Dear All;
As Axel suggested in a reply of my previous question, I modified my input
file to deal with only hydrogeneted graphene sheet.
The flow in my simulation is like that:
read graphenedata
apply AIREBO potential
minimize the structure
start equilibration with fix
get the equlibrated data
unfix fix
but the problem is that the calculation just hang on after giving "NAN" for
potential values. You can find the all data files I have used for the
calculation.
Axel, I am sorry for the same question. But stil its not clear for me what
is wrong. The initial structure is taken from VNL.
Thanks for your valuable suggestions.
--ipek
graphene_only.tar (930 KB)
Dear All;
As Axel suggested in a reply of my previous question, I modified my input
file to deal with only hydrogeneted graphene sheet.
The flow in my simulation is like that:
read graphenedata
apply AIREBO potential
minimize the structure
start equilibration with fix
get the equlibrated data
unfix fix
but the problem is that the calculation just hang on after giving "NAN" for
potential values. You can find the all data files I have used for the
calculation.
Axel, I am sorry for the same question. But stil its not clear for me what
is wrong. The initial structure is taken from VNL.
that structure is *obviously* incorrect. the fact that you have an odd
number of atoms in the data file is a first hint. for the kind of
system you have assembled, logic (and the chemistry of the compound)
dictates, that you have to have an even number of atoms.
if you add the following command to your input, you'll see that there
are two overlapping atoms
delete_atoms overlap 0.1 all all
also a brief visualization shows that you have very obviously an
additional bogus hydrogen in the location of a carbon.
axel.
p.s.: if you compress your tar file with gzip -9 before attaching,
you'll avoid getting your message sent to moderation for excessive
size and reduce the amount of digital noise sent to all subscribers by
over 90%. 