Output bonds information using reax/c

LAMMPS LAMMPS Mailing List Mirror
1

Dear LAMMPS users,

I am using ReaxFF (fix reax/c) to simulate reaction process. Is it possible to output or dump the information concerned with bonds? (e.g. how many O-H bonds are formed)

Regards,

Kira

2

Hi Kira,
Yes, please see “fix reax/c/bonds” command. Also, I believe you are using “pair reax/c”.

Best,
Ray

3

Dear Ray,

Thanks a lot! You’re so helpful. I am using reax/c.

I read from the LAMMPS manual that the output can also be realized by using a control file (e.g. pair_style reax/c lmp_control). The output method is specified in the lmp_control file.

But both methods will only give us the information of all the bonds. We need to do post processing to find out which bonds are newly formed, is it right?

Thanks,

Kira

4

Dear Kira,

You are welcome. Currently the only way to analyze bond information output, either from control file or fix reax/c/bonds, is through post process. Please check out mol_fra.c and reaxc_bond.pl in the /tools/reax directory; they might be helpful to you.

Best,
Ray

5

Dear Ray,

Thanks for your advices. I’ve spent a long time on compiling the mol_fra.c file but still did not make it. I tried gcc and g++ but met errors when compiling it. I wonder what c compiler you use. Thanks.

Regards,

Kira

6

Hi Kira,

I used standard gcc in both RH Linux and Mac. Try add “-lm” at the end and see if it helps. What sizes are your systems?

Best,
Ray