LAMMPS sandia: Help needed to understand the algorithm that LAMMPS uses to calculate the potential energy of the system.

Dear All,

I use LAMMPS version: lammps- 7Aug, 2019. I downloaded it from lammps website.

I was having difficulties replicating the values of potential energy of the system using the theoretical calculations and LAMMPS. I did it for three different systems. To do a sanity check, I tried to get the output of pair potential values for all the systems used, to my surprise these values were different from what was given in all the potential file.

I tried to calculate the potential energy for a 2 atom system which is described as:(For simplicity, I have shown only one of the input atom coordinates)

FeNiCr:
2 atoms

3 atom types

0.0000 5.0035 xlo xhi
0.0000 5.0035 ylo yhi
0.0000 2.3586 zlo zhi

Masses

1 55.845
2 58.6934
3 51.9961

Atoms

1 1 0.0000 0.0000 0.0000
2 1 2.87056 0.000 0.0000

The potential files were downloaded and replicated for research purposes from:
https://www.ctcms.nist.gov/potentials/

The LAMMPS input format looked like the following:

Find minimum energy fcc configuration

Mark Tschopp, 2010

---------- Initialize Simulation ---------------------

clear
units metal
dimension 3
boundary s s s
atom_style atomic
read_data atoms1.dat

---------- Create Atoms ------------------

---------- Define Interatomic Potential ---------------------

pair_style eam/alloy
pair_coeff * * FeNiCr.eam.alloy Fe Ni Cr
pair_write 1 1 5000 r 0.00112 5.6 table.txt RITEEEESH
neighbor 2.0 nsq
neigh_modify every 1 delay 10 check yes

---------- Define Settings ---------------------

compute eng all pe/atom
compute eatoms all reduce sum c_eng

---------- Run Minimization ---------------------

reset_timestep 0
thermo 10
thermo_style custom step pe lx ly lz press pxx pyy pzz c_eatoms
dump 1d all cfg 1000 dump1.all.*.cfg mass type xs ys zs fx fy fz id type c_eng
min_style cg
minimize 1e-25 1e-25 50000 100000

variable natoms equal “count(all)”
variable teng equal “c_eatoms”
variable length equal “lx”
variable ecoh equal “v_teng/v_natoms”

print “Total energy (eV) = {teng};" print "Number of atoms = {natoms};”
print “Lattice constant (Angstroms) = {length};" print "Cohesive energy (eV) = {ecoh};”

print “All done!”

I did similar calculations for different systems using the following potential files with 2 atoms system shown above. But with different spacing which was chosen by critically evaluating the position values used in the reference which was again found at the nist repository:
Ag_Zhou04.eam.alloy

FeNiCr.eam.alloy
Al99.eam.alloy

Unfortunately, by using the following EAM method formula and the values of the pair-potentials, charge density and embedding function from the reference, the values that I get for potential energy is different from LAMMPS:

image.png

I have to format the EAM potential for the system which I am creating right now. Therefore, I want to make sure I understand how the LAMMPS algorithm is calculating the given values of potential energy.

I really appreciate your help. If you need any other information from my end, please, don’t hesitate to reach me out at: [email protected]…2061….

Thanks.

Best,

Ritesh

Thanks.

are you looking at the output in the file from the pair_write command?

axel.

image.png