[lammps-users] Using molecule command for fix_gcmc implementation

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1

Hello All,

I have the following molecule template which I am trying to get read by LAMMPS but I’m encountering the repeated error saying “Unknown section in molecule file”. I cannot seem to find out how my template is differing from the documentation page for molecule command. Can anyone help me out with this? I am using the LAMMPS version of 7th Aug 2019.

LAMMPS molecule file for fix_gcmc command, version 17 Aug 2019

8 atoms
7 bonds
6 angles
5 dihedrals

Coords # line syntax: ID x y z

1 8.655806000694584e-11 3.655472633943652e-10 2.143935356832895e-10
2 9.516117669300782e-10 3.026898792026158e-10 2.255953865385892e-10
3 8.712101384263634e-10 3.423087047366610e-10 9.379577047640335e-11
4 7.286655201220055e-10 2.869197257653652e-10 7.799415167125139e-11
5 6.510311466739685e-10 4.064966101378155e-10 2.004598109885467e-11
6 5.524494431412364e-10 4.761089070836695e-10 1.174327190113998e-10
7 6.157971329664747e-10 5.579013892259024e-10 2.214699296145166e-10
8 7.649805934777869e-10 5.919104211085404e-10 2.410021638431197e-10

Types # line syntax: ID type

1 1
2 2
3 2
4 2
5 2
6 2
7 2
8 1

Molecules # line syntax: ID molecule-ID

1 91
2 91
3 91
4 91
5 91
6 91
7 91
8 91

Charges # line syntax: ID q

1 0.000000000000000e+00
2 0.000000000000000e+00
3 0.000000000000000e+00
4 0.000000000000000e+00
5 0.000000000000000e+00
6 0.000000000000000e+00
7 0.000000000000000e+00
8 0.000000000000000e+00

Bonds # line syntax: ID type atom1 atom2

1 91 1 2
2 91 2 3
3 91 3 4
4 91 4 5
5 91 5 6
6 91 6 7
7 91 7 8

Angles # line syntax: ID type atom1 atom2 atom3

1 91 1 2 3
2 91 2 3 4
3 91 3 4 5
4 91 4 5 6
5 91 5 6 7
6 91 6 7 8

Dihedrals # line syntax: ID type atom1 atom2 atom3 atom4

1 91 1 2 3 4
2 91 2 3 4 5
3 91 3 4 5 6
4 91 4 5 6 7
5 91 5 6 7 8

2

Molecule files may not have comments in the section headers.

axel.

3

Hello All,

Thanks for the clarification. Yes, I have tried removing the comments and keeping just the section headers but it still won’t work. The job script fails with the same error message.

4

that is because you are using an old version of LAMMPS but were looking at the documentation for a more recent version.
support for the “Molecules” section was added in 2020.
so your molecule file does not conform to the documentation (for your version).

axel.

5

FWIW, support for comments in the section headers will be added to LAMMPS soon.