Re: [Wien] lapw0 stuck/drained with seemingly no error message upon launching SCF

[Gavin Abo]

Just to check, do you already have your WIEN2k 23.2 lapw0 built with 
gfortran patched with the fix at:


https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg23272.html

The gfortran compiler on Linux needed the patch, but the Intel ifort 
seemed to work fine without the patch.  However, I don't know about 
gfortran on MAC as I don't have a system with the macOS.


It's unfortunate that only the disk image (.dmg) for the older Lion 10.7 
to Sierra 10.12 are web browser downloadable from [1]. Since, running of 
your particular MacOS might have been possible in a virtual machine on 
Windows or Linux with a disk image.  The MacOS version you are probably 
using is likely among the newer versions that look to be only 
downloadable from the App Store using a compatible Mac.  Meaning access 
to a .dmg is not available to us non-MAC users for trying to help 
troubleshot the issue.


[1] https://support.apple.com/en-us/102662

Kind Regards,
Gavin
WIEN2k user

On 6/23/2024 10:24 PM, Yichen Zhang wrote:

Dear Laurence and Peter,

1) No, I did not run with omp. The above discussions in threads are all in 
sequential mode (no -p). However, indeed I have tested dstart and lapw0 in 
parallel mode, where lapw0 hangs similarly like in serial mode and dstart 
parallel mode runs fine. Just in case, I attach below one version of my 
.machines file when I ran dstart in sequential but lapw0 in parallel mode with 
2 processors:
***
#dstart:localhost localhost
speed:localhost localhost
lapw0:localhost localhost

1:localhost
1:localhost
granularity:1
extrafine:1

omp_global:16
***
And of course, I never made it to lapw1, due to the lapw0 hanging issue.

2) Through inserting a bunch of PRINT *, “BREAKPOINT1,2,3,…”, the exact line of 
the where the programme hangs has been determined. In the output of “time lapw0 
lapw0.def”, it hangs exactly at CALL XCPOT1(luse2,LM,…). The context in lapw0.F 
is:
***
if (.not.xcpot1qq) then
   PRINT *, “BREAKPOINT13”
   CALL XCPOT1(luse2,LM,…)
   PRINT *, “BREAKPOINT14”
***
BREAKPOINT13 is the last printed out. 14 is not printed. Importantly, no any 
BREAKPOINT within the subroutine XCPOT1 is printed. The first “BREAKPOINT” in 
XCPOT1 is at the earliest legit position after all the USE, IMPLICIT NONE, and 
parameters declaration. It doesn’t get printed. That seems to tell XCPOT1 is 
called but never runs, so the code hangs after “BREAKPOINT13” and never prints 
out the BREAKPOINTs in XCPOT1 or BREAKPOINT14.
I don’t understand why, considering XCPOT1 subroutine seems legit and compiled 
fine...

3) My last resort was to ask ChatGPT why subroutines can hang, it suggested 7 
possibilities from programming level to system level. And I provide some of my 
guess and questions on these possibilities.
  a) Infinite loops. I have checked all DO loops in XCPOT1.f, but all loops are 
closed. If there is any, compiler should have found that. So NO.
  b) Large memory allocation. There is no large array allocation in XCPOT1, 
despite three dynamic allocations. So NOT likely.
  c) Recursion without proper termination. NO. XCPOT1 is not a recursive 
subroutine.
  d) Blocking I/O operations. NO. It was not waiting for user input or reading 
from a slow device.
  e) Incorrect use of pointers. NO. I didn’t find pointers in XCPOT1.
  f) Stack overflow. No. Again, I didn’t see any recursion or large arrays. The 
three dynamic allocatables seem small.
  g) Deadlocks. This is the part I don’t quite understand if it could happen, 
but my guess is no. Even though I run lapw0 in sequential mode, could circular 
dependency between tasks still happen when the programme runs on an Apple 
silicon Mac system?

This is where the problem is stuck at the moment, unfortunately.


Best regards
Yichen

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Re: [Wien] MPI Parallelisation confusion.

[Gavin Abo]

To not use OpenMP, set omp_global:1.  That is according to:

https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18967.html

Regarding which of the .machines files, you may want to check the 
mailing list archive to learn about the .machines file syntax difference 
between k-point parallel and mpi parallel.


Mailing list archive posts about k-point parallel

https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg01129.html
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg22747.html

Mailing list archive posts about mpi parallel

https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg05464.html
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg10367.html
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg09599.html

Kind Regards,

Gavin
WIEN2k user

On 6/19/2024 6:45 AM, Pranjal Nandi wrote:


Dear Members,

Version 23.2

I want to do a calculation with only 1 k point (isolated system) using 
MPI parallelisation (Not OPENMPI)


This is my first time doing an MPI parallelisation. Hence, I am highly 
confused after going through the guidebook and the ppts.


Lscpu gives me the information.

CPU(s): 128

On-line CPU(s) list: 0-127

Thread(s) per core: 2

Core(s) per socket: 64

Socket(s): 1

NUMA node(s): 4

echo $OMP_NUM_THREADS gives me as 2.

