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xred generation for orthorhombic cell


Chronological Thread 
  • From: Masayoshi Mikami <mmikami@rc.m-kagaku.co.jp>
  • To: forum@abinit.org
  • Subject: xred generation for orthorhombic cell
  • Date: Thu, 21 Jun 2007 09:43:39 +0900

Dear all,

I have had an interesting situation with ABINIT v.5.3.4.
An input for Pbnm (#62) may not work ? Instead,
the same input for Pnma (converted from Pbnm) works...

Here is my story:
I just tried a computation of Mg2SiO4(forsterite).
The original CIF data is available on the WEB:
http://rruff.geo.arizona.edu/AMS/xtal_data/CIFfiles/00268.cif

1) First, I made an input like this:
## geom part starts ##
spgroup 62
acell 4.79 10.19 5.85 angstrom
angdeg 90 90 90
spgxor 2 spgorig 1 brvltt 1 # Pbnm
nsym 0
natrd 6
typat 2*1 1*2 3*3
xred
0.00000 0.00000 0.00000 # Mg
0.00560 0.26320 0.75000 # Mg
0.09450 0.40780 0.25000 # Si
0.24990 0.09070 0.75000 # O
0.28320 0.05780 0.25000 # O
0.23120 0.33700 0.47070 # O
## geom part ends ##
znucl 12.0 14.0 8.0
ntypat 3 ecut 50
natom 28
ntime 80
ixc 11
ionmov 3
toldff 5.0d-5
tolmxf 5.0d-4

Then, I had an error like this:
operat : ERROR -
The number of atoms obtained from symmetries, 44
is greater than the input number of atoms, natom= 28
This is not allowed.
Action : modify natom or the symmetry data in the input file.

N.B. This unit cell contains 4 times (2+1+4), i.e. 28 !

2) Second, I made "P1" input, i.e., making all xred
from the Pbnm input, with no spgroup information.

## geom part starts ##
acell 4.79 10.19 5.85 angstrom
angdeg 90 90 90
nsym 0
typat 8*1 4*2 16*3
xred
0.00000 0.00000 0.00000 # Mg
0.50000 0.50000 0.00000 # Mg
0.00000 0.00000 0.50000 # Mg
0.50000 0.50000 0.50000 # Mg
0.00560 0.26320 0.75000 # Mg
0.50560 0.23680 0.25000 # Mg
0.99440 0.73680 0.25000 # Mg
0.49440 0.76320 0.75000 # Mg
0.09450 0.40780 0.25000 # Si
0.59450 0.09220 0.75000 # Si
0.90550 0.59220 0.75000 # Si
0.40550 0.90780 0.25000 # Si
0.23120 0.33700 0.47070 # O
0.73120 0.16300 0.52930 # O
0.76880 0.66300 0.97070 # O
0.26880 0.83700 0.02930 # O
0.76880 0.66300 0.52930 # O
0.26880 0.83700 0.47070 # O
0.23120 0.33700 0.02930 # O
0.73120 0.16300 0.97070 # O
0.28320 1.05780 0.25000 # O
0.78320 0.44220 0.75000 # O
0.71680 -0.05780 0.75000 # O
0.21680 0.55780 0.25000 # O
0.24990 0.09070 0.75000 # O
-0.25010 0.40930 0.25000 # O
0.75010 0.90930 0.25000 # O
1.25010 0.59070 0.75000 # O
## geom part ends ##

The ABINIT recognize this crystal as "Pnma" (#62)
in the output, and run without any errors like Case 1).

3) Finally, I converted the Pbnm data into Pnma
(thanks to Material Studio), and make Pnma-based input:

## geom part starts ##
spgroup 62
acell 10.1900 5.8500 4.7900 angstrom
angdeg 90 90 90
spgxor 1 spgorig 1 brvltt 1 # Pnma
nsym 0
natrd 6
typat 2*1 1*2 3*3
xred
-0.50000 -0.00000 0.00000 # Mg
-0.76320 0.75000 -0.00560 # Mg
-0.90780 0.25000 -0.09450 # Si
-0.59070 0.75000 -0.24990 # O
-0.55780 0.25000 -0.28320 # O
-0.83700 0.47070 -0.23120 # O
## geom part ends ##

Then, I had no problems with this again...

Thus, I am just wondering ...
When I looked into the routine,
12geometry/gensymspgr.F90,
I noticed a message (around l.470),
---------
!Orientations for the orthorhombic space groups
!WARNING : XG 000620 : I am not sure that this coding is correct !!
if (spgroup>15 .and. spgroup <75) then
select case (spgaxor)
(snip)
---------

How do you think ?
I will be back if/when I notice something to be added here.

Regards,
Masayoshi

N.B.
(Pbnm)
loop_
_symmetry_equiv_pos_as_xyz
'x,y,z'
'x,y,1/2-z'
'-x,-y,1/2+z'
'1/2+x,1/2-y,1/2+z'
'1/2-x,1/2+y,1/2-z'
'1/2-x,1/2+y,z'
'1/2+x,1/2-y,-z'
'-x,-y,-z'

(Pnma)
loop_
_symmetry_equiv_pos_as_xyz
x,y,z
-x+1/2,-y,z+1/2
-x,y+1/2,-z
x+1/2,-y+1/2,-z+1/2
-x,-y,-z
x+1/2,y,-z+1/2
x,-y+1/2,z
-x+1/2,y+1/2,z+1/2


  • xred generation for orthorhombic cell, Masayoshi Mikami, 06/21/2007

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