Strange result in reax/c/species and other questions.

Hello

I found a strange result from my species.out.

I used species.out as

fix species all reax/c/species 1 1 400 species.out element Si O H H H O O O Si

(Reason why I used lots of element is because I masked some atoms)

and inside the species.out file, I found lines such as

Timestep No_Moles No_Specs Si430H48O260Si146 O H2O H O243H24O914Si124Si451 HO Si H O H2O HO H

3814 117 12 1 1 1 3 1 1 1 1 1 94 6 6

As you can see. H2O appears twice in here. I tried with

fix species all reax/c/species 1 1 400 species.out element H O Si

(without any masking geometry) But the same thing happened in species.out

Is this normal? How can I escape from this situation?

Also, is the mol_fra.c result same with species.out?
I found the mol_fra.c reads connection table. Is the mol_fra.c use updated bond order from connection table for each frame? Or it use fixed bond order given in Cutoff.dic?

Thanks

Best,

Joon

Hello

I found a strange result from my species.out.

I used species.out as

fix species all reax/c/species 1 1 400 species.out element Si O H H H O O O Si

(Reason why I used lots of element is because I masked some atoms)

and inside the species.out file, I found lines such as

Timestep No_Moles No_Specs Si430H48O260Si146 O H2O H O243H24O914Si124Si451 HO Si H O H2O HO H

3814 117 12 1 1 1 3 1 1 1 1 1 94 6 6

As you can see. H2O appears twice in here. I tried with

This is because of your multiple assignments of the elements. It actually thinks all four of your O and three of your H are different elements.

fix species all reax/c/species 1 1 400 species.out element H O Si
(without any masking geometry) But the same thing happened in species.out

Are you sure? It is very unlikely that the species.out are exactly the same. Have you changed the pair_coeff command?

Is this normal? How can I escape from this situation?

Also, is the mol_fra.c result same with species.out?

If fix reax/c/species and fix reax/c/bonds have the same nfreq and nevery and nrepeat are set to 1, then mol_fra.c will give you the same results as species.out.

I found the mol_fra.c reads connection table. Is the mol_fra.c use updated bond order from connection table for each frame? Or it use fixed bond order given in Cutoff.dic?

mol_fra.c reads the output from fix reax/c/bonds. It reads the bond order cutoffs from Cutoff.dic.

Ray

Thanks Ray

  1. Ok, it seems I took a mistake. Their (masked and unmasked) results are different. Still, this means that I can’t trust the species.out result when I mask atoms… A bit sad, because this means I need to run all the simulations again, or I need to use connection table and molfra.c. Is there other way that I can use species.out normally with masked atoms system?

  2. In the fix reax/c/bonds, you can only set Nevery, which was 400 in my case. On the other hand, in reax/c/species, I used 1 1 400 for Nevery Nrepeat Nfreq. I think the output frequency of both are same. Is this good enough?

  3. Ok, that means molfra.c uses fixed bond order… Connection table ( = bond information by reax/c/bonds) also offers the list of bond order for each atoms. Is there anyway that we can use this data to mofra,c?

Thanks

Best,

Thanks Ray

1) Ok, it seems I took a mistake. Their (masked and unmasked) results are
different. Still, this means that I can't trust the species.out result when
I mask atoms... A bit sad, because this means I need to run all the
simulations again, or I need to use connection table and molfra.c. Is there
other way that I can use species.out normally with masked atoms system?

Of course you can use reax/c/species with masked atoms and still "trust"
the results. You just need to combine all repeated results into one via a
post processing tool. I believe you need some kind of text parsing tools
to analyze the species.out, you just need to combine them in your tool.

2) In the fix reax/c/bonds, you can only set Nevery, which was 400 in my
case. On the other hand, in reax/c/species, I used 1 1 400 for Nevery
Nrepeat Nfreq. I think the output frequency of both are same. Is this good
enough?

Yes.

3) Ok, that means molfra.c uses fixed bond order.... Connection table ( =
bond information by reax/c/bonds) also offers the list of bond order for
each atoms. Is there anyway that we can use this data to mofra,c?

You are confusing these two. Yes, mol_fra.c uses fixed bond order values
(defined in Cutoff.dic) to analyze and determine molecules and species -
these are user defined CUTOFFS, just like the cutoffs set in the
reax/c/species command. On the contrary, the bond order values from the
connection table (output from reax/c/bonds) are ReaxFF-calculated bond
orders between pairs of atoms and users do not control them.

Ray

2015-04-02 11:07 GMT-04:00 Ray Shan <[email protected]>:

Thanks Ray

1) Ok, it seems I took a mistake. Their (masked and unmasked) results are
different. Still, this means that I can't trust the species.out result when
I mask atoms... A bit sad, because this means I need to run all the
simulations again, or I need to use connection table and molfra.c. Is there
other way that I can use species.out normally with masked atoms system?

Of course you can use reax/c/species with masked atoms and still "trust"
the results. You just need to combine all repeated results into one via a
post processing tool. I believe you need some kind of text parsing tools
to analyze the species.out, you just need to combine them in your tool.

Yeah, my code is having a hard time to analyze repeating atom type in the
same frame.... (which is not considered in my code) I used gnuawk and other
unix command combinations. It seems I need to find different way to solve
this. Thanks.

2) In the fix reax/c/bonds, you can only set Nevery, which was 400 in my
case. On the other hand, in reax/c/species, I used 1 1 400 for Nevery
Nrepeat Nfreq. I think the output frequency of both are same. Is this good
enough?

Yes.

3) Ok, that means molfra.c uses fixed bond order.... Connection table ( =
bond information by reax/c/bonds) also offers the list of bond order for
each atoms. Is there anyway that we can use this data to mofra,c?

You are confusing these two. Yes, mol_fra.c uses fixed bond order values
(defined in Cutoff.dic) to analyze and determine molecules and species -
these are user defined CUTOFFS, just like the cutoffs set in the
reax/c/species command. On the contrary, the bond order values from the
connection table (output from reax/c/bonds) are ReaxFF-calculated bond
orders between pairs of atoms and users do not control them.

Sorry, my mistake. I confused about bond order and bond order cutoff. Now I
understand that the molfra,c use fixed cutoff only, not the fixed bond
orders. Thanks