Dear users,
I am trying to simulate a mixture of layered structure consisted of graphene nanoribbons and nanoparticles. I have around 30M atoms and 2016 nanoparticles.
I wanted to consider each particle as a separate rigid structure, so I gave specific molecule ID (The molecule ID is a 2nd identifier attached to an atom[from http://lammps.sandia.gov/doc/read_data.html]) to atoms belonging to each nanoparticle and tried to use this command:
“fix rigiddiii ones rigid/nve/small molecule”
where “ones” is the group that includes all the particles and excludes the other components of this layered structure.
I get this error:
“ERROR: Fix rigid/small requires atom attribute molecule (…/fix_rigid_small.cpp:108)”
I should also mention that I am using “atom_style atomic” and do not want to use “atom_style molecular” since I am using only “airebo” and “lj/cut” in a “pair_style hybrid/overlay” potential and have no intention to make the problem more complicated by going to define bonds, angles, etc.
I am using version 15 May 2015. The submission file, a small part of data file, a picture of initial structure and the output file are attached.
{If going to review the submission file: types [124]=graphene nanoribbon; types [252040]=nanoparticles; type 2041=copper substrate}
Any clue to solve this problem would be highly appreciated.
Thanks,
Mojib Saei
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Dear users,
I am trying to simulate a mixture of layered structure consisted of graphene
nanoribbons and nanoparticles. I have around 30M atoms and 2016
nanoparticles.
I wanted to consider each particle as a separate rigid structure, so I gave
specific molecule ID (The molecule ID is a 2nd identifier attached to an
atom[from http://lammps.sandia.gov/doc/read_data.html]) to atoms belonging
to each nanoparticle and tried to use this command:
"fix rigiddiii ones rigid/nve/small molecule"
where "ones" is the group that includes all the particles and excludes the
other components of this layered structure.
I get this error:
"ERROR: Fix rigid/small requires atom attribute molecule
(../fix_rigid_small.cpp:108)"
I should also mention that I am using "atom_style atomic" and do not want to
use "atom_style molecular" since I am using only "airebo" and "lj/cut" in a
"pair_style hybrid/overlay" potential and have no intention to make the
problem more complicated by going to define bonds, angles, etc.
well, you just *made* your situation needlessly complicated by *not*
using a molecular atom style. the fact that it would support defining
bonds does *not* mean that you *have* define them. please also note
that if you do add molecule ids to a data file with atom style atomic,
the data file cannot be read correctly. the format of the data file
has to be consistent with the atom style. if you absolutely insist on
only adding the molecule id to your atom style, you can try using fix
property/atom.
axel.