Dear LAMMPS users
I am using EAM potentials for solid atoms. I used the following commands in the input file:
pair_style eam
pair_coeff 1 1 eam Au_u3.eam
I am having problem while defining pair_coeff for EAM potential in the lammps data file instead of input file. Really appreciate if someone can help me on how to define pair_coeff for EAM potential in the lammps data file.
Thank you very much.
Dear LAMMPS users
I am using EAM potentials for solid atoms. I used the following commands
in the input file:pair_style eam
pair_coeff 1 1 eam Au_u3.eamI am having problem while defining pair_coeff for EAM potential in the
lammps data file instead of input file. Really appreciate if someone can
help me on how to define pair_coeff for EAM potential in the lammps data
file.
why would you need to do that? using the pair_coeff command is completely
sufficient as it is.
axel.
Dear lammps users
Thank you very much Axel for your reply. Actually, I am running a hybrid system to see how complex monomers interact with solids. For the monomers, I am using CHARMM force field and for solid, EAM potential. For CHARMM force field, all the pair_coeff values are defined in the lammps data file. I tried to use pair_coeff in the input file for EAM potentials but getting an error saying,
“Pair coeff for hybrid has invalid style (pair_hybrid.cpp:348)”
That’s why I am thinking to define EAM potential in the lammps data file as well.
Really appreciate if someone can help me on that.
Thank you very much.
Dear lammps users
Thank you very much Axel for your reply. Actually, I am running a hybrid
system to see how complex monomers interact with solids.
now this is not a very smart way of addressing your problem. why don't
you describe the issue *completely* and correctly right away. all you are
achieving is that you are misdirecting people and thus cause irritation and
lower you chances to get helpful advice.
For the monomers, I am using CHARMM force field and for solid, EAM
potential. For CHARMM force field, all the pair_coeff values are defined in
the lammps data file. I tried to use pair_coeff in the input file for EAM
potentials but getting an error saying,
"Pair coeff for hybrid has invalid style (pair_hybrid.cpp:348)"
That's why I am thinking to define EAM potential in the lammps data file
as well.
you are wrong here. the error message is most likely from the PairCoeff
segment in the data file.
if you use a hybrid pair style, the pair coefficient settings must be
prefixed by the pair style.
also, the regular PairCoeff section cannot work, because it depends on
using mixing rules. however, there is no mixing possible between EAM and
lj/charmm interactions.
thus you would have to provide all mixed coefficients directly and do so in
either a PairIJCoeff section or with explicit pair_coeff commands. the
latter is in my opinion much more conr
mind you, this is all explained in the documentation for pair style hybrid
and read_data.
axel.
Thank you very much, Axel. Your suggestions helped a lot.
Dear Lammps users
I am trying to run MD simulation containing complex monomers and solid. I was able to run them separately but when I combined them together I am getting some error.
I am using CHARMM force field for monomers and EAM potential for solid. When I ran the case of monomers only, my pair_coeff constants were defined in the lammps data file. Since there is no mixing possible between lj/charmm and EAM, I chose to define them in the input script explicitly, thanks Axel for this information.
While running the case, I got this error:
“Numeric index is out of bounds (force.cpp:666)”
I double check all the atom ids but still having this error. I also checked the lammps mailing list. Any idea why am I getting this error. I added my input script and data file. Really appreciate your help.
Thank you very much.
…
My input script is like,
dimension 3
units real
boundary p p p
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style hybrid eam lj/charmm/coul/long 8.0 10.0 10.0 lj/cut 9.0
read_data vinyl_pyrolidine_gr_com.data
#pair_coeff 1 1 lj/charmm 0.055 3.8754 0.01 3.3854415
pair_coeff 1 0.055 3.8754 0.01 3.3854415
pair_coeff 2 1 0 0 0 0
pair_coeff 3 1 0 0 0 0
pair_coeff 2 0.2 3.296325 0.2 3.296325
pair_coeff 3 2 0 0 0 0
pair_coeff 3 0.12 3.029056 0.12 2.494516
pair_coeff 4 0 0 0 0
pair_coeff 1 4 0 0 0 0
pair_coeff 2 4 0 0 0 0
pair_coeff 3 4 0 0 0 0
pair_coeff 5 eam Au_u3.eam
pair_coeff 3 5 lj/cut 0.08602 2.95
pair_coeff 1 5 lj/cut 0 0
pair_coeff 2 5 lj/cut 0 0
pair_coeff 4 5 lj/cut 0 0
kspace_style pppm 0.0001
neighbor 2.0 bin
neigh_modify delay 5
velocity all create 280.0 1372109 dist gaussian rot yes units box loop geom
fix 1 all nvt temp 280.0 280.0 100 tchain 1
timestep 1
thermo_style custom step pe ke etotal press vol lx ly lz
thermo 1000
dump 1 all custom 10000 pyro.lammpstrj id type q x y z
restart 200000 mono_300
run 1000000
…
My data file is like,
…
40153 atoms
153 bonds
270 angles
828 dihedrals
36 impropers
5 atom types
9 bond types
17 angle types
47 dihedral types
7 improper types
-101 101 xlo xhi
-101 101 ylo yhi
0 50 zlo zhi
Masses
1 12.011
2 14.0067
3 15.9994
4 1.00794
5 196.97
Atoms
417 0 5 0 -97.7551 -98.1831 19.5044
Bond Coeffs
1 684.039 1.333
Bonds
1 7 1 2
Angle Coeffs
1 38.502 121.004 0 0
Angles
1 10 2 1 5
Dihedral Coeffs
1 3 2 180 1
Dihedrals
1 22 1 2 3 4
Improper Coeffs
1 1.439 0
Impropers
1 4 3 4 2 6
…
Dear Lammps users
I am trying to run MD simulation containing complex monomers and solid. I
was able to run them separately but when I combined them together I am
getting some error.
I am using CHARMM force field for monomers and EAM potential for solid.
When I ran the case of monomers only, my pair_coeff constants were defined
in the lammps data file. Since there is no mixing possible between
lj/charmm and EAM, I chose to define them in the input script explicitly,
thanks Axel for this information.
While running the case, I got this error:
"Numeric index is out of bounds (force.cpp:666)"
I double check all the atom ids but still having this error. I also
checked the lammps mailing list. Any idea why am I getting this error. I
added my input script and data file. Really appreciate your help.
this has nothing to do with atom ids. there are several incorrect
pair_coeff statement. please check the documentation again and more
carefully.
axel.
Dear lammps users
Thank you very much Axel. I managed to correct the pair_coeff statements and got it running. But after few timesteps, I got this new error:
“Out of range atoms - cannot compute PPPM (pppm.cpp:1667)”
I am looking the lammps mailing list. Can anyone help me on that error? Thanks a lot.
The corrected pair_coeff statements are:
…
pair_coeff 1 1 lj/charmm/coul/long 0.055 3.8754 0.01 3.3854415
pair_coeff 2 2 lj/charmm/coul/long 0.2 3.296325 0.2 3.296325
pair_coeff 3 3 lj/charmm/coul/long 0.12 3.029056 0.12 2.494516
pair_coeff 4 4 lj/charmm/coul/long 0 0
pair_coeff 1 2 lj/charmm/coul/long 0 0
pair_coeff 1 3 lj/charmm/coul/long 0 0
pair_coeff 1 4 lj/charmm/coul/long 0 0
pair_coeff 2 3 lj/charmm/coul/long 0 0
pair_coeff 2 4 lj/charmm/coul/long 0 0
pair_coeff 3 4 lj/charmm/coul/long 0 0
pair_coeff 5 5 eam Au_u3.eam
pair_coeff 3 5 lj/cut 0.08602 2.95
pair_coeff 1 5 lj/cut 0 0
pair_coeff 2 5 lj/cut 0 0
pair_coeff 4 5 lj/cut 0 0
Dear lammps users
Thank you very much Axel. After defining all the pair coefficients using mixing rule, I finally got it running. Thanks a lot.
…
pair_style hybrid/overlay lj/charmm/coul/long 8.0 10.0 10.0 eam lj/cut 9.0
read_data vinyl_pyrolidine_gr_com.data
pair_coeff 1 1 lj/charmm/coul/long 0.055 3.875409 0.01 3.3854415
pair_coeff 2 2 lj/charmm/coul/long 0.2 3.296325 0.2 3.296325
pair_coeff 3 3 lj/charmm/coul/long 0.12 3.029056 0.12 2.494516
pair_coeff 4 4 lj/charmm/coul/long 0.022 2.351973 0.022 2.351973
pair_coeff 1 2 lj/charmm/coul/long 0.104880885 3.585867 0.04472136 3.34087
pair_coeff 1 3 lj/charmm/coul/long 0.081240384 3.4522325 0.034641016 2.9399655
pair_coeff 1 4 lj/charmm/coul/long 0.034785054 3.113691 0.014832397 2.868694
pair_coeff 2 3 lj/charmm/coul/long 0.154919334 3.1626905 0.154919334 2.8954205
pair_coeff 2 4 lj/charmm/coul/long 0.066332496 2.824149 0.066332496 2.824149
pair_coeff 3 4 lj/charmm/coul/long 0.05138093 2.6905145 0.05138093 2.4232445
pair_coeff 5 5 eam Au_u3.eam
pair_coeff 3 5 lj/cut 0.08602 2.95
pair_coeff 1 5 lj/cut 0 0
pair_coeff 2 5 lj/cut 0 0
pair_coeff 4 5 lj/cut 0 0
…
Dear Lammps users
Is there any way to convert EAM potential from metal unit to real? I am running a case where all my intra and inter-atomic interactions are defined in real unit. I think it would be easy to convert EAM potential. Really appreciate your help. Thanks a lot.
Dear Lammps users
Is there any way to convert EAM potential from metal unit to real? I am
running a case where all my intra and inter-atomic interactions are defined
in real unit. I think it would be easy to convert EAM potential. Really
appreciate your help. Thanks a lot.
it is *much* easier to convert kcal to ev.
axel.