LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Mailing List Archives
[lammps-users] Methan molecule simulation
[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

[lammps-users] Methan molecule simulation


From: "Kim, Changjae" <cjkim@...1803...>
Date: Wed, 29 Nov 2017 00:17:08 +0000

Hi guys,

 

I was trying to run simulation for methane molecules in nanotubes but I had an error message that all pair coeffs were not set in my model.

My data file and input script

 

a) running error

Reading data file ...

  orthogonal box = (-19.964 -20.0245 5.03305) to (80.036 79.9755 55.124)

  1 by 1 by 1 MPI processor grid

  reading atoms ...

  3700 atoms

  scanning bonds ...

  4 = max bonds/atom

  scanning angles ...

  3 = max angles/atom

  scanning dihedrals ...

  8 = max dihedrals/atom

  scanning impropers ...

  2 = max impropers/atom

  reading bonds ...

  3770 bonds

  reading angles ...

  3480 angles

  reading dihedrals ...

  6870 dihedrals

  reading impropers ...

  1140 impropers

Finding 1-2 1-3 1-4 neighbors ...

  special bond factors lj:   0          0          0

  special bond factors coul: 0          0          0

  4 = max # of 1-2 neighbors

  6 = max # of 1-3 neighbors

  18 = max # of 1-4 neighbors

  18 = max # of special neighbors

500 atoms in group cnt

1000 atoms in group ch4

3700 atoms in group all

ERROR: All pair coeffs are not set (../pair.cpp:228)

 

b) data file

 

LAMMPS data file. CGCMM style. atom_style full generated by VMD/TopoTools v1.7 on Tue Nov 28 21:55:27 +0900 2017

3700 atoms

3770 bonds

3480 angles

6870 dihedrals

1140 impropers

7 atom types

1 bond types

2 angle types

1 dihedral types

2 improper types

-19.963999 80.036001  xlo xhi

-20.024500 79.975500  ylo yhi

5.033046 55.123954  zlo zhi

 

# Pair Coeffs

#

# 1  1H1

# 2  2H1

# 3  3H1

# 4  4H1

# 5  B

# 6  C1

# 7  N

 

# Bond Coeffs

#

# 1  1

 

# Angle Coeffs

#

# 1  1

# 2  2

 

# Dihedral Coeffs

#

# 1  1

 

# Improper Coeffs

#

# 1  1

# 2  2

 

c) input script

#-

#------------------------ INITIALIZATION ----------------------------

 

units real

dimension 3

boundary p p p

atom_style full

 

#------------------------ CONFIGURATION ----------------------------

 

read_data       case1.data

 

# ------------------------ FORCE FIELD ------------------------------

 

# interaction styles

pair_style lj/cut/coul/cut 12.0

bond_style harmonic

angle_style harmonic

 

pair_coeff 1 1 0.00 0.00 #1H

pair_coeff 2 2 0.00 0.00 #2H   

pair_coeff 3 3 0.00 0.00 #3H

pair_coeff 4 4 0.00 0.00 #4H

pair_coeff 5 5 0.102 3.188 #B

pair_coeff 6 6 0.086 3.4 #C1

pair_coeff 7 7 0.102 3.188 #N  

 

pair_coeff 1 6 0.03 2.5 #1H-C

pair_coeff 2 6 0.03 2.5 #2H-C

pair_coeff 3 6 0.03 2.5 #3H-C

pair_coeff 4 6 0.03 2.5 #4H-C

 

bond_coeff 5 340 1.09

 

angle_coeff 5 33 107.8

 

If you have experienced or solved this problem, please give me your own solution or share your experience.

Thanks