Dear all,
I am working crosslinking of monomers with curing agent molecules to get resin. I have located reactive sites at both the molecules by specifying the atom types. I am trying with fix bond/create … command but not able to do it. With cross-linking, we have to create new bonds and remove some of the existing bonds (on both of the molecules). Please suggest what i need to do complete the cross-linking.
There is also a fix bond/break command you can look at.
You can search the mail list for recent posts by
Jan Michael-Carrillo who was working on a new fix
that both added and deleted bonds. He is CCd on this
message.
Steve
It's not clear how many cross-links you want to generate and how you
want to generate them.
If you want LAMMPS to generate the cross-links automatically whenever
two atoms are close to eachother then "fix bond/create" should do
exactly what you want. I would recommend to keep trying this. It
should work. (I have not tried it, so I can not help you with that
problem.)
Alternately, if you don't have to add too-many cross-links, then it be
difficult to edit the data file, and add a few lines to the "Bonds"
section containing the pairs of atoms you want to connect.
To figure out which atoms you want to connect, you can visualise the
molecule in VMD using topotools using commands like this:
topo readlammpsdata YOURFILE.data full
animate write psf YOURPSFFILE.psf
If you use a different atom_type (such as "molecular") then replace
"full" with "molecular".
Then in the 3-D window, rotate the molecule into position and type %
and click on the atoms you want to connect. VMD will write the atom
ID number in the terminal. These are the numbers you want to put in
the lines of text you will add to the "Bonds" section of your data
file. (Note: You may have to add 1 to them. This will require some
experimentation.)
(To rotate or move the molecule again, use the "r" and "t" keys.)
Of course, be sure to use VMD to visualise your new data file again
before you start your simulation to make sure you connected the
correct pairs of atoms.
I hope this helps.
Andrew
Hello lammps users,
I found what is seem to be a problem with the fix_gcmc.
I did one run just on one processor, and then I wanted to compare the efficiency increasing the number of processors, so I did another run in 8 processors, I got different results, after going through the fix_gcmc.cpp I found that the energies that I was geting for the insertion or deletion of a particle where different depending on the number of processors i run my script, I think this should not happen.
I wrote some printf in the code in order for you to see what I’m talking about, I attached two outs in 1 and 8 processors that says the energy of the particle that’s being deleted or inserted.
thank you in advance
Matias
1proc (1.54 KB)
8procs (1.54 KB)