Dear all
I am using BNC.tersoff potential from lammps library to minimize the energy of Boron doped graphene. but it gives me total energy zero. i think there is something wrong in my input script or coordinate file. please have a look.
coordinate file
LAMMPS data file. CGCMM style. atom_style full generated by VMD/TopoTools v1.7 on Tue Oct 23 11:46:54 IST 2018
260 atoms
367 bonds
690 angles
0 dihedrals
0 impropers
2 atom types
2 bond types
3 angle types
0 dihedral types
0 improper types
-2.50000 30.50000 xlo xhi
-1.56000 20.50000 ylo yhi
-1.500000 1.500000 zlo zhi
Masses
1 10.811000 # B
2 12.010700 # CA
Atoms # full
1 1 2 0.000000 0.000000 0.000000 0.000000 # CA GRA
2 2 2 0.000000 -1.228024 0.709000 0.000000 # CA GRA
3 3 2 0.000000 -1.228024 2.127000 0.000000 # CA GRA
4 4 2 0.000000 0.000000 2.836000 0.000000 # CA GRA
5 5 2 0.000000 2.456048 0.000000 0.000000 # CA GRA
6 6 2 0.000000 1.228024 0.709000 0.000000 # CA GRA
7 7 2 0.000000 1.228024 2.127000 0.000000 # CA GRA
8 8 2 0.000000 2.456048 2.836000 0.000000 # CA GRA
9 9 2 0.000000 4.912096 0.000000 0.000000 # CA GRA
10 10 2 0.000000 3.684072 0.709000 0.000000 # CA GRA
11 11 2 0.000000 3.684072 2.127000 0.000000 # CA GRA
12 12 1 0.000000 4.912096 2.836000 0.000000 # B
13 13 2 0.000000 7.368144 0.000000 0.000000 # CA GRA
14 14 2 0.000000 6.140120 0.709000 0.000000 # CA GRA
15 15 2 0.000000 6.140120 2.127000 0.000000 # CA GRA
16 16 2 0.000000 7.368144 2.836000 0.000000 # CA GRA
17 17 2 0.000000 9.824192 0.000000 0.000000 # CA GRA
18 18 2 0.000000 8.596169 0.709000 0.000000 # CA GRA
19 19 2 0.000000 8.596169 2.127000 0.000000 # CA GRA
20 20 2 0.000000 9.824192 2.836000 0.000000 # CA GRA
21 21 2 0.000000 12.280240 0.000000 0.000000 # CA GRA
22 22 2 0.000000 11.052217 0.709000 0.000000 # CA GRA
23 23 1 0.000000 11.052217 2.127000 0.000000 # B
24 24 2 0.000000 12.280240 2.836000 0.000000 # CA GRA
25 25 2 0.000000 14.736288 0.000000 0.000000 # CA GRA
26 26 2 0.000000 13.508265 0.709000 0.000000 # CA GRA
27 27 2 0.000000 13.508265 2.127000 0.000000 # CA GRA
28 28 2 0.000000 14.736288 2.836000 0.000000 # CA GRA
29 29 2 0.000000 17.192337 0.000000 0.000000 # CA GRA
30 30 2 0.000000 15.964313 0.709000 0.000000 # CA GRA
31 31 2 0.000000 15.964313 2.127000 0.000000 # CA GRA
32 32 2 0.000000 17.192337 2.836000 0.000000 # CA GRA
33 33 2 0.000000 19.648384 0.000000 0.000000 # CA GRA
34 34 1 0.000000 18.420361 0.709000 0.000000 # B
35 35 2 0.000000 18.420361 2.127000 0.000000 # CA GRA
.
.
;
script:
Mark Tschopp, 2010
---------- Initialize Simulation ---------------------
clear
units metal
dimension 3
boundary p p p
#read data
atom_style full
read_data gra_B2.coor
---------- Define Interatomic Potential ---------------------
pair_style tersoff
pair_coeff * * BNC.tersoff B C
neighbor 2.0 bin
neigh_modify delay 1
---------- Define Settings ---------------------
compute eng all pe/atom
compute eatoms all reduce sum c_eng
---------- Run Minimization ---------------------
reset_timestep 0
fix 1 all box/relax iso 0.0 vmax 0.001
thermo 10
thermo_style custom step pe lx ly lz press pxx pyy pzz c_eatoms
dump 2 all custom 1000 md.lammpstrj id type x y z
min_style cg
minimize 1e-25 1e-25 5000 10000
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 (Angstoms) = {length};"
print "Cohesive energy (eV) = {ecoh};”
print “All done!”
another question is how to use tersoff potential for Hydrogen containing system as there as there is no parameter for hydrogen in BNC.tersoff.
thank you
regards
Mohd Riyaz
MSc
panjan university
candigarh india (160014)