I was trying to generate a sheet of graphene in the simulation box. I have all the coordinates of the the carbon atoms, and what I wanted to do was using “create_bonds” command to generate bonds between atoms, to save the trouble of generating bonds list in the data file. See this: http://lammps.sandia.gov/doc/create_bonds.html
But it gives me an error message of:
ERROR: All pair coeffs are not set (…/pair.cpp:218)
Here’s part of my input script:
#Initialization
units real
boundary p p f
atom_style full
bond_style harmonic
pair_style lj/cut 2.5
#Atom definition
read_data data.graphene
create_bonds all all 1 1.3 1.5
pair_coeff 1 1 1.0 1.0
I was trying to generate a sheet of graphene in the simulation box. I have
all the coordinates of the the carbon atoms, and what I wanted to do was
using “create_bonds” command to generate bonds between atoms, to save the
trouble of generating bonds list in the data file. See this: http://lammps.sandia.gov/doc/create_bonds.html
this will create *even more* trouble, since it cannot generate the
necessary angles and dihedral angles.
But it gives me an error message of:
ERROR: All pair coeffs are not set (../pair.cpp:218)
well, it means just what it says. your pair coefficients are not yet
set, but it is required for the bond creating process to have a
"runnable" system.
you set the coefficients only later in the input, but LAMMPS processes
its input line-by-line.
if you *really* want to save yourself some troubles, think about using
a tool like this: http://www.ks.uiuc.edu/Research/vmd/plugins/nanotube/
VMD can write out the generated topology/geometry directly via the
topotools plugin.