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Re: [lammps-users] Methan molecule simulation
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Re: [lammps-users] Methan molecule simulation


From: Andrew Jewett <jewett@...1937...>
Date: Tue, 28 Nov 2017 18:17:31 -0800

On Tue, Nov 28, 2017 at 6:16 PM, Andrew Jewett <jewett@...1937...> wrote:
> On Tue, Nov 28, 2017 at 4:17 PM, Kim, Changjae <cjkim@...1803...> wrote:
>> ERROR: All pair coeffs are not set (../pair.cpp:228)
> :
>> 7 atom types
>
> I'd like to say I know the reason, but somehow I'm not seeing the
> problem either.
> Checking pair.cpp line 228:
>
>   for (i = 1; i <= atom->ntypes; i++)
>     if (setflag[i][i] == 0) error->all(FLERR,"All pair coeffs are not set");
>
> Either somehow LAMMPS thinks atom->ntypes is larger than 7, or it got
> confused by these lines:
>
>> 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
>
> Curious: Did you place these lines before or after the other
> pair_coeff commands in your script?
>
> To help diagnose the problem, try replacing the code above with:
>
>   for (i = 1; i <= atom->ntypes; i++) {
>     fprintf(stderr,"i=%d, ntypes=%d\n");
>     if (setflag[i][i] == 0) error->all(FLERR,"All pair coeffs are not set");
>   }

ugh.  My apologies.  I meant to say:

  for (i = 1; i <= atom->ntypes; i++) {
    fprintf(stderr,"i=%d, ntypes=%d\n", i, atom->ntypes);
    if (setflag[i][i] == 0) error->all(FLERR,"All pair coeffs are not set");
  }

>
> compile LAMMPS, run your code, and let us know what you found.
>
> Andrew
>
>> 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
>>
>>
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