Fix bond/react: Bond type affected by reaction myrxn1 is too close to template edge

LAMMPS LAMMPS General Discussion
1

Hi All,
I’m trying to model polymer structure based on DGEBA and AFD. However, when I run the program it shows the following error : “Fix bond/react: Bond type affected by reaction myrxn1 is too close to template edge” I really appreciate your answer.

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Based on our recent (private) correspondence, this issue arises when using reaction templates generated by Automapper tool. Have you reached out to the developer of that tool (Matt Bone)?

That error indicates that certain bond types close to edge atoms in your reaction template might not be getting updated correctly. You can either correct the reaction templates, or comment out that error check in the source code if you are confident that the bond types you want to be updated are sufficiently far from edge atoms.

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Data_input.txt (59.3 KB)
Polymer.txt (983 Bytes)
rxn1_stp1_map.data (418 Bytes)
rxn1_stp1_posttmplt.txt (11.4 KB)
rxn1_stp1_pretmplt.txt (10.9 KB)
Hi Dr. Jake,
I have generated the map, pre, and post reaction template files manually following the examples given in the LAMMPS Packages. Please see the attached files. But it still shows the error.

Thanks again for the support.

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To clarify, the issue is that bond types change type that are too close the edge atom. The error is warning you that these bond types will not be updated. You can avoid the error by correcting the post-reaction template, such that bond types near the edge atom do not change types. For example, referring to your files, change bond 11 in your post-reaction template from type 8 to type 7, to match your pre-reaction template (you might have to do the same thing for a couple more bonds near the edge atom).

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Thanks a lot. It’s now working. After fixing the types of bonds between pre-reaction and post-reaction templates, there is no error. But no reaction occurs between two molecules (f_rxns[1] and f_rxns[2] show 0 in every step). Is there anything else that I’m missing? Should the types of atoms and bonds in the data file also be the same as the pre-reaction and post-reaction templates?

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The atom types of the data file must match those of the pre-reaction template if you want that reaction to occur (but the bond types do not need to be the same). Let me know if that helps.

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Hi Dr. Jake,
Thanks a lot. It is now working. After making all the atom types same, now the reaction is happening.

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Hi sheraj, how to fix bond type affected by reaction myrxn1 is too closed the edged atom?

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Hi Liang,
The bond types of the pre- and post-reaction templates should be the same, especially closer to the reacted atoms. Hope, it will solve the problem.

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trimer.data (17.5 KB)
pre.molecule_template (3.8 KB)
post.molecule_template (5.8 KB)
grow.map (342 Bytes)
in.grow_styrene (1.5 KB)

Hi sheraj ,
input files are attached, it can run normally, but there is no reaction for growth, I have tried to keep the bond type same between pre.molecule_template and post.molecule_template,

Could you please help me check out ?
Thanks

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Hi Liang
Did you resolve your problem?

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hello, sheraj
my simulation run but f_rxns[1] and f_rxns[2] come out zero
as @jrgissing mention that the atom types must be match my atom types in reaction template and data file are same
Could you please tell me how to match the atom types in data file and reaction template file
thank you

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In your main structure, the trimer.data file, there is only one molecule. But it should be at least two molecules that will react and form new molecules.

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thank you for your quick response, but the above is not my file, i am not able to upload my data file, but still the f_rxns[] come out zero after the matching of the types in the data file and in the reaction templates

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Are you sure of that?

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Hello, i try multiple time but after some time the uploading of file is failed

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Then the file is likely too large. Try creating a small test system. That is a good idea for testing and learning anyway.

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Thank you teacher for on time reply, the attached is my file, i created my data and reaction templates using molteplate,

densification polymer.zip (98.9 KB)

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matching atoms types between a data files and one or more sets of reaction templates is made much more straightforward using ‘type labels’, a new LAMMPS feature that allows using strings instead of just numbers for atom types, bond types, etc.

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thank you so much teacher, the issue has been solved, i make a mistake in map file, you are right sir using labels is more convenient but i am using moltemplate for in put date and this software give me data in numbers.
thank you teacher