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Re: [lammps-users] How to build a cubic box
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Re: [lammps-users] How to build a cubic box


From: Andrew Jewett <jewett@...1937...>
Date: Mon, 30 Oct 2017 20:43:33 -0700

It's not clear what you are asking for.

1) If you have started a simulation that is currently using triclinic
boundaries, and you want to use rectangular boundary conditions, then
you will have to deform your simulation.  In that case, read the
following documentation:
http://lammps.sandia.gov/doc/fix_deform.html

2) If you are trying to build a system from scratch using cubical or
rectangular boundary conditions, read on.

I'm assuming you are using "read_data" to read a data file containing
the shape of the simulations boundary box.  In that case, read the
documentation for "read_data"
http://lammps.sandia.gov/doc/read_data.html
(specifically, scroll down to the the section named "Format of the
header of a data file")

Here's an example from the top of a "data" file

     91956  atoms
    113911  bonds
    157283  angles
    215912  dihedrals
    175273  impropers
     139  atom types
     180 bond types
     259 angle types
     481 dihedral types
      33 improper types

  -1114.56616515 1199.16204377 xlo xhi
  -1268.33024819 1343.74509338 ylo yhi
  -1188.7937261 1174.97203135 zlo zhi

A few obligatory moltemplate examples with rectangular boundary conditions:
http://moltemplate.org/visual_examples.html#translocation
http://moltemplate.org/visual_examples.html#nanotube+water
http://moltemplate.org/visual_examples.html#3bodyWater+hydrocarbons
http://moltemplate.org/visual_examples.html#2bead_heteropolymer
No email from me is complete without promoting moltemplate in some fashion
Many other useful LAMMPS data file builders are listed at:
http://lammps.sandia.gov/prepost.html

Andrew

On Fri, Oct 27, 2017 at 1:19 PM, Khourshaei Shar, Ali
<akhoursh@...6666...> wrote:
> Dear LAMMPS users,
>
> Hi,
>
>
> Currently I'm working on a simulation and My initial simulation box is
> triclinic. However, I have to make a cubic one for some mechanical
> simulation. So, any help on how to make a cubic simulation box fast and easy
> ?!
>
> Thanks in advance,
>
> Ali
>
>
>
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