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Dear Collegues<br>
I want to <a style="direction: ltr; text-decoration: none;"
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data mail<br>
Thanks<br>
Dr F. TERKI<br>
Le 19/03/2015 18:29, Peter Blaha a écrit :<br>
</div>
<blockquote cite="mid:550B158D.5000902@theochem.tuwien.ac.at"
type="cite">For low symmetry structures (eg. monoclinic) one can
generate several unit cells
<br>
which are absolutely equivalent (same volume, same number of
atoms, ...)
<br>
<br>
This happens with sgroup, which transforms your structure such
that the
<br>
monoclinic angle is less than 90. In addition the fractional
coordinates
<br>
have been changed austomatically. Nevertheless, these two cells
will give
<br>
identical neighbor-distances, which you can verify with nn and
comparing the
<br>
resulting outputnn files. There is nothing wrong with either your
original cell
<br>
or the one from sgroup. You can use either one for the
calculations.
<br>
<br>
If you want the conventional cell (which contains of course 2x as
many atoms),
<br>
you can use x supercell (1x1x1, no shifts/vacuum). It simply
changes
<br>
the lattice type to "P", and adds the centered atoms.
<br>
With this struct file, however, you cannot make the calculations
unless you
<br>
make these atoms "non-equivalent" and break symmetry, eg. by
labeling one
<br>
atom as "Al1".
<br>
<br>
What you have been trying was to express the lattice
vectors/positions in carthesian
<br>
coordinates.
<br>
You can check your calculations again using the distances of
outputnn and
<br>
compare them to your own calculations.
<br>
<br>
<br>
<br>
Am 19.03.2015 um 17:03 schrieb David Olmsted:
<br>
<blockquote type="cite">Dear reader,
<br>
I am trying to determine the primitive cell and positions for
a
<br>
case.struct file I am running. But I am not determining the
either
<br>
primitive cell or the conventional cell correctly.
<br>
<br>
I need to either:
<br>
1. Figure out what I am doing wrong. or
<br>
2. Find a place in the code where I can print out the
positions in terms
<br>
of the primitive cell.
<br>
<br>
Does anyone know the answer to either question?
<br>
<br>
This is a base-centered monoclinic system, space group 15.
<br>
<br>
<blockquote type="cite">From case.struct:
<br>
</blockquote>
MODE OF CALC=RELA unit=bohr
<br>
<br>
35.704486 13.533274 13.533274 90.000000 90.000000 99.990000
<br>
<br>
The full case.struct is given below.
<br>
<br>
sgroup reports 15 (C 2/c) [unique axis c] cell choice 2.
<br>
The struct file output from sgroup is:
<br>
CXZ LATTICE,NONEQUIV.ATOMS: 14 15 C2/c
<br>
MODE OF CALC=RELA unit=bohr
<br>
<br>
35.704486 13.533274 13.533274 90.000000 90.000000 80.010000
<br>
The case.struct file I am using has the 99.99 degree entry as
above.
<br>
<br>
In angstroms, my lattice constants (and angles in degrees) are
<br>
18.894 7.1615 7.1615 90 90 99.99
<br>
<br>
The userguide gives (on page 39) the primitive cell as:
<br>
CXZ [a sin(\gamma)/2, a cos(\gamma)/2, -c/2], [0, b, 0], [a
<br>
sin(\gamma)/2, acos(\gamma)/2, c/2]
<br>
<br>
So I have for a primitive cell (each row is a vector):
<br>
9.3038 -1.6388 -3.5808
<br>
0 7.1615 0
<br>
9.3038 -1.6388 3.5808
<br>
<br>
With lengths of 10.1029 7.1615 10.1029 and angles 99.34 41.52
99.34.
<br>
<br>
The positions in case.struct are given in terms of the
conventional unit
<br>
cell, and I must convert them to the primitive cell. So I need
the
<br>
conventional cell in cartesian coordinates.
