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I am trying to simulate a mixture of CO2 and N2 but I keep getting ERROR: lost atoms: original 1500 current 1495. I have performed several energy minimizations and even tried increasing the size of the box, yet I am still getting this error. Can anyone help? Below is the input script and data files.

units           real      
atom_style      full        
boundary        p p p

read_data       CO2_initial.data

pair_style      lj/cut/coul/long 12
pair_modify     tail yes                
bond_style      harmonic
angle_style     harmonic
kspace_style    pppm 1.0e-4  

include PARM.lammps
    
molecule N2 N2.mol
create_atoms 0 random 5 428515 NULL mol N2 645341

group CO2 type 1 2
group n2 type 3 4
#neighbor       2.0 bin
#neigh_modify   every 1 delay 0 check yes
                                             
#Minimization
                                               
thermo 10                                               
min_style sd
minimize    1.0e-4 1.0e-6 1000 10000

variable        dt equal 1
timestep        ${dt}

reset_timestep 0

velocity all create 300 4932567 dist uniform
variable        kinetic_energy equal ke
variable        potential_energy equal pe
variable        pressure equal press   
variable        Temperature equal temp   
variable        Density equal density    
variable        total_energy equal etotal

fix             1 all npt temp 300 300 100 iso 78.9539 78.9539 1000
thermos          1000
#fix            myave1 all ave/time 10 100 1000 v_Temperature v_kinetic_energy v_potential_energy v_total_energy v_pressure file energy1.data
thermo_style    custom step temp density epair ke etotal press vol
run             500000

DATA FILES

**N2**
# N2 molecule file. TraPPE model.

3 atoms
2 bonds
1 angles

Coords
    
1   0.0 0.00 0.00
2   -0.55 0.00 0.00
3   0.55 0.00 0.00

Types

1   3
2   4 
3   4 
 

Charges

1    0.964
2   -0.482
3   -0.482

Bonds

1   1      1      2
2   1      1      3

Angles

1   1      2      1      3
--------------------------------------------------------------------------


**PARM**

# Masses

mass            1   12.0107  #C
mass            2   15.9994  #O
mass            3   1e-20    #COM
mass            4   14.005 #N

# Pair coeff

pair_coeff      1 1 0.05365359 2.8000       
pair_coeff      2 2 0.15698643 3.05000          
pair_coeff      1 2 0.09177627989 2.9250   
pair_coeff      4 4 0.07153812 3.31000
pair_coeff      1 4 0.06195382926 3.055
pair_coeff      2 4 0.1059741198 3.180 
pair_coeff      * 3 0.000000000000 0.000    

# Bond coeff

bond_coeff      1 5000.00 1.16 
bond_coeff      2 5000.00 0.55

# Angle coeff

angle_coeff     1 500.0 180.00
angle_coeff     2 500.0 180.00
```
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1 Answer 1

3
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Your $\require{mhchem} \ce{N2}$ molecule template has a virtual charge site with a stated mass of 1e-20 units, but your input file has no means of rigidifying the $\ce{N2}$ molecules, and thus the dynamics cannot be integrated with any reasonable timestep.

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  • 1
    $\begingroup$ please how can I rigidify the N2 in my input file $\endgroup$ Oct 4, 2023 at 12:11
  • $\begingroup$ can you please assist me? $\endgroup$ Oct 4, 2023 at 17:29
  • 1
    $\begingroup$ See fix shake or fix rigid. Please note that at some point you have to justify your simulation choices to another scientist reviewing your paper, and you cannot say "an Internet stranger told me on StackExchange" to argue that your results are correct or wrong. $\endgroup$ Oct 5, 2023 at 1:58
  • $\begingroup$ please how do I apply the fix rigid since we have two different molecules $\endgroup$ Oct 6, 2023 at 6:13
  • $\begingroup$ You can create groups in LAMMPS script and apply fixes to specific groups. $\endgroup$
    – Roni Saiba
    Oct 8, 2023 at 5:46

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