[Wien] Determine primitive cell and positions, CXZ LATTICE 15_B2/b
David Olmsted
olmsted at berkeley.edu
Thu Mar 19 21:36:03 CET 2015
Peter,
Thank you for your prompt reply.
I apologize profusely, I failed to explain what I was trying to do.
The cell was generated from an ICSD cif. There is indeed no problem with
case.struct file, the neighbor distances seem fine. But I am having
terrible trouble getting this to run because the ghostbands are even harder
to get rid of than in the other Al-P-O-H structure. I also know that the H
positions are very different from what GGA is going to give, because I had
already done a VASP run for the conventional cell.
I am thinking that if I relaxed the structure in VASP first, the positions
would be better and it might be easier to converge the WIEN2k computation.
(I am using WIEN2k even though I already have a VASP run because I am trying
to compute XPS.) But to set up a VASP run, I need to figure out the correct
primitive cell and the positions that go with them. That is why I am trying
to convert from the conventional cell description given in case.struct to a
description in terms of a primitive cell. But I do have one (or both) of
those two cells wrong with respect to WIEN2k.
Best regards,
David
--------------------------
Peter Blaha Thu, 19 Mar 2015 11:30:41 -0700
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.
-----Original Message-----
From: David Olmsted [mailto:olmsted at berkeley.edu]
Sent: Thursday, March 19, 2015 9:04 AM
To: 'wien at zeus.theochem.tuwien.ac.at'
Subject: Determine primitive cell and positions, CXZ LATTICE 15_B2/b
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
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