[Wien] cleaning up scratch dir

[Luc Fruchter]

Dear all,

I am running parallel k-points over several nodes, which run fine (19.1 
version).
However, I have defined local scratch directories on nodes to reduce 
file transfers (defining the scratch variable in .bashrc), as recommended.
I see that .vector files accumulate there at each case run. I would 
expect that the scratch dir be cleaned, for instance using "clean_lapw", 
but the only way to clean up these accumulating files seems to remove 
them by hand. Is this the expected behavior for the scratch dir files ?


Thanks
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Re: [Wien] cleaning up scratch dir

[Peter Blaha]

It is the expected behaviour.

Of course, it would be easy to remove such files on the local SCHRATCH 
directory. However, in many cases you may run such calculations on 
different nodes (and thus different local scratch directories), while 
eg. on the frontend, where you "clean", there are no such files anyway.


If you are running only "locally" (eg. on your own PC), there is hardly 
any benefit of using a SCRATCH directory and I would set it to "./".


Thus at least "in general", there is no way one can clean the actually 
used scratch, because you may not know on which machine the calculations 
were done.


PS: We have a cron-job on all our nodes, which deletes automatically all 
files older than 4 weeks on scratch (find command).


Regards

Am 23.07.2020 um 15:37 schrieb Luc Fruchter:

Dear all,

I am running parallel k-points over several nodes, which run fine (19.1 
version).
However, I have defined local scratch directories on nodes to reduce 
file transfers (defining the scratch variable in .bashrc), as recommended.
I see that .vector files accumulate there at each case run. I would 
expect that the scratch dir be cleaned, for instance using "clean_lapw", 
but the only way to clean up these accumulating files seems to remove 
them by hand. Is this the expected behavior for the scratch dir files ?


Thanks

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--
--
Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
Email: bl...@theochem.tuwien.ac.atWIEN2k: http://www.wien2k.at
WWW: 
http://www.imc.tuwien.ac.at/tc_blaha- 


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Re: [Wien] Mailing List

[Tran, Fabien]

You need to construct a super cell which contains several Mn atoms (at least 
one for each orientation of the magnetic moment).
Then, you need to put labels (1, 2) in case.struct to avoid to reobtain the 
original cell after init_lapw.
See for instance discussion here
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19513.html

From: Wien  on behalf of djamel 
slamnia 
Sent: Thursday, July 23, 2020 5:25 PM
To: A. Mailing List for WIEN2k Users
Subject: [Wien] Mailing List
  
Dear wien2k user's 

for antiferromagnetic calculation : i have to split the position of Mn atom to 
get 2 atoms in unit cell but 
in my case.struct the Mn atom has only one position 

so what i have to do ???

can i displace Mn atom ??

thanks in advance  
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[Wien] Mailing List

[djamel slamnia]

Dear wien2k user's 
for antiferromagnetic calculation : i have to split the position of Mn atom to 
get 2 atoms in unit cell but in my case.struct the Mn atom has only one 
position 
so what i have to do ???
can i displace Mn atom ??


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[Wien] Space group change during running x sgroup

[Peeyush Kumar Kamlesh]

Dear Wien2k users,
Greetings!
I am working on XYZ half-Heusler compounds with space group no.-216. When I
do initialization of a struct  file of a supercell. then output of x sgroup
shows some warning:

warning: !!! Number of inequivalent atoms has changed. !!! Old value= 34
New value= 40 warning: !!! Bravais lattice has changed.
sgroup found: 35 (C m m 2) Note that shift vectors for this space group are
defined.
Bravais lattice: Orthorhombic C-base centred.
Kindly help me to solve the problem.

Thank you!
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Re: [Wien] Space group change during running x sgroup

[Peeyush Kumar Kamlesh]

Before that when I run the command x nn, it shows following error:

WARNING: Mult not equal. PLEASE CHECK outputnn-file
 WARNING: ityp not equal. PLEASE CHECK outputnn-file

I have tried by putting different values for nn, but it is not changing.

What will be its solution?


