Hello everyone.
I want to relax my nano wire with fix npt but it keeps giving me this error:
“ERROR: Domain too large for neighbor bins (src/nbin_standard.cpp:133)
Last command: run 500”
I’ve put my code below
thanks
Pouya
------------------------------------------------------------
dimension 3
boundary p p p
atom_style atomic
units metal
variable dt equal 0.002
variable inputTemp equal 0.01
variable inputPress equal 1.0
variable w equal 0.018
variable periodOfRotation equal 360/${w}
variable tdamp equal 20*${dt}
variable pdamp equal 50*${dt}
----- create lattice -----
region boxRegion block -110 110 -30 30 -30 30 units box
region aluminaRegion block -110 110 -15 15 -15 15 units box
region region_a block -110 -100 -15 15 -15 15 units box
region region_b block -5 5 -15 15 -15 15 units box
region region_c block 100 110 -15 15 -15 15 units box
region surfaceStress block -100 100 -15 15 -15 15 units box
create_box 2 boxRegion
lattice custom 1 a1 4.76570 0.00000 0.00000 a2 -2.38285 4.12722 0.00000 a3 0.00000 0.00000 13.01000 &
basis 0.00000 0.00000 0.35200 &
basis 0.30600 0.00000 0.25000 &
basis 0.00000 0.00000 0.14800 &
basis 0.00000 0.00000 0.64800 &
basis 0.00000 0.00000 0.85200 &
basis 0.66667 0.33333 0.68533 &
basis 0.66667 0.33333 0.48133 &
basis 0.66667 0.33333 0.98133 &
basis 0.66667 0.33333 0.18533 &
basis 0.33333 0.66667 0.01867 &
basis 0.33333 0.66667 0.81467 &
basis 0.33333 0.66667 0.31467 &
basis 0.33333 0.66667 0.51867 &
basis 0.00000 0.30600 0.25000 &
basis 0.69400 0.69400 0.25000 &
basis 0.69400 0.00000 0.75000 &
basis 0.00000 0.69400 0.75000 &
basis 0.30600 0.30600 0.75000 &
basis 0.97267 0.33333 0.58333 &
basis 0.66667 0.63933 0.58333 &
basis 0.36067 0.02733 0.58333 &
basis 0.36067 0.33333 0.08333 &
basis 0.66667 0.02733 0.08333 &
basis 0.97267 0.63933 0.08333 &
basis 0.63933 0.66667 0.91667 &
basis 0.33333 0.97267 0.91667 &
basis 0.02733 0.36067 0.91667 &
basis 0.02733 0.66667 0.41667 &
basis 0.33333 0.36067 0.41667 &
basis 0.63933 0.97267 0.41667
create_atoms 2 region aluminaRegion &
basis 1 1 &
basis 2 2 &
basis 3 1 &
basis 4 1 &
basis 5 1 &
basis 6 1 &
basis 7 1 &
basis 8 1 &
basis 9 1 &
basis 10 1 &
basis 11 1 &
basis 12 1 &
basis 13 1 &
basis 14 2 &
basis 15 2 &
basis 16 2 &
basis 17 2 &
basis 18 2 &
basis 19 2 &
basis 20 2 &
basis 21 2 &
basis 22 2 &
basis 23 2 &
basis 24 2 &
basis 25 2 &
basis 26 2 &
basis 27 2 &
basis 28 2 &
basis 29 2 &
basis 30 2 &
units lattice
mass 1 26.98
mass 2 15.999
neigh_modify binsize 10
neighbor 3 bin
----- potentials -----
pair_style eam/alloy
pair_coeff * * AlO.eam.alloy Al O
----- define groups -----
group aluminaGroup region aluminaRegion
group group_a region region_a
group group_b region region_b
group group_c region region_c
----- initial velocities -----
velocity aluminaGroup create ${inputTemp} 123456 mom yes rot yes dist gaussian
----- computation -----
compute keneticenergy aluminaGroup ke
----- thermo dump -----
thermo 100
thermo_style custom step cpu temp pe c_keneticenergy press pxx pyy pzz
timestep ${dt}
----- run -----
minimize 1e-6 1e-8 10000 10000
reset_timestep 0
dump myDumpHeavy all xyz 50 dumpH.xyz
dump_modify myDumpHeavy element Al O
dump myDumpLight all xyz 1000 dumpL.xyz
dump_modify myDumpLight element Al O
fix relax all npt temp $inputTemp $inputTemp $tdamp aniso $inputPress $inputPress $pdamp
run 500
unfix relax
write_data data.relax pair ij
thermo 100
thermo_style custom step cpu temp pe c_keneticenergy press pxx pyy pzz
fix aluminaTempFix aluminaGroup nvt temp $inputTemp $inputTemp $tdamp
fix fix_b group_b move linear 0 0 0
fix aluminaRotationFixA group_a move rotate 0 0 0 0 -1 0 $periodOfRotation units box
fix aluminaRotationFixC group_c move rotate 0 0 0 0 1 0 $periodOfRotation units box
run 1000