Creating an Input File

Hi All,
I want to use the results of my previous run ( updated atomic positions and velocities) as an input for another run. For the first run, i did not use any software to prepare an input file - I used create lattice, atoms etc

Which pre-processing software should i use to be able to import updated atomic positions and velocities ? Also, is there any tutorial which explains how to prepare the data files?

Thanks,
Rose

Hi,

there are many ways, actually.

http://lammps.sandia.gov/doc/read_data.html
http://lammps.sandia.gov/doc/read_dump.html
http://lammps.sandia.gov/doc/read_restart.html

Data file format (if you want to create it yourself) is described in read_data doc page. There are also data files in lammps distribution, that you can use as an example. But in fact you don't need to prepare the data file by hand, just use http://lammps.sandia.gov/doc/write_data.html or http://lammps.sandia.gov/doc/dump.html or http://lammps.sandia.gov/doc/restart.html during the first run.

Oleg

Rose Dalyan <[email protected]> 31 октября 2014 г. 2:50:25 написал:

Hi Oleg,
I think i could not state the question clearly. I am trying to prepare a data.xxx file to read data from it, and i was wondering which pre-processing software can i use to create a data file. ( I already have the positions and velocities for the data file)
Thanks,
Rose

Hi Oleg,
I think i could not state the question clearly. I am trying to prepare a data.xxx file to read data from it, and i was wondering which pre-processing software can i use to create a data file. ( I already have the positions and velocities for the data file)

No, oleg’s response was spot on. You can use all of these to restart your simulation, but most importantly, you should learn how to do proper restarting with the restart/write_restart/read_restart commands. It also looks as if you need to talk with your adviser about MD basics. Restarting is one of the core tasks of managing MD simulations and it is quite surprising that you are not aware of it.

Axel

Hi Axel,
Thanks for your response. I do not want to restart my simulation. What i want to do is that I want to introduce an gas molecule on top of heated solid surface. ( it is warm-up by using a thermostat and i wanna use the updated atomic positions and velocities for the data file i will use for the second simulation). That is why; i need to create a new data file with the gas molecule and the surface atoms with updated atomic positions and velocities.

I do not have an advisor.
Thanks,
Rose

Hi Axel,
Thanks for your response. I do not want to restart my simulation. What i want to do is that I want to introduce an gas molecule on top of heated solid surface. ( it is warm-up by using a thermostat and i wanna use the updated atomic positions and velocities for the data file i will use for the second simulation). That is why; i need to create a new data file with the gas molecule and the surface atoms with updated atomic positions and velocities.

again, i repeat. oleg was pointing you into the right direction. only,
he cannot give you a good answer, if you omit important details.
the only additional thing to mention would be this link and the tools
it is pointing to: http://lammps.sandia.gov/prepost.html

nevertheless, the update of positions that you want can indeed be done
by using a regular system setup and then just overwriting the subset
that you equilibrated with read_dump. it really helps to read the
links that get pointed out to you. and if you insist on a custom data
file *with* the velocities *and* additional components, there is
little else than generating a custom data file from scratch according
to the description in the read_data documentation.

if that doesn't help you enough, then i don't know much else to
suggest. it should be plenty information. the rest is just a little
legwork and piecing the pieces of information that are pertinent to
your particular situation together.

I do not have an advisor.

too bad. it looks like you need one.