Wrong indexing in "Data Angles" of moltemplate

LAMMPS LAMMPS General Discussion
1

Hi,

I’m encountering a problem with the indexing of the output file “Data Angles,” which is generated in the output_ttree by employing the moltemplate.sh system.lt script. While I managed to obtain correct indexing for Data Bonds, I’m facing an inconsistency with the indexing for angles. Ideally, the indexing for angles should follow a sequence like 1, 2, 3… instead of 1, 3, 5…as highlighted in bold. Could anyone please help me on how to resolve this issue?

1 1 1 2 3
3 1 2 3 4
5 1 3 4 5
7 1 4 5 6
9 1 5 6 7
11 1 6 7 8
13 1 7 8 9
15 1 8 9 10
17 1 9 10 11
19 1 10 11 12
21 1 11 12 13
23 1 12 13 14
25 1 13 14 15
.
.
.

Thanks
TPal

2

Can you supply your .lt file?

3

This is happening because Moltemplate looks for duplicate terms and delete them. Try building a data file using only one molecule, and that will help you point out to duplicate angle definitions, e.g. there should be three instances of angle between atoms 1 2 and 3 in the definition of the first molecule.
EDIT it looks like every angle is defined twice.

4

Thanks. Corrected

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