[Wien] Type II AFM MnO

[Manish Jain]

Dear WIEN2K Users,

Does Wien2K write the lattice vectors out to a file somewhere?

I am trying to calculate the AFM II rock-salt structure of MnO. However, 
as MnO has several AFM configurations possible, I would like to be able to 
check which one of the attached structure files corresponds to which 
configuration. Unfortunately mere visualization of the struct file with 
xcryden does not help much as I would like to transform all the lattice 
vectors to (pseudo-) cubic supercells and then visualize the structures.


Could you please tell me where to look for the lattice vectors in the 
output files?


Thanks for all your help.

Regards,
Manish

--
Manish Jain
Assistant Professor
Department of Physics
Indian Institute of Science
Bangalore KA 560 012
India

email: mj...@physics.iisc.ernet.in
Phone: +91 80 2293 2858
web  : http://www.physics.iisc.ernet.in/~mjain
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MnO
P   LATTICE,NONEQUIV.ATOMS:  3 
MODE OF CALC=RELA unit=ang 
  5.921270  5.921270 11.842540 60.00 60.00 60.00   
ATOM  -1: X=0. Y=0. Z=0.
  MULT= 1  ISPLIT= 8
Mn NPT=  781  R0=0.5000 RMT=2.2400   Z: 25.0   
LOCAL ROT MATRIX:1.000 0.000 0.000
 0.000 1.000 0.000
 0.000 0.000 1.000
ATOM  -2: X=0. Y=0. Z=0.5000
  MULT= 1  ISPLIT= 8
Mn NPT=  781  R0=0.5000 RMT=2.2400   Z: 25.0   
LOCAL ROT MATRIX:1.000 0.000 0.000
 0.000 1.000 0.000
 0.000 0.000 1.000
ATOM  -3: X=0.5000 Y=0.5000 Z=0.2500
  MULT= 2  ISPLIT= 8
  -3: X=0.5000 Y=0.5000 Z=0.7500
O  NPT=  781  R0=0.0001 RMT=1.9200   Z:  8.0   
LOCAL ROT MATRIX:1.000 0.000 0.000
 0.000 1.000 0.000
 0.000 0.000 1.000
   2  NUMBER OF SYMMETRY OPERATIONS
-1 0 0 0.
 0-1 0 0.
 0 0-1 0.
   1
 1 0 0 0.
 0 1 0 0.
 0 0 1 0.
   2
Wien97 struct file generated by XCrySDen program   
R   LATTICE,NONEQUIV.ATOMS:  3 166 R-3m
MODE OF CALC=NREL unit=bohr
  5.921312  5.921312 29.008386 90.00 90.00120.00   
ATOM  -1: X=0. Y=0. Z=0.
  MULT= 1  ISPLIT= 4
Mn1NPT=  781  R0=0.5000 RMT=   2.24  Z: 25.0   
LOCAL ROT MATRIX:1.000 0.000 0.000
 0.000 1.000 0.000
 0.000 0.000 1.000
ATOM  -2: X=0.2500 Y=0.2500 Z=0.2500
  MULT= 2  ISPLIT= 4
  -2: X=0.7500 Y=0.7500 Z=0.7500
O 1NPT=  781  R0=0.0001 RMT=   1.92  Z:  8.0   
LOCAL ROT MATRIX:1.000 0.000 0.000
 0.000 1.000 0.000
 0.000 0.000 1.000
ATOM  -3: X=0.5000 Y=0.5000 Z=0.5000
  MULT= 1  ISPLIT= 4
Mn2NPT=  781  R0=0.5000 RMT=   2.24  Z: 25.0   
LOCAL ROT MATRIX:1.000 0.000 0.000
 0.000 1.000 0.000
 0.000 0.000 1.000
  12  NUMBER OF SYMMETRY OPERATIONS
 1 0 0 0.
 0 1 0 0.
 0 0 1 0.
   1
 0 0 1 0.
 1 0 0 0.
 0 1 0 0.
   2
 0 1 0 0.
 0 0 1 0.
 1 0 0 0.
   3
 0-1 0 0.
-1 0 0 0.
 0 0-1 0.
   4
-1 0 0 0.
 0 0-1 0.
 0-1 0 0.
   5
 0 0-1 0.
 0-1 0 0.
-1 0 0 0.
   6
-1 0 0 0.
 0-1 0 0.
 0 0-1 0.
   7
 0 0-1 0.
-1 0 0 0.
 0-1 0 0.
   8
 0-1 0 0.
 0 0-1 0.
-1 0 0 0.
   9
 0 1 0 0.
 1 0 0 0.
 0 0 1 0.
  10
 1 0 0 0.
 0 0 1 0.
 0 1 0 0.
  11
 0 0 1 0.
 0 1 0 0.
 1 0 0 0.
  12
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Re: [Wien] Type II AFM MnO

[tran]

Hi,

This is MnO.struct which corresponds to AFM II.
In xcrysden you can increase the number of units shown
on the screen with Shift-n.