<br>
<br>
The README file in SRC_sgroup talks about base-centered
monoclinic being
<br>
restricted to A centered. Page 39 of the userguide shows only
<br>
B-base-centered,
<br>
which is what I have. The README gives:
<br>
<br>
The vectors of the conventional cell in cartesian basis
<br>
( 1 vector is 1 column ... )
<br>
<br>
a b*Cos[gamma] 0
<br>
0 b*Sin[gamma] 0 A - centred
<br>
0 0 c
<br>
<br>
This is a valid conventional cell in my case, and switching to
each row
<br>
being a vector, I have:
<br>
18.894 0 0
<br>
-1.24235 7.0529 0
<br>
0 0 7.1615
<br>
<br>
However the location of the second primitive cell is (0.5, 0,
0.5) in terms
<br>
of the conventional cell. When transformed to primitive cell
coordinates it
<br>
must be a lattice vector. But it is not. So one of my cells is
wrong. (I
<br>
believe the vector for the second primitive cell is correct
because it is
<br>
what is given in the International Tables, page 199, for unique
axis c, cell
<br>
choice 2. And it matches to the neighbor positions in
case.outputnn.)
<br>
<br>
Quite possibly the conventional cell is different for B-centered
than for
<br>
A-centered, but I do not find it described anywhere.
<br>
<br>
My thanks for any help.
<br>
David
<br>
<br>
David Olmsted
<br>
Assistant Research Engineer
<br>
Materials Science and Engineering
<br>
210 Hearst Memorial Mining Building
<br>
University of California
<br>
Berkeley, CA 94720-1760
<br>
<br>
<br>
<br>
------- case.struct
<br>
troll_icsd
<br>
<br>
CXZ LATTICE,NONEQUIV.ATOMS: 14 15_B2/b
<br>
<br>
MODE OF CALC=RELA unit=bohr
<br>
<br>
35.704486 13.533274 13.533274 90.000000 90.000000 99.990000
<br>
<br>
ATOM -1: X=0.16778000 Y=0.32059000 Z=0.00654000
<br>
MULT= 4 ISPLIT= 8
<br>
-1: X=0.83222000 Y=0.67941000 Z=0.99346000
<br>
-1: X=0.83222000 Y=0.17941000 Z=0.00654000
<br>
-1: X=0.16778000 Y=0.82059000 Z=0.99346000
<br>
Al NPT= 781 R0=0.00010000 RMT= 1.6300 Z: 13.0
<br>
<br>
LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
<br>
0.0000000 1.0000000 0.0000000
<br>
0.0000000 0.0000000 1.0000000
<br>
ATOM -2: X=0.07570000 Y=0.41714000 Z=0.72882000
<br>
MULT= 4 ISPLIT= 8
<br>
-2: X=0.92430000 Y=0.58286000 Z=0.27118000
<br>
-2: X=0.92430000 Y=0.08286000 Z=0.72882000
<br>
-2: X=0.07570000 Y=0.91714000 Z=0.27118000
<br>
Al NPT= 781 R0=0.00010000 RMT= 1.6300 Z: 13.0
<br>
<br>
LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
<br>
0.0000000 1.0000000 0.0000000
<br>
0.0000000 0.0000000 1.0000000
<br>
ATOM -3: X=0.00000000 Y=0.25000000 Z=0.11731000
<br>
MULT= 2 ISPLIT= 8
<br>
-3: X=0.00000000 Y=0.75000000 Z=0.88269000
<br>
P NPT= 781 R0=0.00010000 RMT= 1.3000 Z: 15.0
<br>
<br>
LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
