[Wien] Determine primitive cell and positions, CXZ LATTICE 15_B2/b
Terki Férial
ferial.terki at univ-montp2.fr
Thu Mar 19 19:38:58 CET 2015
Dear Collegues
I want to */unsubscribe/* <javascript:void(0)> to this data mail
Thanks
Dr F. TERKI
Le 19/03/2015 18:29, Peter Blaha a écrit :
> For low symmetry structures (eg. monoclinic) one can generate several
> unit cells
> which are absolutely equivalent (same volume, same number of atoms, ...)
>
> This happens with sgroup, which transforms your structure such that the
> monoclinic angle is less than 90. In addition the fractional coordinates
> have been changed austomatically. Nevertheless, these two cells will give
> identical neighbor-distances, which you can verify with nn and
> comparing the
> resulting outputnn files. There is nothing wrong with either your
> original cell
> or the one from sgroup. You can use either one for the calculations.
>
> If you want the conventional cell (which contains of course 2x as many
> atoms),
> you can use x supercell (1x1x1, no shifts/vacuum). It simply changes
> the lattice type to "P", and adds the centered atoms.
> With this struct file, however, you cannot make the calculations
> unless you
> make these atoms "non-equivalent" and break symmetry, eg. by labeling one
> atom as "Al1".
>
> What you have been trying was to express the lattice
> vectors/positions in carthesian
> coordinates.
> You can check your calculations again using the distances of outputnn and
> compare them to your own calculations.
>
>
>
> Am 19.03.2015 um 17:03 schrieb David Olmsted:
>> Dear reader,
>> I am trying to determine the primitive cell and positions for a
>> case.struct file I am running. But I am not determining the either
>> primitive cell or the conventional cell correctly.
>>
>> I need to either:
>> 1. Figure out what I am doing wrong. or
>> 2. Find a place in the code where I can print out the positions in
>> terms
>> of the primitive cell.
>>
>> Does anyone know the answer to either question?
>>
>> This is a base-centered monoclinic system, space group 15.
>>
>>> From case.struct:
>> MODE OF CALC=RELA unit=bohr
>>
>> 35.704486 13.533274 13.533274 90.000000 90.000000 99.990000
>>
>> The full case.struct is given below.
>>
>> sgroup reports 15 (C 2/c) [unique axis c] cell choice 2.
>> The struct file output from sgroup is:
>> CXZ LATTICE,NONEQUIV.ATOMS: 14 15 C2/c
>> MODE OF CALC=RELA unit=bohr
>>
>> 35.704486 13.533274 13.533274 90.000000 90.000000 80.010000
>> The case.struct file I am using has the 99.99 degree entry as above.
>>
>> In angstroms, my lattice constants (and angles in degrees) are
>> 18.894 7.1615 7.1615 90 90 99.99
>>
>> The userguide gives (on page 39) the primitive cell as:
>> CXZ [a sin(\gamma)/2, a cos(\gamma)/2, -c/2], [0, b, 0], [a
>> sin(\gamma)/2, acos(\gamma)/2, c/2]
>>
>> So I have for a primitive cell (each row is a vector):
>> 9.3038 -1.6388 -3.5808
>> 0 7.1615 0
>> 9.3038 -1.6388 3.5808
>>
>> With lengths of 10.1029 7.1615 10.1029 and angles 99.34 41.52 99.34.
>>
>> The positions in case.struct are given in terms of the conventional unit
>> cell, and I must convert them to the primitive cell. So I need the
>> conventional cell in cartesian coordinates.
>>
>> The README file in SRC_sgroup talks about base-centered monoclinic being
>> restricted to A centered. Page 39 of the userguide shows only
>> B-base-centered,
>> which is what I have. The README gives:
>>
>> The vectors of the conventional cell in cartesian basis
>> ( 1 vector is 1 column ... )
>>
>> a b*Cos[gamma] 0
>> 0 b*Sin[gamma] 0 A - centred
>> 0 0 c
>>
>> This is a valid conventional cell in my case, and switching to each row
>> being a vector, I have:
>> 18.894 0 0
>> -1.24235 7.0529 0
>> 0 0 7.1615
>>
>> However the location of the second primitive cell is (0.5, 0, 0.5) in
>> terms
>> of the conventional cell. When transformed to primitive cell
>> coordinates it
>> must be a lattice vector. But it is not. So one of my cells is
>> wrong. (I
>> believe the vector for the second primitive cell is correct because
>> it is
>> what is given in the International Tables, page 199, for unique axis
>> c, cell
>> choice 2. And it matches to the neighbor positions in case.outputnn.)
>>
>> Quite possibly the conventional cell is different for B-centered than
>> for
>> A-centered, but I do not find it described anywhere.
>>
>> My thanks for any help.