Xcrysden can also write the lattice vectors (in file .xsf with
"Save XSF Structure").

F. Tran

On Thu, 5 Nov 2015, Manish Jain wrote:



Dear WIEN2K Users,

Does Wien2K write the lattice vectors out to a file somewhere?

I am trying to calculate the AFM II rock-salt structure of MnO. However, as 
MnO has several AFM configurations possible, I would like to be able to check 
which one of the attached structure files corresponds to which configuration. 
Unfortunately mere visualization of the struct file with xcryden does not 
help much as I would like to transform all the lattice vectors to (pseudo-) 
cubic supercells and then visualize the structures.


Could you please tell me where to look for the lattice vectors in the output 
files?


Thanks for all your help.

Regards,
Manish

--
Manish Jain
Assistant Professor
Department of Physics
Indian Institute of Science
Bangalore KA 560 012
India

email: mj...@physics.iisc.ernet.in
Phone: +91 80 2293 2858
web  : http://www.physics.iisc.ernet.in/~mjain
--
This message has been scanned for viruses and
dangerous content by MailScanner, and is
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Re: [Wien] question

[Fecher, Gerhard]

I guess you like to calculate the Seebeck coefficient of some materials based 
the electronic structure calculated by Wien2k ,
therefore, please check the program Boltztrap.
Xou will find it on the "Unsupported software goodies " page: 
http://www.wien2k.at/reg_user/unsupported/

Next time, please ask a clear question.

Ciao
Gerhard

DEEP THOUGHT in D. Adams; Hitchhikers Guide to the Galaxy:
"I think the problem, to be quite honest with you,
is that you have never actually known what the question is."


Dr. Gerhard H. Fecher
Institut of Inorganic and Analytical Chemistry
Johannes Gutenberg - University
55099 Mainz
and
Max Planck Institute for Chemical Physics of Solids
01187 Dresden

Von: wien-boun...@zeus.theochem.tuwien.ac.at 
[wien-boun...@zeus.theochem.tuwien.ac.at] im Auftrag von Dj Fati 
[fatid...@yahoo.fr]
Gesendet: Mittwoch, 4. November 2015 13:20
An: wien@zeus.theochem.tuwien.ac.at
Betreff: [Wien] question

calculs of seebeck coefficient in wien2k
thank's
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Re: [Wien] Some error messages during Installation of WIEN2k_14.2 on CentOS6.5

[Laurence Marks]

What you wrote is right...and wrong.

If you are just running 1 process at a time in the non-parallel mode, what
you wrote is correct.

However, in many cases one either runs  many different processes
simultaneously, often as many as you have cores (ignoring hyperthreading
which is rarely useful in my experience). For larger calculations you may
also want to use mpi in which case every core will have the same memory
usage.

You have a relatively small cluster, so I suggest that you leave it with
the default values, particularly if you are relatively new to Wien2k. While
the values you used probably won't matter, they are not that safe. I
suggest leaving them for now and running a number of test calculations.

On Wed, Nov 4, 2015 at 8:04 AM, tongwei  wrote:

> Thanks.
> For the NMATMAX and NUME values, I am following the prompt during
> installation:
> "NMATMAX=1 ==>   1GB (real) (==> cells with about 50-150
> atoms/unitcell)
> ==> for lapw1c:NMATMAX will be reduced internally to NMATMAX/sqrt2
> ==> for lapw1_mpi: NMATMAX will be increased internally to
> NMATMAX*sqrt(NP)
>
> NUME determines the number of states to output. As a rule of thumb one can
> estimate 100 basis functions per atom in the cell and 10 occupied states
> per
> atom, so setNUME=NMATMAX/10.
> "
> I have 128GB at node1 and 64GB memory at node2 . So, I assume that 32GB
> should be available for WIEN2k. Then 32*1=32, NUME=NMATMAX/10=32000.
>
> Is this wrong? Then, where to change this value?
>
> Best,
> WT
>
> --
> Date: Mon, 2 Nov 2015 09:01:41 -0600
> From: l-ma...@northwestern.edu
> To: wien@zeus.theochem.tuwien.ac.at
> Subject: Re: [Wien] Some error messages during Installation of WIEN2k_14.2
> on CentOS6.5
>
> I am 99.9% certain that none of these is an error. The compile script will
> tell you if there are any at the end, these are flagged with "Error".
>
> N.B., the values
> set value for NMATMAX=32
> set value for NUME=32000
>
> are large, you could run into problems with these if you are running
> k-point parallel for larger jobs. Since you only have a 2 node cluster with
> 1G ethernet (?) you may be only intending to run smaller jobs in which case
> it will be fine. You could get an OOM (Out Of Memory) OS crash with larger
> jobs.
>
>
> --
Professor Laurence Marks
Department of Materials Science and Engineering
Northwestern University
www.numis.northwestern.edu
Corrosion in 4D: MURI4D.numis.northwestern.edu
Co-Editor, Acta Cryst A
"Research is to see what everybody else has seen, and to think what nobody
else has thought"
Albert Szent-Gyorgi
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[Wien] question

