Hi,
I was trying to simulate Cu2O...cubic...O tetrahedrally coordinated by
Cu...Cu linearly coordinated by O.
There are two origin choices for space group 224 (Pn-3m).
If using origin choice 1, then atom positions would be
O 0,0,0
Cu 0.25,0.25,0.25
If using origin choice 2, translate by -0.25,-0.25,-0.25 to get
O 0.75,0.75,0.75
Cu 0,0,0
(or use the shift vector in Atoms...)
My understanding is that Demeter defaults to the 2nd origin choice.
Problem I am having is that neither gives me linearly coordinated copper
using current Atoms.
If I read in the attached atoms.inp (choice 2) and Run Atoms, the ATOMS
list in the
Feff output begins with:
ATOMS * this list contains 87 atoms
* x y z ipot tag distance
0.00000 0.00000 0.00000 0 cu1 0.00000
-1.06675 1.06675 1.06675 2 o1.1 1.84767
-1.06675 -1.06675 1.06675 2 o1.1 1.84767
1.06675 1.06675 -1.06675 2 o1.1 1.84767
-1.06675 -1.06675 -1.06675 2 o1.1 1.84767
2.13350 2.13350 0.00000 1 cu1.1 3.01722
I get 4-coordinate instead of 2-coordinate.
If I try origin choice 1, almost the same result....
ATOMS * this list contains 83 atoms
* x y z ipot tag distance
0.00000 0.00000 0.00000 0 cu1 0.00000
-1.06675 1.06675 1.06675 2 o1.1 1.84767
1.06675 -1.06675 1.06675 2 o1.1 1.84767
1.06675 1.06675 -1.06675 2 o1.1 1.84767
-1.06675 -1.06675 -1.06675 2 o1.1 1.84767
2.13350 2.13350 0.00000 1 cu1.1 3.01722
If I run choice 1 with the shift vector, I do reproduce the choice 2 result.
If I use the old dos version of Atoms with origin choice 2,
I do get linearly coordinated copper:
ATOMS
.00000 .00000 .00000 0 cu1 .00000
-1.06675 -1.06675 -1.06675 1 o1 1.84767
1.06675 1.06675 1.06675 1 o1 1.84767
.00000 -2.13350 2.13350 2 cu1 3.01722
SPECS:
Demeter 0.9.26 (pre2)
Win10x64
AMD64
-R.
## This Atoms file was generated by Demeter 0.9.26
## Demeter written by and copyright (c) Bruce Ravel, 2006-2017
title = Cuprite
space = 224
a = 4.26700 b = 4.26700 c = 4.26700
alpha = 90.00000 beta = 90.00000 gamma = 90.00000
rmax = 6.00000 core = cu1
polarization = 0.0 0.0 0.0
shift = 0.00000 0.00000 0.00000
atoms
# el. x y z tag
Cu 0.00000 0.00000 0.00000 cu1
O 0.75000 0.75000 0.75000 o1
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