>> David
>>
>> David Olmsted
>> Assistant Research Engineer
>> Materials Science and Engineering
>> 210 Hearst Memorial Mining Building
>> University of California
>> Berkeley, CA 94720-1760
>>
>>
>>
>> ------- case.struct
>> troll_icsd
>>
>> CXZ LATTICE,NONEQUIV.ATOMS: 14 15_B2/b
>>
>> MODE OF CALC=RELA unit=bohr
>>
>> 35.704486 13.533274 13.533274 90.000000 90.000000 99.990000
>>
>> ATOM -1: X=0.16778000 Y=0.32059000 Z=0.00654000
>> MULT= 4 ISPLIT= 8
>> -1: X=0.83222000 Y=0.67941000 Z=0.99346000
>> -1: X=0.83222000 Y=0.17941000 Z=0.00654000
>> -1: X=0.16778000 Y=0.82059000 Z=0.99346000
>> Al NPT= 781 R0=0.00010000 RMT= 1.6300 Z: 13.0
>>
>> LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
>> 0.0000000 1.0000000 0.0000000
>> 0.0000000 0.0000000 1.0000000
>> ATOM -2: X=0.07570000 Y=0.41714000 Z=0.72882000
>> MULT= 4 ISPLIT= 8
>> -2: X=0.92430000 Y=0.58286000 Z=0.27118000
>> -2: X=0.92430000 Y=0.08286000 Z=0.72882000
>> -2: X=0.07570000 Y=0.91714000 Z=0.27118000
>> Al NPT= 781 R0=0.00010000 RMT= 1.6300 Z: 13.0
>>
>> LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
>> 0.0000000 1.0000000 0.0000000
>> 0.0000000 0.0000000 1.0000000
>> ATOM -3: X=0.00000000 Y=0.25000000 Z=0.11731000
>> MULT= 2 ISPLIT= 8
>> -3: X=0.00000000 Y=0.75000000 Z=0.88269000
>> P NPT= 781 R0=0.00010000 RMT= 1.3000 Z: 15.0
>>
>> LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
>> 0.0000000 1.0000000 0.0000000
>> 0.0000000 0.0000000 1.0000000
>> ATOM -4: X=0.16844000 Y=0.08109000 Z=0.63272000
>> MULT= 4 ISPLIT= 8
>> -4: X=0.83156000 Y=0.91891000 Z=0.36728000
>> -4: X=0.83156000 Y=0.41891000 Z=0.63272000
>> -4: X=0.16844000 Y=0.58109000 Z=0.36728000
>> P NPT= 781 R0=0.00010000 RMT= 1.3000 Z: 15.0
>>
>> LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
>> 0.0000000 1.0000000 0.0000000
>> 0.0000000 0.0000000 1.0000000
>> ATOM -5: X=0.06458000 Y=0.32611000 Z=0.98827000
>> MULT= 4 ISPLIT= 8
>> -5: X=0.93542000 Y=0.67389000 Z=0.01173000
>> -5: X=0.93542000 Y=0.17389000 Z=0.98827000
>> -5: X=0.06458000 Y=0.82611000 Z=0.01173000
>> O NPT= 781 R0=0.00010000 RMT= 0.8700 Z: 8.0
>>
>> LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
>> 0.0000000 1.0000000 0.0000000
>> 0.0000000 0.0000000 1.0000000
>> ATOM -6: X=0.02064000 Y=0.09579000 Z=0.23728000
>> MULT= 4 ISPLIT= 8
>> -6: X=0.97936000 Y=0.90421000 Z=0.76272000
>> -6: X=0.97936000 Y=0.40421000 Z=0.23728000
>> -6: X=0.02064000 Y=0.59579000 Z=0.76272000
>> O NPT= 781 R0=0.00010000 RMT= 0.8700 Z: 8.0
>>
>> LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
>> 0.0000000 1.0000000 0.0000000
>> 0.0000000 0.0000000 1.0000000
>> ATOM -7: X=0.23738000 Y=0.16861000 Z=0.53512000
>> MULT= 4 ISPLIT= 8
>> -7: X=0.76262000 Y=0.83139000 Z=0.46488000
>> -7: X=0.76262000 Y=0.33139000 Z=0.53512000
>> -7: X=0.23738000 Y=0.66861000 Z=0.46488000
>> O NPT= 781 R0=0.00010000 RMT= 0.8700 Z: 8.0
>>
>> LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
>> 0.0000000 1.0000000 0.0000000
>> 0.0000000 0.0000000 1.0000000
>> ATOM -8: X=0.11140000 Y=0.00803000 Z=0.49156000
>> MULT= 4 ISPLIT= 8
>> -8: X=0.88860000 Y=0.99197000 Z=0.50844000
>> -8: X=0.88860000 Y=0.49197000 Z=0.49156000
>> -8: X=0.11140000 Y=0.50803000 Z=0.50844000
>> O NPT= 781 R0=0.00010000 RMT= 0.8700 Z: 8.0
>>
>> LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
>> 0.0000000 1.0000000 0.0000000