[Dj Fati]

the step of transport calculs
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[Wien] question

[Dj Fati]

calculs of seebeck coefficient in wien2kthank's
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Re: [Wien] question

[Fecher, Gerhard]

the answer is 42, see reference given below

Ciao
Gerhard

DEEP THOUGHT in D. Adams; Hitchhikers Guide to the Galaxy:
"I think the problem, to be quite honest with you,
is that you have never actually known what the question is."


Dr. Gerhard H. Fecher
Institut of Inorganic and Analytical Chemistry
Johannes Gutenberg - University
55099 Mainz
and
Max Planck Institute for Chemical Physics of Solids
01187 Dresden

Von: wien-boun...@zeus.theochem.tuwien.ac.at 
[wien-boun...@zeus.theochem.tuwien.ac.at] im Auftrag von Dj Fati 
[fatid...@yahoo.fr]
Gesendet: Mittwoch, 4. November 2015 13:20
An: wien@zeus.theochem.tuwien.ac.at
Betreff: [Wien] question

calculs of seebeck coefficient in wien2k
thank's
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Re: [Wien] Some error messages during Installation of WIEN2k_14.2 on CentOS6.5

[Peter Blaha]

Yes it is wrong.

a) The memory count usually as memory/core, so if you have a 64GB node, 
you should most likely divide by the number of cores (and then maybe 
multiply by 2, because you can use multithreading with 2 cores and use 2 
cores/job.
b) The memory is calculated as:  NMATMAX**2 * 10 (actually it should be 
8 bytes/number, but we need also some overhead)

1**2*10=10**9 bytes = 1GB
NMATMAX=2: ~4GB (per core !!)

c) larger values than 2 are most likely useless, because as was said 
by L.Marks, for larger cases there is no k-parallism but even when it 
would fit in memory, it would run much too long. Therefore we switch to 
mpi-parallelization with many cores (on a good cluster AND big problem 
we have used up to 1000 cores).
And for these problems NMTMAX will be internally increased by 
NMATMAX*sqrt(NP)


On 11/04/2015 03:04 PM, tongwei wrote:

Thanks.
For the NMATMAX and NUME values, I am following the prompt during
installation:
"NMATMAX=1 ==>   1GB (real) (==> cells with about 50-150 atoms/unitcell)
 ==> for lapw1c:NMATMAX will be reduced internally to NMATMAX/sqrt2
 ==> for lapw1_mpi: NMATMAX will be increased internally to
NMATMAX*sqrt(NP)

NUME determines the number of states to output. As a rule of thumb one can
estimate 100 basis functions per atom in the cell and 10 occupied states
per
atom, so setNUME=NMATMAX/10.
"
I have 128GB at node1 and 64GB memory at node2 . So, I assume that 32GB
should be available for WIEN2k. Then 32*1=32,
NUME=NMATMAX/10=32000.
Is this wrong? Then, where to change this value?

Best,
WT


Date: Mon, 2 Nov 2015 09:01:41 -0600
From: l-ma...@northwestern.edu
To: wien@zeus.theochem.tuwien.ac.at
Subject: Re: [Wien] Some error messages during Installation of
WIEN2k_14.2 on CentOS6.5

I am 99.9% certain that none of these is an error. The compile script
will tell you if there are any at the end, these are flagged with "Error".

N.B., the values
set value for NMATMAX=32
set value for NUME=32000

are large, you could run into problems with these if you are running
k-point parallel for larger jobs. Since you only have a 2 node cluster
with 1G ethernet (?) you may be only intending to run smaller jobs in
which case it will be fine. You could get an OOM (Out Of Memory) OS
crash with larger jobs.