On Fri, Jul 24, 2020 at 1:33 AM Peeyush Kumar Kamlesh <
peeyush.physik@gmail.com> wrote:

> Dear Wien2k users,
> Greetings!
> I am working on XYZ half-Heusler compounds with space group no.-216. When
> I do initialization of a struct  file of a supercell. then output of x
> sgroup shows some warning:
>
> warning: !!! Number of inequivalent atoms has changed. !!! Old value= 34
> New value= 40 warning: !!! Bravais lattice has changed.
> sgroup found: 35 (C m m 2) Note that shift vectors for this space group
> are defined.
> Bravais lattice: Orthorhombic C-base centred.
> Kindly help me to solve the problem.
>
> Thank you!
>
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Re: [Wien] Mailing List

[djamel slamnia]

 thanks for replay :my compound has one Mn atom with one position , i'm trying 
to split it to get tow atoms of Mn in unit cell but i cant  because Mn has one 
position can i do for exemple : displace (at least one) atoms
Le jeudi 23 juillet 2020 à 17:49:26 UTC+2, Tran, Fabien 
 a écrit :  
 
 You need to construct a super cell which contains several Mn atoms (at least 
one for each orientation of the magnetic moment).
Then, you need to put labels (1, 2) in case.struct to avoid to reobtain the 
original cell after init_lapw.
See for instance discussion here
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19513.html

From: Wien  on behalf of djamel 
slamnia 
Sent: Thursday, July 23, 2020 5:25 PM
To: A. Mailing List for WIEN2k Users
Subject: [Wien] Mailing List
  
Dear wien2k user's 

for antiferromagnetic calculation : i have to split the position of Mn atom to 
get 2 atoms in unit cell but 
in my case.struct the Mn atom has only one position 

so what i have to do ???

can i displace Mn atom ??

thanks in advance     
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Re: [Wien] Space group change during running x sgroup

[Peter Blaha]

The solution is to create a correct struct file.

Your struct file is NOT a half-Heusler structure with spacegroup 216.

Am 23.07.2020 um 22:23 schrieb Peeyush Kumar Kamlesh:

Before that when I run the command x nn, it shows following error:

WARNING: Mult not equal. PLEASE CHECK outputnn-file WARNING: ityp not 
equal. PLEASE CHECK outputnn-file


I have tried by putting different values for nn, but it is not changing.

What will be its solution?


On Fri, Jul 24, 2020 at 1:33 AM Peeyush Kumar Kamlesh 
mailto:peeyush.physik@gmail.com>> wrote:


Dear Wien2k users,
Greetings!
I am working on XYZ half-Heusler compounds with space group no.-216.
When I do initialization of a struct  file of a supercell. then
output of x sgroup shows some warning:

warning: !!! Number of inequivalent atoms has changed. !!! Old
value= 34 New value= 40 warning: !!! Bravais lattice has changed.
sgroup found: 35 (C m m 2) Note that shift vectors for this space
group are defined.
Bravais lattice: Orthorhombic C-base centred.
Kindly help me to solve the problem.

Thank you!


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--
--
Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
Email: bl...@theochem.tuwien.ac.atWIEN2k: http://www.wien2k.at
WWW: 
http://www.imc.tuwien.ac.at/tc_blaha- 


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Re: [Wien] Space group change during running x sgroup

[Peeyush Kumar Kamlesh]

Dear Blaha Sir,
1. First I prepared a case.struct file with optimized lattice parameters,
having F43m spacegroup (216). Which F lattice. it is as follows:
--

F   LATTICE,NONEQUIV.ATOMS:  3 216_F-43m
MODE OF CALC=RELA unit=ang
 13.647608 13.647608 13.647608 90.00 90.00 90.00
ATOM   1: X=0.5000 Y=0.5000 Z=0.5000
  MULT= 1  ISPLIT= 2
Rb NPT=  781  R0=0.1000 RMT=2.5000   Z: 37.000
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= 1  ISPLIT= 2
Zn NPT=  781  R0=0.5000 RMT=2.5000   Z: 30.000
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. Y=0. Z=0.
  MULT= 1  ISPLIT= 2
Bi NPT=  781  R0=0.0500 RMT=2.5000   Z: 83.000
LOCAL ROT MATRIX:1.000 0.000 0.000
 0.000 1.000 0.000
 0.000 0.000 1.000
24  NUMBER OF SYMMETRY OPERATIONS

2. Then I created a supercell (1x1x1) using wien2k, having P lattice but
with the same space group. case_super .struct file is as follows:
---

P   LATTICE,NONEQUIV. ATOMS 12
MODE OF CALC=RELA unit=ang
 13.647608 13.647608 13.647608 90.00 90.00 90.00
ATOM   1: X=0.5000 Y=0.5000 Z=0.5000
  MULT= 1  ISPLIT= 2
Rb NPT=  781  R0=0.1000 RMT=2.5000   Z: 37.0
LOCAL ROT MATRIX:1.000 0.000 0.000
 0.000 1.000 0.000
 0.000 0.000 1.000
And so on . till
ATOM  12: X=0. Y=0.5000 Z=0.5000
  MULT= 1  ISPLIT= 2
Bi NPT=  781  R0=0.0500 RMT=2.5000   Z: 83.0
LOCAL ROT MATRIX:1.000 0.000 0.000
 0.000 1.000 0.000
 0.000 0.000 1.000
   0  NUMBER OF SYMMETRY OPERATIONS
-
3. Then I copied case_super.struct to case.struct file and used the command
(phonopy --wien2k -d --dim="2 2 2" -c case.struct) to run phonopy with a
supercell of (2x2x2). its output is as follows:
---
   _
  _ __ | |__   ___  _ __   ___   _ __  _   _
 | '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
 | |_) | | | | (_) | | | | (_) || |_) | |_| |
 | .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
 |_||_||___/
   2.7.0

