Basic question about the command and output of reax/c/bonds and reax/c/species

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1

Dear lammps users

I used reax/c/bonds and reax/c/species in my input, and then the outcome was written into two different files. I have some basic questions about the commands and information in output files. I used following commands.

fix 3 all reax/c/species 10 10 100 species.tatb

fix 4 all reax/c/bonds 1000 bonds.reaxc

My questions are:

(1) According to the manual, the first command means that the bonder order value on timpstep within first 10,20,30….,80,90,100 will be used to compute the average bond-order for the species analysis output on timestep 100. However, I am confused about how to calculate the average bond order for next 100 timestep. One understanding is that the bonder order value on timpstep 110,120,130….,180,190,200 within next 100 tiemstep will be used to compute the average bond-order for the species analysis output on timestep 200. Or the bonder order value on timpstep 10,20,30….,80,90,100, 110,120,130,…180,190,200 will be used to compute the average bond-order for the species analysis output on timestep 200. Which one is right?

(2) If the first understanding in (1) is right, the second command means that only the bond order information on 1000th timestep is written into file. Is that right?

(3)Is there any criteria for choosing the parameter (I mean 10 10 100) for reax/c/species?

The first picture is the output reax/c/bonds. I understand some of items. For example, items give information about id of the atom and atoms that are bond with them from the first (id) to fifth item (id_nb). And bo_nb is bond order information. My question is

(4)What are “mol”, “abo” and nlp?

The second picture is output of reax/c/species. I know that “No_Moles” and “No_Spacs” are the number of molecules and species My question are

(5)Is there any difference between molecules and species?

(6)What “1” represents?

The third and fourth picture are my data file and input file. I am very sorry to ask such basic questions.

output of reaxc bonds.png

output of speices.png

input.docx (13.8 KB)

corodata.pdf (35.6 KB)

2

Dear lammps users

I used reax/c/bonds and reax/c/species in my input, and then the outcome
was written into two different files. I have some basic questions about the
   commands and information in output files. I used following commands.

fix 3 all reax/c/species 10 10 100 species.tatb

fix 4 all reax/c/bonds 1000 bonds.reaxc

My questions are:

(1) According to the manual, the first command means that the bonder order
value on timpstep within first 10,20,30….,80,90,100 will be used to compute
the average bond-order for the species analysis output on timestep 100.
However, I am confused about how to calculate the average bond order for
next 100 timestep. One understanding is that the bonder order value on
timpstep 110,120,130….,180,190,200 within next 100 tiemstep will be used to
compute the average bond-order for the species analysis output on timestep
200. Or the bonder order value on timpstep 10,20,30….,80,90,100,
110,120,130,…180,190,200 will be used to compute the average bond-order for
the species analysis output on timestep 200. Which one is right?

​the former. you get output every 100 steps and that output is averaged
from 10 samples of data each taken 10 steps a​part.

(2) If the first understanding in (1) is right, the second command means
that only the bond order information on 1000th timestep is written into
file. Is that right?

​yes.
​

(3)Is there any criteria for choosing the parameter (I mean 10 10 100) for
reax/c/species?

​you choose what is meaningful for your system. if changes are frequent,
you need to output more often. if data is noisy, you need to average more.
if files get too large you output data farther apart.

The first picture is the output reax/c/bonds. I understand some of items.
For example, items give information about id of the atom and atoms that are
bond with them from the first (id) to fifth item (id_nb). And bo_nb is bond
order information. My question is

(4)What are “mol”, “abo” and nlp?

​not sure about "mol", but "abo" is ​obviously the accumulated bond order
(i.e. the sum of all individual bond orders) and "nlp" should be referring
to lone pairs

The second picture is output of reax/c/species. I know that “No_Moles”
and “No_Spacs” are the number of molecules and species My question are

(5)Is there any difference between molecules and species?

​number of molecules is the total number of molecules. number of species is
the number of *kinds* of molecules and then the following columns are the
formula for each species and the number of molecules of that kind
(species). i.e. you have one kind of molecule and two molecules of that
kind. ​

(6)What “1” represents?
The third and fourth picture are my data file and input file. I am very
sorry to ask such basic questions.

​see my answer to 5.

axel.​

3

Thanks a lot, I understand.