LAMMPS Chain Tool

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1

Dear All,

Any body know how to generate two type monomers polymer system (like backbone and end bead ) by using LAMMPS chain tool? (http://lammps.sandia.gov/doc/Section_tools.html#chain)

Best Wishes!

2

I think you’d have to edit the chain tool code to do that.

Wouldn’t be hard.

Steve

3

Thanks.

I looked the chain.f file, I don’t know how to modify that, any hints?

do i = 1,natoms
write (6,903) i,molecule(i),type(i),x(i),y(i),z(i),
$ imagex(i),imagey(i),imagez(i)
enddo

Also, after edit that, how should I compile that, I am working in the windows enviroment.

I want to get the following:

Atoms

1 1 1 5.09947 3.82766 14.0409
2 1 2 5.31344 4.58832 14.6584
3 1 2 4.43393 4.39559 14.7277
4 1 2 4.14197 3.50991 14.5647
5 1 2 3.43304 2.99959 14.1035
6 1 2 2.6999 3.58894 14.1031
7 1 2 2.40869 4.3579 14.5307
8 1 2 3.31303 4.28386 14.4763
9 1 2 3.07994 4.70254 15.344
10 1 1 2.24471 5.13303 15.2155

11 2 1 5.09947 3.82766 18.0409
12 2 2 5.31344 4.58832 18.6584
13 2 2 4.43393 4.39559 18.7277
14 2 2 4.14197 3.50991 18.5647
15 2 2 3.43304 2.99959 18.1035
16 2 2 2.6999 3.58894 18.1031
17 2 2 2.40869 4.3579 18.5307
18 2 2 3.31303 4.28386 18.4763
19 2 2 3.07994 4.70254 19.344
20 2 1 2.24471 5.13303 19.2155

Best Wishes!

4

Thanks.

I looked the chain.f file, I don't know how to modify that, any hints?

read the code, make sense of it, and modify it as needed for your
system. that is how this works.

    do i = 1,natoms
        write (6,903) i,molecule(i),type(i),x(i),y(i),z(i),
     $ imagex(i),imagey(i),imagez(i)
      enddo

Also, after edit that, how should I compile that, I am working in the
windows enviroment.

how to compile executables on windows is not a LAMMPS issue. please
search in the appropriate places.

5

Hi,

Thanks for the information.

I used python to post process the output of the chain tool , which is easy to me .

Best Wishes!

6

You could easily re-write the chain tool in Python.
It is a simple short code.

Steve