Hello everyone,
I’m reaching out to get your insights on a challenge I’m facing with stacking faults refinement in hydromagnesite using TOPAS.
When splitting my hydromagnesite structure into two stacking layers (top: z≥0.5, bottom:
z<0.5, stacking vector and distance = 0.5 along c), the calculated powder diffraction pattern changes significantly and no longer matches hydromagnesite pattern. Using a single-layer model works perfectly, so I’m puzzled by the result when introducing two layers. What am I missing in defining the layers or their stacking?
What I Did
Model 1 (Works):
Used only one layer — the transformed hydromagnesite structure — stacking along c.
Layer-to-layer distance h1 = c parameter.
Transition matrix:
Transition(A, h1)
to A = 1; a_add = 0; b_add = 0;
site Mg x 0.000000 y 0.000000 z= 0.000000/Nv; occ Mg 1.0 beq 1 layer A
.
.
.
' Full crystal structure of hydromagnesite
.
.
.
site O x 0.852950 y 0.817900 z= 0.996850/Nv; occ O 1.0 beq 1 layer A
Model 2 (Issue):
Broke the structure into two layers:
Layer A: all atoms with z<0.5
Layer B: all atoms with z≥0.5 (z coordinates shifted by –0.5)
Layer-to-layer distance = h2 = c/2.
Transition matrix:
Transition(A, h2)
to A = 0; a_add = 0; b_add = 0;
to B = 1; a_add = 0.0; b_add = 0;
Transition(B, h2)
to A = 1; a_add = 0.0; b_add = 0.0;
to B = 0; a_add = 0.0; b_add = 0.0;
Sites redefined appropriately for A and B layers (z values adjusted as stated above).
site Mg1 x 0.000000 y 0.000000 z= 0.000000/Nv; occ Mg 1.0 beq 1 layer A
.
.
.
site O2 x 0.852950 y 0.682100 z= 0.496850/Nv; occ O 1.0 beq 1 layer A
site Mg3 x 0.500000 y 0.000000 z=(0.500000-0.5)/Nv; occ Mg 1.0 beq 1 layer B
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.
.
site O4 x 0.852950 y 0.817900 z= (0.996850-0.5)/Nv; occ O 1.0 beq 1 layer B
The issue: This two-layer model yields a calculated pattern quite different from hydromagnesite powder pattern.
The same approach in FAULTS and GSAS-II yields the correct structural stacking (verified via Vesta), but a similarly wrong powder pattern.
My expectation: If I simply decompose original structure in to 2 layers and stack them one over another, pattern should be identical to the original structure. But it is not.
What am I missing in the way I’m defining or stacking the layers? Is there a fundamental step in the stacking vector, coordinates’ transformation, or layer placement that I’m overlooking? Any pointers on best practice for defining layers when decomposing crystal structures like this?
Even brief suggestions, hints, or references to documentation are much appreciated!
Thank you in advance!
- .inp file
- .xy XRD pattern
- .cif file of P1 hydromagnesite