On Mon, Nov 2, 2015 at 8:51 AM, tongwei > wrote:

Dear Everyone,

During installing WIEN2k_14.2, I watched the screen and saw a few
errors in the following.  I am not sure it is OK or not.
---after save compiler options---
No Makefile.orig in SRC_structeditor/SRC_lib, leaving directory.
No Makefile.orig in SRC_BerryPI, leaving directory.
No Makefile.orig in SRC_lib, leaving directory.
No Makefile.orig in SRC_structeditor, leaving directory.
No Makefile.orig in SRC_templates, leaving directory.
  No Makefile.orig in SRC_usersguide_html, leaving directory.
No Makefile.orig in SRC_w2web, leaving directory.
-During compiling-
RC_BerryPI ...
make: *** No rule to make target `clean'.  Stop.
make: *** No targets specified and no makefile found.  Stop.

SRC_clmcopy ...
make: Circular modules.o <- modules.o dependency dropped.
make: Circular reallocate.o <- modules.o dependency dropped.
make: Circular reallocate.o <- reallocate.o dependency dropped.

make[1]: Leaving directory `/usr/local/WIEN2k_14.2/SRC_dstart'
make: *** No rule to make target `complex'.  Stop.
---

Waiting for solution.
Thanks!

WT

+++Here is my situation and installation process

1. Hardware: A simple cluster with TWO DELL T760/T7600 workstations
communicating through 1000M switch:
Master (node1)--- 2*Xeon E5-2690 (2*8core), 128G memory
Slave (node2)  2*Xeon E5-2690 v2 (2*10core), 64G memory
---Installation is on Master.
2. OS: CentOS 6.5 64bit final
3. Required package installed
F90 compiler Intel parallel_studio_xe_2013_update4 inluding
ifort version 13.1.3, icc version 13.1.3, MKL, installed at /opt/intel
perl 5   v5.10.1 installed at  /usr/bin/perl)
emacs --- GNU Emacs 23.1.1 installed at /usr/bin/emacs）
ghostscript  v8.70 installed at /usr/bin/ghostscript)
gnuplot - gnuplot 4.2 patchlevel 6 installed at /usr/bin/gnuplot ）
www-browser - firefox 38.2.1 installed
Tcl/Tk-Toolkit - tcl.x86_64/tk.x86_64 v8.5.7 installed
FFTW v.2 or 3 -Both installed with yum (fftw2-2.1.5, fftw-3.2.1),
   and also installed fftw3.3.4 from source through
   "./configure --prefix=/usr/local/fftw3.3.4
CC="icc" --enable-mpi --enable-threads"
   and "make", "make install" at
/usr/local/fftw3.3.4 with parallel 

Re: [Wien] RMTs changing on their own?

[Elias Assmann]

On 11/03/2015 02:47 PM, Laurence Marks wrote:
> a) :FCHECK (bottom of case.scf) was large. This is the sum of all
> the forces, and should be small. Particularly for cells without
> inversion one can get bad, highly asymmetric densities in which case
> MSR1a can have problems.

True, I had not notice this before.  :FCHECK was already quite large
(hundreds for x and y, even >1000 for z) before ‘clminter’ and “jumped”
to even larger values afterwards.

> b) The greed is small. Too small a value can be as bad as too large.
> I have struggled with this for years and failed to find a strong
> ansatz for this, although I believe the next release of the mixer
> will be better.

AFAIK, the greed in MSR1(a) is set internally by the mixer (the
corresponding value in case.inm being ignored), so there is nothing I
can do directly to influence this, is there?

> I am not sure what the calculation is, perhaps an oxide surface
> where you have made a guess at the initial structure and want to
> minimize to something more reasonable.

Quite a good guess, it is an oxide heterostructure including a slab of
vacuum, but the initial structure is derived (cut out) from a converged
one from an older calculation, so I would have expected only relatively
minor adjustments.  As such, the large forces also come as something of
a surprise.

> I strongly suggest trying to use cells with inversion, they behave
> much, much better.

In this case, inversion symmetry could only be achieved by adding an
additional “film” on the back side of the “substrate”.

> I also strongly suggest that you look at the Bond Valence Sums (BVS)
> and tweak the initial positions until they are reasonable. (x nn ; 
> grep Bond *tnn). If, for instance, you have highly underbonded O
> (e.g. 0.8) it can take forever and the calculations can be unstable
> -- convergence is faster the more physical are the atomic positions.

I guess the expectation is that the BVS should be close to the “formal
valence” of the ion, right?  In this case, it seems okay: The first BVS
value is between 1.4 and 2.2 for O, deviations for other species are
rather smaller).

> Good luck.

Thanks, and thank you for your tips.


Elias

-- 
Elias Assmann
Institute of Theoretical and Computational Physics
TU Graz   ⟨https://itp.tugraz.at/⟩



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