Ni structure relaxation

Dear lammps user


I want to simulate nanoindentation on single crystal nickel.

I create a simulation box = (0 0 -20 ) to (180 180 220) and deleted atoms upper side and bottom side for forming free surface.

---------------------------- INITIALLIZE ----------------------------

units metal

dimension 3

boundary p p p

atom_style atomic

-------------------------- ATOM DEFINITION --------------------------

lattice fcc 3.52

region sample block 0 180 0 180 -20 220 units box

create_box 1 sample

create_atoms 1 region sample

mass 1 58.6934

---------------------------- FORCE FIELD ---------------------------

pair_style eam

pair_coeff * * Ni_u3.eam

------------------------ Making free surface -----------------------

region up block INF INF INF INF 150 INF units box

group slap1 region up

delete_atoms group slap1

region down block INF INF INF INF INF 0 units box

group slap2 region down

delete_atoms group slap2

------------------- Calculate/Extract energy of each atom -------------------

compute csym all centro/atom fcc

compute eng all pe/atom

compute eatoms all reduce sum c_eng

thermo 50

thermo_style custom step temp pe ke press pxx pyy pzz lx ly lz

thermo_modify norm no

---------------------- Setting ensemble (NVE) ----------------------

fix 1 all nve

Before indentation test, I do minimize the structure by using below scripts.

-------------------- Minimization/Stress relaxation --------------------

dump 2 all custom 500 dump.initialnickel id type xs ys zs c_csym c_eng fx fy fz

min_style cg

minimize 1e-10 1e-12 10000 100000

run 10000

velocity all create 300.0 4928459

fix 3 all temp/rescale 10 300.0 300.0 0.01 1.0

min_style cg

minimize 1e-10 1e-12 10000 100000

run 350000

region fixed block INF INF INF INF INF 30 units box

group bottom region fixed

fix 4 bottom setforce 0.0 0.0 0.0 region fixed

From the log file, I knew that the pressure decrease from 825276.87 to 4567.8092 at 0K and stabilized.

And after increasing temperature up to 300 K, pressure increase again to ~16800 and it is fluctuated for a long time step and finally stabilized.

When I check the dump file, however, there are so many dislocations in the Ni structure at both 0 K and 300 K.

(different points at between two temperature: at 0K it is possible to simulate indentation test although there are so many dislocations. But at 300K, LAMMPS show the warning message, which is that ¡°WARNING: Building an occasional neighbor list when atoms may have moved too far (…/neighbor.cpp:1401)¡±, every 200 time step and finally simulation failed with error like ¡°ERROR: Lost atoms: original 450882 current 450880 (…/thermo.cpp:389)¡±)

timestep 0.001

reset_timestep 0

variable b equal “155.0+stepdt0.1”

fix 6 all indent 10.0 sphere 90.0 90.0 v_b 20.0 units box

fix 8 all ave/time 2 5 10 v_a f_6 f_6[1] f_6[2] f_6[3] file PhcurveNi2_unload.indentation

run 155000

I cannot fix this problem. How can I fix it? I appreciate if you can help me solving this problem.

Thanks in advanced.

You’re the best person to debug your script. For anything
complicated you have to run it one stage at a time and carefully
monitor what the results are (viz, dump files, thermodyanmics, etc).

The warning is an indication you should be checking more
frequently for the need to re-neighbor, via the neigh_modify command.