is there some way to work around this problem without modifying the source code of the tool? Thanks.

BTW, another question: can one redefine a orthogonal simulation box to be triclinic (i.e. adding 0 0 0 xy yz xz) in the input script instead of modifying the data file? Thanks.

Best
Shaorui

Hello Lammps users:

I just found out that the restart2data tool will generate data file
containing type 0 bonds if the MD process prior to the restart file is
associated with bond breakage (like for quartic bonds, broken bond is set to
type zero). Using the generated data file will cause error but directly
using the restart file seems to be fine. Now I need to use the data file, is
there some way to work around this problem without modifying the source code
of the tool? Thanks.

no. but the change shouldn't be too difficult.

BTW, another question: can one redefine a orthogonal simulation box to be
triclinic (i.e. adding 0 0 0 xy yz xz) in the input script instead of
modifying the data file? Thanks.

have you tried "change_box"?

axel.

Hello Lammps users:

I just found out that the restart2data tool will generate data file
containing type 0 bonds if the MD process prior to the restart file is
associated with bond breakage (like for quartic bonds, broken bond is set to
type zero). Using the generated data file will cause error but directly
using the restart file seems to be fine. Now I need to use the data file, is
there some way to work around this problem without modifying the source code
of the tool? Thanks.

do you have a simple example input deck (not restart) to demonstrate this?
i've looked through the restart2data code and the necessary change
seems to be pretty simple to implement. so with a test example, i
could test and debug (if needed) the changes.

thanks,
   axel.

Hi Axel:

I am a bit swamped right now. I will generate a smaller system and send it to you later. Sorry for the delay.

Shaorui

Hi Axel:

I am a bit swamped right now. I will generate a smaller system and send it
to you later. Sorry for the delay.

FYI,

i decided to just go ahead and implement the
(rather simple) changes. the modified version
of restart2data is available here:

http://git.icms.temple.edu/git/?p=lammps-icms.git;a=history;f=tools/restart2data.cpp;hb=HEAD

axel.

this will be part of today's patch - thanks for the upgrade Axel

Steve