Lost Atom Error in MD simulation of LiMn2O4

Dear Lammps users, Dear LAMMPS-creators

I am trying to simulate the LiMn2O4 crystal with spinel structure as a cathode material in Li-ion batteries using MD.The unit cell of this crystal consist of 56 atom(ion).for definition of this spinel structure I use the lattice command.then I create a 222 cubic simulation BOX with a periodic boundary in all three directions as an initial configuration.

My problem is An error about lost atoms.I ran the input file for the nve ensemble and checked the output. When I do this simulation with smaller time steps it lost atoms again.

I checking the outputs and saw that if in thermo_modify use the “lost ignore” keywords, the temperature and Kinetic Energy goes up very much at second step of run .now my questions are :

1-The causes of this error ? bad timestep, bad geometry, bad boundary conditions, etc?
2-how to control the temperature when the Temperature goes up very much in nve ensemble?
I am also attaching my input file with this email. I would really appreciate if somebody can help me with this.
 
# MD Run LiMn2O4 As a chatode material in Li-ion Batteries - V1
#------------------------------- Initialization -----------------------------------------
clear
units           metal
dimension          3
atom_style         charge
boundary           p p p
#------------------------Atomic Structure Definition---------------------------------------------variable alat    equal 8.24
lattice                 custom ${alat}             &
                        a1 1.0 0.0 0.0             &
                        a2 0.0 1.0 0.0             &
                        a3 0.0 0.0 1.0             & 
                        basis 0.1875 0.1875 0.4375 &
                        basis 0.6875 0.1875 0.9375 &
                        basis 0.4375 0.4375 0.6875 &
                        basis 0.9375 0.4375 0.1875 &
                        basis 0.6875 0.6875 0.4375 &
                        basis 0.4375 0.9375 0.1875 &
                        basis 0.9375 0.9375 0.6875 &
                        basis 0.1875 0.6875 0.9375 &
                        basis 0.0625 0.0625 0.0625 &
                        basis 0.3125 0.3125 0.0625 &
                        basis 0.5625 0.5625 0.0625 &
                        basis 0.8125 0.8125 0.0625 &
                        basis 0.0625 0.8125 0.3125 &
                        basis 0.3125 0.5625 0.3125 &
                        basis 0.5625 0.3125 0.3125 &
                        basis 0.8125 0.0625 0.3125 &
                        basis 0.0625 0.5625 0.5625 &
                        basis 0.3125 0.8125 0.5625 &
                        basis 0.5625 0.0625 0.5625 &
                        basis 0.8125 0.3125 0.5625 &
                        basis 0.0625 0.3125 0.8125 &
                        basis 0.3125 0.0625 0.8125 &
                        basis 0.5625 0.8125 0.8125 &
                        basis 0.8125 0.5625 0.8125 &
                        basis 0.3125 0.0625 0.0625 &
                        basis 0.0625 0.3125 0.0625 &
                        basis 0.0625 0.8125 0.0625 &
                        basis 0.8125 0.0625 0.0625 &
                        basis 0.5625 0.3125 0.0625 &
                        basis 0.3125 0.5625 0.0625 &
                        basis 0.8125 0.5625 0.0625 &
                        basis 0.5625 0.8125 0.0625 &
                        basis 0.0625 0.0625 0.3125 &
                        basis 0.0625 0.5625 0.3125 &
                        basis 0.3125 0.3125 0.3125 &
                        basis 0.3125 0.8125 0.3125 &
                        basis 0.5625 0.5625 0.3125 &
                        basis 0.8125 0.3125 0.3125 &
                        basis 0.8125 0.8125 0.3125 &
                        basis 0.5625 0.0625 0.3125 &
                        basis 0.0625 0.3125 0.5625 &
                        basis 0.0625 0.8125 0.5625 &
                        basis 0.3125 0.0625 0.5625 &
                        basis 0.3125 0.5625 0.5625 &
                        basis 0.5625 0.3125 0.5625 &
                        basis 0.5625 0.8125 0.5625 &
                        basis 0.8125 0.0625 0.5625 &
                        basis 0.8125 0.5625 0.5625 &
                        basis 0.0625 0.0625 0.8125 &
                        basis 0.0625 0.5625 0.8125 &
                        basis 0.3125 0.3125 0.8125 &
                        basis 0.3125 0.8125 0.8125 &
                        basis 0.5625 0.0625 0.8125 &
                        basis 0.5625 0.5625 0.8125 &
                        basis 0.8125 0.3125 0.8125 &
                        basis 0.8125 0.8125 0.8125  

region         LMObox block 0 2 0 2 0 2  
create_box     4 LMObox 

create_atoms   4 box basis 1 1  basis 2  1  basis 3 1  basis 4 1  basis 5 1  basis 6 1  basis 7 1  basis 8 1  &
                     basis 9 2  basis 10 2 basis 11 2 basis 12 2 basis 13 2 basis 14 2 basis 15 2 basis 16 2  &
                     basis 17 3 basis 18 3 basis 19 3 basis 20 3 basis 21 3 basis 22 3 basis 23 3 basis 24 3  & 
                     basis 25 4 basis 26 4 basis 27 4 basis 28 4 basis 29 4 basis 30 4 basis 31 4 basis 32 4  &
                     basis 33 4 basis 34 4 basis 35 4 basis 36 4 basis 37 4 basis 38 4 basis 39 4 basis 40 4  &
                     basis 41 4 basis 42 4 basis 43 4 basis 44 4 basis 45 4 basis 46 4 basis 47 4 basis 48 4  &
                     basis 49 4 basis 50 4 basis 51 4 basis 52 4 basis 53 4 basis 54 4 basis 55 4 basis 56 4
mass            1 6.94               
mass            2 54.94                     
mass            3 54.94
mass            4 15.999                  
 
group Lithium    type 1
group Manganese3 type 2
group Manganese4 type 3
group Oxygen     type 4
 
set group Lithium    charge +1
set group Manganese3 charge +1.4
set group Manganese4 charge +2.4
set group Oxygen     charge -1.2
 
