Hello,
I am using the December 15, 2015, intel complied version of lammps and have come into a pickle with comparing potential energies with HOOMD.
My inputs and data file are shown below after this section.
I am switching from HOOMD to LAMMPS because of some core pinning issues and want to get the correct energies for a 2D simulation of a simple model. The potential energies from the HOOMD run and lammps run are not consistent(-4.7 reduced energy units vs -0.5). I calculated the potential energy by hand to see which energy it was nearest too and it was hoomd. I feel confident in my calculation of the potential energy( ~ -4.6) so I am wondering what I am doing wrong in my process in LAMMPS. I checked both end results which give me the roughly the same final configuration and distance between atoms (important in verifying my potential energy calculation). I have interconverted between lammps and hoomd before in 3D and had no problems but that was with units real in LAMMPS in which I constructed similar units in HOOMD. Wondering if there might be a bug or if I am not accounting for something right.
Thanks,
Michael Goytia
in.mol
units lj
atom_style full
boundary p p p
dimension 2
variable tempi equal 0.75
variable tempf equal 0.0123
read_data random.data
pair_style lj/cut 2.5
pair_coeff 1 1 0.182097851198 1.04308220858 2.60770552144
pair_coeff 1 2 0.702854451025 0.866639911779 2.16659977945
pair_coeff 1 3 0.973685740843 0.777251743894 1.94312935973
pair_coeff 2 2 0.169736804547 0.690197614981 1.72549403745
pair_coeff 2 3 0.570151175955 0.600809447096 1.50202361774
pair_coeff 3 3 0.24318312159 0.600809447096 1.27855319803
#pair_modify shift yes
neigh_modify exclude molecule all
timestep 0.005
fix 2d all enforce2d
thermo 1000
thermo_style custom step temp pe ke etotal press vol
dump myDump all dcd 1000 random.dcd
write_dump all custom random.lammpstrj id mol type x y z
restart 100000 2d.restart
fix 1 all rigid molecule langevin \{tempi\} {tempf} 500 10
run 4000000
.data file
#Goytia's random molecule generator
6 atoms
3 atom types
-6.0 6.0 xlo xhi
-6.0 6.0 ylo yhi
-5.0 5.0 zlo zhi
Masses
1 5.00065548514
2 1.44874411347
3 0.589396705833
Atoms
1 1 1 0 -5.01247611056 0 0
2 1 2 0 -3.5 0 0
3 1 3 0 -3.83528420926 0.66167837418 0
4 2 1 0 1.98752388944 0 0
5 2 2 0 3.5 0 0
6 2 3 0 3.16471579074 0.66167837418 0