<br>
0.0000000 1.0000000 0.0000000
<br>
0.0000000 0.0000000 1.0000000
<br>
ATOM -4: X=0.16844000 Y=0.08109000 Z=0.63272000
<br>
MULT= 4 ISPLIT= 8
<br>
-4: X=0.83156000 Y=0.91891000 Z=0.36728000
<br>
-4: X=0.83156000 Y=0.41891000 Z=0.63272000
<br>
-4: X=0.16844000 Y=0.58109000 Z=0.36728000
<br>
P NPT= 781 R0=0.00010000 RMT= 1.3000 Z: 15.0
<br>
<br>
LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
<br>
0.0000000 1.0000000 0.0000000
<br>
0.0000000 0.0000000 1.0000000
<br>
ATOM -5: X=0.06458000 Y=0.32611000 Z=0.98827000
<br>
MULT= 4 ISPLIT= 8
<br>
-5: X=0.93542000 Y=0.67389000 Z=0.01173000
<br>
-5: X=0.93542000 Y=0.17389000 Z=0.98827000
<br>
-5: X=0.06458000 Y=0.82611000 Z=0.01173000
<br>
O NPT= 781 R0=0.00010000 RMT= 0.8700 Z: 8.0
<br>
<br>
LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
<br>
0.0000000 1.0000000 0.0000000
<br>
0.0000000 0.0000000 1.0000000
<br>
ATOM -6: X=0.02064000 Y=0.09579000 Z=0.23728000
<br>
MULT= 4 ISPLIT= 8
<br>
-6: X=0.97936000 Y=0.90421000 Z=0.76272000
<br>
-6: X=0.97936000 Y=0.40421000 Z=0.23728000
<br>
-6: X=0.02064000 Y=0.59579000 Z=0.76272000
<br>
O NPT= 781 R0=0.00010000 RMT= 0.8700 Z: 8.0
<br>
<br>
LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
<br>
0.0000000 1.0000000 0.0000000
<br>
0.0000000 0.0000000 1.0000000
<br>
ATOM -7: X=0.23738000 Y=0.16861000 Z=0.53512000
<br>
MULT= 4 ISPLIT= 8
<br>
-7: X=0.76262000 Y=0.83139000 Z=0.46488000
<br>
-7: X=0.76262000 Y=0.33139000 Z=0.53512000
<br>
-7: X=0.23738000 Y=0.66861000 Z=0.46488000
<br>
O NPT= 781 R0=0.00010000 RMT= 0.8700 Z: 8.0
<br>
<br>
LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
<br>
0.0000000 1.0000000 0.0000000
<br>
0.0000000 0.0000000 1.0000000
<br>
ATOM -8: X=0.11140000 Y=0.00803000 Z=0.49156000
<br>
MULT= 4 ISPLIT= 8
<br>
-8: X=0.88860000 Y=0.99197000 Z=0.50844000
<br>
-8: X=0.88860000 Y=0.49197000 Z=0.49156000
<br>
-8: X=0.11140000 Y=0.50803000 Z=0.50844000
<br>
O NPT= 781 R0=0.00010000 RMT= 0.8700 Z: 8.0
<br>
<br>
LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
<br>
0.0000000 1.0000000 0.0000000
<br>
0.0000000 0.0000000 1.0000000
<br>
ATOM -9: X=0.14191000 Y=0.23708000 Z=0.75449000
<br>
MULT= 4 ISPLIT= 8
<br>
-9: X=0.85809000 Y=0.76292000 Z=0.24551000
<br>
-9: X=0.85809000 Y=0.26292000 Z=0.75449000
<br>
-9: X=0.14191000 Y=0.73708000 Z=0.24551000
<br>
O NPT= 781 R0=0.00010000 RMT= 0.8700 Z: 8.0
<br>
<br>
LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
<br>
0.0000000 1.0000000 0.0000000
<br>
0.0000000 0.0000000 1.0000000
<br>
ATOM -10: X=0.18216000 Y=0.92446000 Z=0.76484000
<br>
MULT= 4 ISPLIT= 8
<br>
-10: X=0.81784000 Y=0.07554000 Z=0.23516000
<br>
-10: X=0.81784000 Y=0.57554000 Z=0.76484000
<br>
