I’ve not used molecule files before and am having some basic problems which I can’t resolve. This is with a very simple test run involving a CO2 molecule only, configured in the molecule file as 2 atom types (1 & 2 for C & O respectively).
The input file has pair_coeff definitions for 11, 12, 22, which should be all I need for these 2 types. However I am getting an error “All pair coeffs are not set”. This goes away if I add pair_coeff lines for 13, 23 & 33; so it seems to think there are 3 atom types (or it is expecting coefficients to be defined at the atom level).
I am also getting a warning “WARNING: Molecule attributes do not match system attributes” which may relate to the problem but I’m unclear what it is referring to.
The dump confirms only 2 atom types are created (I uncommented the extra pair_coeff lines to generate the dump but that was the only change from the input file that produced the error).
Attached below are the input script, molecule file, piped screen output and dump file.
I’m sure this is very simple but I can’t identify the problem.
I’ve not used molecule files before and am having some basic problems which
I can’t resolve. This is with a very simple test run involving a CO2
molecule only, configured in the molecule file as 2 atom types (1 & 2 for C
& O respectively).
The input file has pair_coeff definitions for 11, 12, 22, which should be
all I need for these 2 types. However I am getting an error “All pair
coeffs are not set”. This goes away if I add pair_coeff lines for 13, 23 &
33; so it seems to think there are 3 atom types (or it is expecting
coefficients to be defined at the atom level).
LAMMPS is set up to expect (or rather require) 3 atom types, because
you told LAMMPS so with your
create_box 3 container
command. this locks in the system configuration with 3 atom types.
This doesn't mean, that there have to be atom present for all atom
types, but you need to provide (dummy) force field parameters for all
of them.
I am also getting a warning “WARNING: Molecule attributes do not match
system attributes” which may relate to the problem but I’m unclear what it
is referring to.
i suspect this is referring to the lack of charge information in atom
style template.
try with atom style full or use fix property/atom to add the charge property.
axel.