>> 0.0000000 0.0000000 1.0000000
>> ATOM -9: X=0.14191000 Y=0.23708000 Z=0.75449000
>> MULT= 4 ISPLIT= 8
>> -9: X=0.85809000 Y=0.76292000 Z=0.24551000
>> -9: X=0.85809000 Y=0.26292000 Z=0.75449000
>> -9: X=0.14191000 Y=0.73708000 Z=0.24551000
>> O NPT= 781 R0=0.00010000 RMT= 0.8700 Z: 8.0
>>
>> LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
>> 0.0000000 1.0000000 0.0000000
>> 0.0000000 0.0000000 1.0000000
>> ATOM -10: X=0.18216000 Y=0.92446000 Z=0.76484000
>> MULT= 4 ISPLIT= 8
>> -10: X=0.81784000 Y=0.07554000 Z=0.23516000
>> -10: X=0.81784000 Y=0.57554000 Z=0.76484000
>> -10: X=0.18216000 Y=0.42446000 Z=0.23516000
>> O NPT= 781 R0=0.00010000 RMT= 0.8700 Z: 8.0
>>
>> LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
>> 0.0000000 1.0000000 0.0000000
>> 0.0000000 0.0000000 1.0000000
>> ATOM -11: X=0.00000000 Y=0.25000000 Z=0.63572000
>> MULT= 2 ISPLIT= 8
>> -11: X=0.00000000 Y=0.75000000 Z=0.36428000
>> O NPT= 781 R0=0.00010000 RMT= 0.8700 Z: 8.0
>>
>> LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
>> 0.0000000 1.0000000 0.0000000
>> 0.0000000 0.0000000 1.0000000
>> ATOM -12: X=0.16141000 Y=0.06966000 Z=0.12100000
>> MULT= 4 ISPLIT= 8
>> -12: X=0.83859000 Y=0.93034000 Z=0.87900000
>> -12: X=0.83859000 Y=0.43034000 Z=0.12100000
>> -12: X=0.16141000 Y=0.56966000 Z=0.87900000
>> O NPT= 781 R0=0.00010000 RMT= 0.8700 Z: 8.0
>>
>> LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
>> 0.0000000 1.0000000 0.0000000
>> 0.0000000 0.0000000 1.0000000
>> ATOM -13: X=0.00000000 Y=0.25000000 Z=0.51600000
>> MULT= 2 ISPLIT= 8
>> -13: X=0.00000000 Y=0.75000000 Z=0.48400000
>> H NPT= 781 R0=0.00010000 RMT= 0.4700 Z: 1.0
>>
>> LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
>> 0.0000000 1.0000000 0.0000000
>> 0.0000000 0.0000000 1.0000000
>> ATOM -14: X=0.19000000 Y=0.07200000 Z=0.19100000
>> MULT= 4 ISPLIT= 8
>> -14: X=0.81000000 Y=0.92800000 Z=0.80900000
>> -14: X=0.81000000 Y=0.42800000 Z=0.19100000
>> -14: X=0.19000000 Y=0.57200000 Z=0.80900000
>> H NPT= 781 R0=0.00010000 RMT= 0.4700 Z: 1.0
>>
>> LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
>> 0.0000000 1.0000000 0.0000000
>> 0.0000000 0.0000000 1.0000000
>> 4 NUMBER OF SYMMETRY OPERATIONS
>> -1 0 0 0.00000000
>> 0-1 0 0.00000000
>> 0 0-1 0.00000000
>> 1
>> 1 0 0 0.00000000
>> 0 1 0 0.00000000
>> 0 0 1 0.00000000
>> 2
>> -1 0 0 0.00000000
>> 0-1 0 0.50000000
>> 0 0 1 0.00000000
>> 3
>> 1 0 0 0.00000000
>> 0 1 0 0.50000000
>> 0 0-1 0.00000000
>> 4
>>
>>
>> _______________________________________________
>> Wien mailing list
>> Wien at zeus.theochem.tuwien.ac.at
>> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
>> SEARCH the MAILING-LIST at:
>> http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
>>
>
--
------------------------------------------------------------------------
_*Attention nouvelle adresse*_
*ferial.terki at univ-montp2.fr*
Férial TERKI
Institut Charles Gerhardt UMR 5253 CNRS-UM2
Université Montpellier 2, cc 1701
Place Eugène Bataillon
34095 Montpellier cedex 5
Tel: +33 (0) 4 67 14 37 68 / 49 14
Fax: +33 (0) 4 67 14 38 53
Thème "Magnétisme Moléculaire"
------------------------------------------------------------------------
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://zeus.theochem.tuwien.ac.at/pipermail/wien/attachments/20150319/a234eb96/attachment.html>
More information about the Wien
mailing list