Python version 3.8.4
Spglib version 1.15.1

Calculator interface: wien2k
Crystal structure was read from "RbZnBi.struct".
Unit of length: au
Displacements creation mode
Settings:
  Supercell: [2 2 2]
Spacegroup: F-43m (216)
Use -v option to watch primitive cell, unit cell, and supercell structures.

Number of non-equivalent atoms in RbZnBi.structS-001.in: 40
Number of non-equivalent atoms in RbZnBi.structS-002.in: 38
Number of non-equivalent atoms in RbZnBi.structS-003.in: 40
"phonopy_disp.yaml" and supercells have been created.

Summary of calculation was written in "phonopy_disp.yaml".
 _
   ___ _ __   __| |
  / _ \ '_ \ / _` |
 |  __/ | | | (_| |
  \___|_| |_|\__,_|


4. It is clear from the output that the space group is not changed. It
generates one file for a perfect supercell and 3 files (case-xxx.struct)
for supercells with displacements. case-xxx.struct is as follows:
---
Title
P   LATTICE,NONEQUIV.ATOMS: 96
MODE OF CALC=RELA
 27.295216 27.295216 27.295216 90.00 90.00 90.00
ATOM  -1: X=0.25073273 Y=0.2500 Z=0.2500
  MULT= 1  ISPLIT= 8
Rb NPT=  781  R0=0.1000 RMT=   2.5   Z: 37.0
LOCAL ROT MATRIX:1.000 0.000 0.000
 0.000 1.000 0.000
 0.000 0.000 1.000
And so on.till
ATOM -96: X=0.5000 Y=0.7500 Z=0.7500
  MULT= 1  ISPLIT= 8
Bi NPT=  781  R0=0.0500 RMT=3.   Z: 83.000
LOCAL ROT MATRIX:1.000 0.000 0.000
 0.000 1.000 0.000
 0.000 0.000 1.000
   0  NUMBER OF SYMMETRY OPERATIONS
--
5. Then I picked one of the case-xxx.struct files and put in another
directory for initialization and started step by step initialization.

Re: [Wien] Space group change during running x sgroup

[Peter Blaha]

            _
   _ __ | |__   ___  _ __   ___   _ __  _   _
  | '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |
  | |_) | | | | (_) | | | | (_) || |_) | |_| |
  | .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |
  |_|                            |_|    |___/
                                        2.7.0

Python version 3.8.4
Spglib version 1.15.1

Calculator interface: wien2k
Crystal structure was read from "RbZnBi.struct".
Unit of length: au
Displacements creation mode
Settings:
   Supercell: [2 2 2]
Spacegroup: F-43m (216)
Use -v option to watch primitive cell, unit cell, and supercell structures.

Number of non-equivalent atoms in RbZnBi.structS-001.in 
: 40
Number of non-equivalent atoms in RbZnBi.structS-002.in 
: 38
Number of non-equivalent atoms in RbZnBi.structS-003.in 
: 40

"phonopy_disp.yaml" and supercells have been created.

Summary of calculation was written in "phonopy_disp.yaml".
                  _
    ___ _ __   __| |
   / _ \ '_ \ / _` |
  |  __/ | | | (_| |
   \___|_| |_|\__,_|


4. It is clear from the output that the space group is not changed. It 
generates one file for a perfect supercell and 3 files (case-xxx.struct) 
for supercells with displacements. case-xxx.struct is as follows:



NO !!! It is NOT clear. It only tells you that the starting symmetry was 
216, but the different displaced structures (S-001 ... S-003) have a 
different number of non-equivalent atoms. And it tells you, that S-001 
should have 40 non-equivalent atoms, which is what sgroup gave you.


In fact, it is clear that when you have a high-symmetry structure and 
you displace an atom in a supercell, it MUST reduce symmetry and change 
the space group.


Accept the changes by nn about equivalent atoms. Usually you can then 
neglect the suggestions of sgroup (provided the number of non-equivalent 
atoms did not change and symmetry finds exactly the same number of 
symmetry operations as sgroup), because you do not want to change the 
basis vectors of the cell.





--

  P.Blaha
--
Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
Email: bl...@theochem.tuwien.ac.atWIEN2k: http://www.wien2k.at
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