Errors in Stacking Faults Refinements

kibeom

Hi, I'm kibeom

Recently, I'm struggling with the stacking fault refinement. Honestly, I'm really new to this kind of refinement and never have tried before. After reading John's stacking fault tutorial and TOPAS book, I understood just a little bit of the concept.

So for now, I'm trying to follow the earlier works, usually conducted with FAULTS of FullProf suite, with TOPAS.

The material that I'm interested is Li, Mn-rich cathode material for Li-ion battery
Serrano-Sevillano et al(2018), https://www.rsc.org/suppdata/c8/cp/c8cp04181d/c8cp04181d1.pdf
did stacking fault refinement on Li, Mn-rich cathode material. and I'm trying to adapting those to my data with TOPAS.

Here is the lines that I'm writing (Li2MnO3 phase with C2/m space group, transformed to P-1 space group) based on the paper above.
(number of stacks and sequences are set to small numbers, because of the poor computing performance of my labtop)

str
space_group P-1
a a_LMO 4.91660 b a_LMO 4.91660 c = Get(generated_c); ga @ 60
prm !pa 0.9999 prm !h 4.7416
prm s 497.07306` min 1e-15 scale = s 1e-6 / (Nv Nstr);
generate_stack_sequences {
number_of_sequences Nstr 10
number_of_stacks_per_sequence Nv 20
Transition(L1, h)
to L2 = pa; a_add = 1/3; b_add = -1/3; z_add = 1/2 h;
to L3 = 1 - 0.5*pa; a_add = 2/3; b_add = 0; z_add = 1/2 h;
to L4 = 1 - 0.5*pa; a_add = 0; b_add = -2/3; z_add = 1/2 h;
Transition(L2, h)
to L1 = 1 ; a_add = 1/3; b_add = -1/3; z_add = 1/2 h;
Transition(L3, h)
to L1 = 1 ; a_add = 1/3; b_add = -1/3; z_add = 1/2 h;
Transition(L4, h)
to L1 = 1 ; a_add = 1/3; b_add = -1/3; z_add = 1/2 h;
}

site Li1_L1 num_posns 1 x 0 y 0 z 0 occ Li+1 1 beq B 1 layer L1
site Li2_L1 num_posns 1 x = 1/3 y = 1/3 z 0 occ Li+1 1 beq B 1 layer L1
site Li3_L1 num_posns 1 x = 2/3 y = 2/3 z 0 occ Li+1 1 beq B 1 layer L1

site Li1_L2 num_posns 1 x 0 y 0 z 0 occ Li+1 1 beq B 1 layer L2
site Mn1_L2 num_posns 1 x = 1/3 y = 1/3 z 0 occ Mn+4 1 beq B 1 layer L2
site Mn2_L2 num_posns 1 x = 2/3 y = 2/3 z 0 occ Mn+4 1 beq B 1 layer L2
site O1_L2 num_posns 1 x 0.3400 y 0 z 0.2250 occ O-2 1 beq B 1 layer L2
site O2_L2 num_posns 1 x 0.6500 y 0 z -0.2250 occ O-2 1 beq B 1 layer L2
site O3_L2 num_posns 1 x 0 y 0.3400 z -0.2250 occ O-2 1 beq B 1 layer L2
site O4_L2 num_posns 1 x 0.3400 y 0.6500 z -0.2250 occ O-2 1 beq B 1 layer L2
site O5_L2 num_posns 1 x 0.6500 y 0.3400 z 0.2250 occ O-2 1 beq B 1 layer L2
site O6_L2 num_posns 1 x 0 y 0.6500 z 0.225 occ O-2 1 beq B 1 layer L2

site Li1_L3 num_posns 1 x 0 y 0 z 0 occ Li+1 1 beq B 1 layer L3
site Mn1_L3 num_posns 1 x = 1/3 y = 1/3 z 0 occ Mn+4 1 beq B 1 layer L3
site Mn2_L3 num_posns 1 x = 2/3 y = 2/3 z 0 occ Mn+4 1 beq B 1 layer L3
site O1_L3 num_posns 1 x 0.3400 y 0 z 0.2250 occ O-2 1 beq B 1 layer L3
site O2_L3 num_posns 1 x 0.6500 y 0 z -0.2250 occ O-2 1 beq B 1 layer L3
site O3_L3 num_posns 1 x 0 y 0.3400 z -0.2250 occ O-2 1 beq B 1 layer L3
site O4_L3 num_posns 1 x 0.3400 y 0.6500 z -0.2250 occ O-2 1 beq B 1 layer L3
site O5_L3 num_posns 1 x 0.6500 y 0.3400 z 0.2250 occ O-2 1 beq B 1 layer L3
site O6_L3 num_posns 1 x 0 y 0.6500 z 0.225 occ O-2 1 beq B 1 layer L3

site Li1_L4 num_posns 1 x 0 y 0 z 0 occ Li+1 1 beq B 1 layer L4
site Mn1_L4 num_posns 1 x = 1/3 y = 1/3 z 0 occ Mn+4 1 beq B 1 layer L4
site Mn2_L4 num_posns 1 x = 2/3 y = 2/3 z 0 occ Mn+4 1 beq B 1 layer L4
site O1_L4 num_posns 1 x 0.3400 y 0 z 0.2250 occ O-2 1 beq B 1 layer L4
site O2_L4 num_posns 1 x 0.6500 y 0 z -0.2250 occ O-2 1 beq B 1 layer L4
site O3_L4 num_posns 1 x 0 y 0.3400 z -0.2250 occ O-2 1 beq B 1 layer L4
site O4_L4 num_posns 1 x 0.3400 y 0.6500 z -0.2250 occ O-2 1 beq B 1 layer L4
site O5_L4 num_posns 1 x 0.6500 y 0.3400 z 0.2250 occ O-2 1 beq B 1 layer L4
site O6_L4 num_posns 1 x 0 y 0.6500 z 0.225 occ O-2 1 beq B 1 layer L4

peak_buffer_based_on = Xo; peak_buffer_based_on_tol = 1;

SF_smooth( @, 1, 1)

and I encountered many error messages.

- cannot locate peak_buffer_based_on_tol from x in data structures

if i remove "peak_buffer_..." line, then

- generate_stack_sequences: use_layer L2 not found

How can I avoid those errors? and I'm not sure if I'm doing right or not.
This might be silly, but any tips and advice for the stacking fault refinement is welcome.

Kibeom.

alancoelho

Hi Kibeom

Some equations in yours text does not have an ending semicolon; include a semicolon as in:

y = 1/3;

cheers
alan

kibeom

Hi Alan,

I'm still not good at TOPAS syntax ..
It's technically working now :-)

But the overall fitting is much far from satisfaction.
Looks like I'll have to do another tries on the stacking sequence lines

Thank you much, Alan.

rabailabbasi

kibeom Hi! I am also working on this material. I was curious if you were able to make it work?

kibeom

rabailabbasi
Hi, Yes, I've done some refinements with stacking faults and got some results.
In my case, however, the differences of samples were quite subtle.
So I didn't exploit this approach as much as I expected.

rabailabbasi

kibeom Thanks for the reply! I have tried to use your str lines for my refinement but my fitting is far from satisfactory, Would you be able to share any additions you made to the INP file to make it work?
Thanks in advance!!

kibeom

rabailabbasi
I'm afraid but I'm not allowed to share. (I'm a industrial researcher)
But I think you can do well if you try further on your file.
Serrano-Sevillano et al(2018) paper about this material helped me much.
And maybe you can get some syntax help on this forum.
I'm deeply sorry.

rabailabbasi

kibeom Of course I understand, thank you regardless!