# -----------------------------------Force Field----------------------------------------- 
 
pair_style born/coul/long 7.5 8 
kspace_style ewald 1e-05
variable f0 equal 0.04335               
variable a1 equal 1.043
variable a2 equal 1.038
variable a3 equal 0.958
variable a4 equal 1.503
variable b1 equal 0.080
variable b2 equal 0.070
variable b3 equal 0.070
variable b4 equal 0.075
 
variable rho11 equal ${b1}+${b1}
variable rho12 equal ${b1}+${b2}
variable rho13 equal ${b1}+${b3}
variable rho14 equal ${b1}+${b4}
variable rho22 equal ${b2}+${b2}
variable rho23 equal ${b2}+${b3}
variable rho24 equal ${b2}+${b4}
variable rho33 equal ${b3}+${b3}
variable rho34 equal ${b3}+${b4}
variable rho44 equal ${b4}+${b4}
 
variable A11 equal ${f0}*${rho11}
variable A12 equal ${f0}*${rho12}
variable A13 equal ${f0}*${rho13}
variable A14 equal ${f0}*${rho14}
variable A22 equal ${f0}*${rho22}
variable A23 equal ${f0}*${rho23}
variable A24 equal ${f0}*${rho24}
variable A33 equal ${f0}*${rho33}
variable A34 equal ${f0}*${rho34}
variable A44 equal ${f0}*${rho44}
 
variable sigma11 equal ${a1}+${a1}
variable sigma12 equal ${a1}+${a2}
variable sigma13 equal ${a1}+${a3}
variable sigma14 equal ${a1}+${a4}
variable sigma22 equal ${a2}+${a2}
variable sigma23 equal ${a2}+${a3}
variable sigma24 equal ${a2}+${a4}
variable sigma33 equal ${a3}+${a3}
variable sigma34 equal ${a3}+${a4}
variable sigma44 equal ${a4}+${a4}
  

pair_coeff 1 1 ${A11} ${sigma11} ${rho11} 0 0
pair_coeff 1 2 ${A12} ${sigma12} ${rho12} 0 0  
pair_coeff 1 3 ${A13} ${sigma13} ${rho13} 0 0
pair_coeff 1 4 ${A14} ${sigma14} ${rho14} 0 0
 
pair_coeff 2 2 ${A22} ${sigma22} ${rho22} 0 0
pair_coeff 2 3 ${A13} ${sigma23} ${rho23} 0 0
pair_coeff 2 4 ${A14} ${sigma24} ${rho24} 0 0
 
pair_coeff 3 3 ${A33} ${sigma33} ${rho33} 0 0
pair_coeff 3 4 ${A34} ${sigma34} ${rho34} 0 0
 
pair_coeff 4 4 ${A44} ${sigma44} ${rho44} 0 0
 
neighbor        2 bin
neigh_modify    every 1 delay 1 check yes page 1000000 

velocity all create 300 43454 dist gaussian  

# ----------------------------------------Running-------------------------------------------
 fix        1 all nve
thermo          100
thermo_style    custom step temp etotal pe ke lx 
thermo_modify   lost error  
timestep             0.001 
dump            1 all atom 1 dump_LiMn2O4.lammpstrj
run             10000
  

Thanks
Ali.A
 
[[email protected]](mailto:[email protected])

Dear Lammps users, Dear LAMMPS-creators

I am trying to simulate the LiMn2O4 crystal with spinel structure as a
cathode material in Li-ion batteries using MD.The unit cell of this crystal
consist of 56 atom(ion).for definition of this spinel structure I use the
lattice command.then I create a 2*2*2 cubic simulation BOX with a
periodic boundary in all three directions as an initial configuration.

My problem is An error about lost atoms.I ran the input file for the nve
ensemble and checked the output. When I do this simulation with smaller
time steps it lost atoms again.

I checking the outputs and saw that if in thermo_modify use the "lost
ignore" keywords, the temperature and Kinetic Energy goes up very much at
second step of run .now my questions are :

1-The causes of this error ? bad timestep, bad geometry, bad boundary conditions, etc?

All of the above, in addition to bad pair coefficients.

2-how to control the temperature when the Temperature goes up very much in nve ensemble?

You can't cure a disease by suppressing its symptoms. You need to fix your
bad dynamics first.

Ray

Hi,

it is likely a very bad initial structure (you need page 1000000 for some - the same? - reason). The good way to see what’s going on is to compute pe/atom and then dump it on step 0 - it will indicate high PE parts of a system, that then “explode”.

You don’t control temperature in nve ensemble. If the temperature goes up and up (after initial equilibration), it means something going wrong.

Regards,
Oleg

Ali Asadi <[email protected]…24…> 27 октября 2014 г. 18:34:22 написал: