Temperature control under non-periodic boundary conditions

LAMMPS LAMMPS General Discussion
1

Dear Lammps users,
Hello, I was simulating a deformation recently. I need a non-periodic boundary condition ssp. The target temperature is simulated at 100K; but during the simulation, the temperature of my input file can only be set to 10K. If the temperature is higher, an error will be reported: ERROR on proc 55: Bond length> table outer cutoff: type 3 length 3.72526 (…/bond_table.cpp:622);
But there is no problem with the model that simulates this process, because this model can set the temperature arbitrarily under periodic boundary conditions without reporting an error, and it will report an error when encountering non-periodic boundary conditions. I don’t know why this is. How to solve this problem?
Greatful.

Jackie

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

atom_style full

units metal

boundary s s p

atom_modify map array sort 0 0.0

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

read_data data.Cubicbto6488

------------------------------------ Create Regions -----------------------------------

region bto_fixed1 block 0.0 80.32 0 32.128 0 32.128 units box # 0 20 0 8 0 8 units lattice #

region bto_middle block 80.32 240.96 0 32.128 0 32.128 units box # 20 60 0 8 0 8 units lattice #

region bto_fixed2 block 240.96 257.024 0 32.128 0 32.128 units box # 60 64 0 8 0 8 units lattice #

region bto_mobile union 2 bto_middle bto_fixed2

region bto_total union 3 bto_middle bto_fixed1 bto_fixed2

group Gr_bto_fixed1 region bto_fixed1

group Gr_bto_middle region bto_middle

group Gr_bto_fixed2 region bto_fixed2

group Gr_bto_mobile region bto_mobile

group Gr_bto_total region bto_total

#------------------------------------ potential ------------------------------

bond_style table linear 151

bond_coeff 1 table_bond.dat Bas

bond_coeff 2 table_bond.dat Tis

bond_coeff 3 table_bond.dat Os

pair_style born/coul/wolf 0.25 12.0 12.0

pair_coeff * * 0.0 1.0 0.0 0.0 0.0

pair_coeff 4 6 1061.3 0.374 0.0 0.0 0.0

pair_coeff 5 6 3769.93 0.2589 0.0 0.0 0.0

pair_coeff 6 6 4740.0 0.2686 0.0 160.0 0.0

#------------------------------------ neighbor -------------------------------

neighbor 1.0 bin

neigh_modify every 1 delay 0 check yes

#---------------------------------- Equilibration ----------------------------

velocity Gr_bto_total create 300 12345 mom yes rot no

#---------------------------------- minimize--------------------------------------------

min_style cg

minimize 1e-10 1e-10 10000 10000

--------------------------------- Define Compute -------------------------------------

compute d_atom all displace/atom

#--------------------------Thermo information shows--------------------------------------

thermo_style custom step temp etotal ke pe cella cellb cellc cellalpha cellbeta cellgamma vol press

#---------------------------------------Display thermo-------------------------

timestep 0.0004

thermo 1

fix 1 Gr_bto_total npt temp 300 300 0.04 z 1.0 1.0 0.04

dump 1 all custom 10 dumps/stab1_*.txt id type x y z q c_d_atom[1] c_d_atom[2] c_d_atom[3] c_d_atom[4]

run 1200

unfix 1

undump 1

2

There are multiple possible reasons. For example:
Atoms can move more freely without being confined by other neighboring atoms.
Your initial geometry has atoms with nonzero image flags on a non-periodic dimension.
Your initial box is much larger than the shrink-wrap size.

It is unlikely to be caused by applying a thermostat fix.

3

Always appear ERROR on proc 55: Bond length> table outer cutoff: type 3 length 3.72526 (…/bond_table.cpp:622);
Is this a problem with the potential function? ?

4

You are in a much better position to answer that question than everybody else. The message clearly states you have a bond of length 3.72526 and says that that is larger than your upper bond cutoff. You prepared the table and created you input file, so you can best see whether that is correct and only you can know how long your bonds should be and what the potential function is and where your table stops.