-10: X=0.18216000 Y=0.42446000 Z=0.23516000
<br>
O NPT= 781 R0=0.00010000 RMT= 0.8700 Z: 8.0
<br>
<br>
LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
<br>
0.0000000 1.0000000 0.0000000
<br>
0.0000000 0.0000000 1.0000000
<br>
ATOM -11: X=0.00000000 Y=0.25000000 Z=0.63572000
<br>
MULT= 2 ISPLIT= 8
<br>
-11: X=0.00000000 Y=0.75000000 Z=0.36428000
<br>
O NPT= 781 R0=0.00010000 RMT= 0.8700 Z: 8.0
<br>
<br>
LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
<br>
0.0000000 1.0000000 0.0000000
<br>
0.0000000 0.0000000 1.0000000
<br>
ATOM -12: X=0.16141000 Y=0.06966000 Z=0.12100000
<br>
MULT= 4 ISPLIT= 8
<br>
-12: X=0.83859000 Y=0.93034000 Z=0.87900000
<br>
-12: X=0.83859000 Y=0.43034000 Z=0.12100000
<br>
-12: X=0.16141000 Y=0.56966000 Z=0.87900000
<br>
O NPT= 781 R0=0.00010000 RMT= 0.8700 Z: 8.0
<br>
<br>
LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
<br>
0.0000000 1.0000000 0.0000000
<br>
0.0000000 0.0000000 1.0000000
<br>
ATOM -13: X=0.00000000 Y=0.25000000 Z=0.51600000
<br>
MULT= 2 ISPLIT= 8
<br>
-13: X=0.00000000 Y=0.75000000 Z=0.48400000
<br>
H NPT= 781 R0=0.00010000 RMT= 0.4700 Z: 1.0
<br>
<br>
LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
<br>
0.0000000 1.0000000 0.0000000
<br>
0.0000000 0.0000000 1.0000000
<br>
ATOM -14: X=0.19000000 Y=0.07200000 Z=0.19100000
<br>
MULT= 4 ISPLIT= 8
<br>
-14: X=0.81000000 Y=0.92800000 Z=0.80900000
<br>
-14: X=0.81000000 Y=0.42800000 Z=0.19100000
<br>
-14: X=0.19000000 Y=0.57200000 Z=0.80900000
<br>
H NPT= 781 R0=0.00010000 RMT= 0.4700 Z: 1.0
<br>
<br>
LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
<br>
0.0000000 1.0000000 0.0000000
<br>
0.0000000 0.0000000 1.0000000
<br>
4 NUMBER OF SYMMETRY OPERATIONS
<br>
-1 0 0 0.00000000
<br>
0-1 0 0.00000000
<br>
0 0-1 0.00000000
<br>
1
<br>
1 0 0 0.00000000
<br>
0 1 0 0.00000000
<br>
0 0 1 0.00000000
<br>
2
<br>
-1 0 0 0.00000000
<br>
0-1 0 0.50000000
<br>
0 0 1 0.00000000
<br>
3
<br>
1 0 0 0.00000000
<br>
0 1 0 0.50000000
<br>
0 0-1 0.00000000
<br>
4
<br>
<br>
<br>
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<br>
<br>
</blockquote>
<br>
</blockquote>
<br>
<br>
<div class="moz-signature">-- <br>
<hr>
<h5><font color="#FF0000"><u><b>Attention nouvelle adresse</b></u><br>
<b><a class="moz-txt-link-abbreviated" href="mailto:ferial.terki@univ-montp2.fr">ferial.terki@univ-montp2.fr</a></b></font></h5>
<h6><font color="blue">Férial TERKI<br>
Institut Charles Gerhardt UMR 5253 CNRS-UM2<br>
Université Montpellier 2, cc 1701<br>
Place Eugène Bataillon <br>
34095 Montpellier cedex 5<br>
Tel: +33 (0) 4 67 14 37 68 / 49 14<br>
Fax: +33 (0) 4 67 14 38 53<br>
Thème "Magnétisme Moléculaire"</font></h6>
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