Dear Axel,
Thank you for your advice! I’ve really ignored the important information in manual. However, I encounter another problem after I moved the files to my working directory. I have tested the case in three different devices,
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LAMMPS( 31, Oct, 2015) in Windows-64bit, as long as i set up to run the case, a pop-up window appears that shows lmp_serial.exe has stop working and it is forced to be terminated.
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LAMMPS(29, Mar, 2015) in Window-32bit, it can set up to run but the thermo is weird.
Step Temp E_pair E_mol TotEng Press
0 274.50995 -1.#IND 106087.82 -1.#IND 1.#QNAN
Error on proc 0: Out of range atoms - cannot compute pppm
3)LAMMPS (15 May 2015) in Linux HPC-cluster, it is also forced to be terminated and the output and error files is enclosed.
My last question, I want to simulate that water go through three graphene oxide (graphene with hydroxy) layers. The graphene oxide atoms interact with each other via an comb3 potential. i want to use a REBO potential at first, but it can’t present the interaction with O atoms. And the water atoms interact with each other via a lj/cut/coul/long potential, the same as water/GO interaction. i don’t understand why it cannot work. Is comb3 potential improper in GO? or the hybrid pattern?
My complete input is as followed.
Initialzation
units metal
atom_style full
boundary p p p
Force fields
pair_style hybrid lj/cut/coul/long 10 12 comb3 polar_off
bond_style harmonic
angle_style harmonic
read_data waterGO-$rnm.data
kspace_style pppm 1.0e-6
set type 2 charge -1.0 # Cl charge
set type 4 charge 0.41 # Hw charge
set type 5 charge 1.0 # Na charge
set type 7 charge -0.82 # Ow charge
pair_coeff * * comb3 ffield.comb3 C NULL H NULL NULL O NULL NULL # GO comb3
pair_coeff 2 2 lj/cut/coul/long 0.00464007 4.446297312 # Cl unit parameter
pair_coeff 4 4 lj/cut/coul/long 0 0 # Hw 23.06
pair_coeff 5 5 lj/cut/coul/long 0.069693966 1.897438886 # Na
pair_coeff 7 7 lj/cut/coul/long 0.006739654 3.165520088 # Ow
pair_coeff 8 8 lj/cut/coul/long 0.681613182 2.542 # Pt
pair_coeff 1 2 lj/cut/coul/long 0.005457119 4.031673056 # C & Cl
pair_coeff 1 4 lj/cut/coul/long 0 0 # C & Hw
pair_coeff 1 5 lj/cut/coul/long 0.021149436 2.757243843 # C & Na
pair_coeff 1 7 lj/cut/coul/long 0.004545944 3.19 # C & Ow
pair_coeff 1 8 lj/cut/coul/long 0.066140915 3.0795244 # C & Pt
pair_coeff 2 3 lj/cut/coul/long 0 0 # Cl & H
pair_coeff 2 4 lj/cut/coul/long 0 0 # Cl & Hw
pair_coeff 2 5 lj/cut/coul/long 0.017982904 3.1718695 # Cl & Na
pair_coeff 2 6 lj/cut/coul/long 0.006773296 3.653041092 # Cl & O
pair_coeff 2 7 lj/cut/coul/long 0.005592179 3.8059087 # Cl & Ow
pair_coeff 2 8 lj/cut/coul/long 0.056238177 3.494148656 # Cl & Pt
pair_coeff 3 45 lj/cut/coul/long 0 0 # H & Hw Na
pair_coeff 3 78 lj/cut/coul/long 0 0 # H & Ow Pt
pair_coeff 4 * lj/cut/coul/long 0 0 # H & other
pair_coeff 5 6 lj/cut/coul/long 0.026250367 2.378611879 # Na & O
pair_coeff 5 7 lj/cut/coul/long 0.021672868 2.531479487 # Na & Ow
pair_coeff 5 8 lj/cut/coul/long 0.217954871 2.219719443 # Na & Pt
pair_coeff 6 7 lj/cut/coul/long 0.008163127 3.01265428 # O & Ow
pair_coeff 6 8 lj/cut/coul/long 0.082093122 2.700892436 # O & Pt
pair_coeff 7 8 lj/cut/coul/long 0.067777849 2.853760044 # Ow & Pt
Settings
neighbor 2.0 bin
neigh_modify delay 5
velocity sys create ${temp1} 123456
velocity fix set 0 0 0
velocity Pt set 0 0 0
timestep 0.001
write_dump all atom dump.setup_Watergraphene_rnm_{temp2}K.lammpstrj
Run for equlibrium
Fix
fix fixedatom fix setforce 0 0 0
fix Piston1 Pt1 rigid group 1 Pt1
fix Piston1 Pt2 rigid group 1 Pt2
fix 1 sys nvt temp {temp1} {temp1} 100 drag 0.2
fix p1 Pt1 aveforce NULL NULL 0.0004154
fix p2 Pt2 aveforce NULL NULL -0.0004154
Output
thermo 1000
restart 50000 restartWatergraphene_rnm_{temp2}K.*
Dump
dump 1 all atom 10 dump_Watergraphene_rnm_equil_{temp2}K.lammpstrj # 10000
Run
run 10000#0
error.22868 (1.68 KB)
output.22868 (6.76 KB)