Which format of the machines files is correct so that I can allow the 
calculations to use maximum number of nodes ? I am highly confused


 1. granularity:1

64:localhost  #(later I will change from 64 to 32, 16, 8 , 4 and 2 to 
check the efficiency)

omp_global:2

 2. granularity:1

1:localhost:1  1:localhost:1  1:localhost:1  1:localhost:1 
 1:localhost:1  1:localhost:1  …….. 64 times (later I will change from 
64 to 32, 16, 8 , 4 and 2 to check the efficieny)

omp_global:2

 3. set OMP_NUM_Threads to 128
granularity:1

128:localhost  #(later I will change from 64 to 32, 16, 8 , 4 
and 2 to check the efficiency)

    omp_global:2

Your guidance will be very helpful.

Thank you.

With warm regards,

Pranjal



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Re: [Wien] Charge leakage too large

[Gavin Abo]

Does attached struct file give same NEC error for you?  It has some 
differences.  For example, it doesn't have the special labels such as 
"Zn1" like in your struct.


ZnO structure parameters were used from

https://next-gen.materialsproject.org/materials/mp-2133#summary

They were put in StructGen, after clicking "set automatically RM and 
continue editing" the Reduce RMTs by 0% using new scheme was used for 
creating the ZnO.struct file.


Below is what happened on my system:

username@computername:~/wiendata/ZnO$ lsb_release -a
No LSB modules are available.
Distributor ID:    Ubuntu
Description:    Ubuntu 24.04 LTS
Release:    24.04
Codename:    noble
username@computername:~/wiendata/ZnO$ cat $WIENROOT/WIEN2k_VERSION
WIEN2k_23.2 (Release 9/3/2022)
username@computername:~/wiendata/ZnO$ ls -l
total 4
-rw-rw-r-- 1 username username 954 Jun 13 22:44 ZnO.struct
username@computername:~/wiendata/ZnO$ init_lapw -b
 next is setrmt
 next is nn
 specify nn-bondlength factor: (usually=2) [and optionally dlimit, 
dstmax (about 1.d-5, 20)]

 dfac,DSTMAX:   2.    20.000
 iix,iiy,iiz   4   4   3 
24.4908601    24.4908601 29.5931221


    ATOM  1  Zn ATOM  2  O
 RMT(  1)=1.99000 AND RMT(  2)=1.72000
 SUMS TO 3.71000  LT.  NN-DIST= 3.73063

    ATOM  2  O  ATOM  1  Zn
 RMT(  2)=1.72000 AND RMT(  1)=1.99000
 SUMS TO 3.71000  LT.  NN-DIST= 3.73063
STOP NN ENDS
0.003u 0.000s 0:00.00 0.0%    0+0k 0+56io 0pf+0w
 next is sgroup
>   sgroup     (22:46:00) 0.000u 0.000s 0:00.00 0.0%    0+0k 0+8io 0pf+0w
  Names of point group: 3m1    3m1    C3v
  Names of point group: 3m1    3m1    C3v
Number and name of space group: 186 (P 63 m c)
 next is symmetry
>   symmetry     (22:46:00)  SPACE GROUP DOES NOT CONTAIN INVERSION
0.000u 0.000s 0:00.00 0.0%    0+0k 192+40io 1pf+0w
 next is lstart
 2 Atoms found:  with labels Zn   O
generate atomic configuration for atom 1 : Zn
generate atomic configuration for atom 2 : O
  SELECT XCPOT:
  recommended: PBE    [(13) GGA of Perdew-Burke-Ernzerhof 96]
   LDA    [( 5)]
   WC [(11)  GGA of Wu-Cohen 2006]
   PBESOL [(19) GGA of Perdew etal. 2008]
  SELECT ENERGY to separate core and valence states:
  recommended: -6.0 Ry (check how much core charge leaks out of MT-sphere)
  ALTERNATIVELY: specify charge localization (between 0.97 and 1.0) to 
select core state

STOP LSTART ENDS
 file .lcore created, scf-cycle with core-density superposition !
1.7200 8
 set RKmax = 6.2533
 set LVNS = 6
 set GMAX = 16.0
 set IFFTfac = 2.0
>   inputfiles prepared    (22:46:00)
 inputfiles prepared
 inversion is NOT present
>   inputfiles for lapw1c/2c prepared, no inversion present (22:46:00)
 next is kgen
STOP KGEN ENDS
NUMK: 1000
basic k-mesh: 12, 12, 7 = 1008,  kfactor = 1
  12  symmetry operations without inversion
 inversion added (non-spinpolarized non-so calculation)
  NUMBER OF K-POINTS IN WHOLE CELL: (0 for 3 divisions of K, -1 for 
delta-K)

 length of reciprocal lattice vectors (bohr^-1):   1.185   1.185 0.637
  76  k-points generated, ndiv=  12 12   6
 delta-K (bohr^-1): 0.0987    0.0987    0.1062
STOP KGEN ENDS
 next is dstart
>   dstart  -c -p  > & .mist    (22:46:00) running dstart in single mode
STOP DSTART ENDS
0.528u 0.007s 0:00.54 96.2%    0+0k 4096+1288io 13pf+0w

-> new ZnO.in0 generated
  init_lapw finished ok
username@computername:~/wiendata/ZnO$ run_lapw
STOP  LAPW0 END
STOP  LAPW1 END
STOP  LAPW2 END
STOP  CORE  END
STOP DSTART ENDS
STOP  MIXER END
ec cc fc and str_conv 0 1 1 1
in cycle 2    ETEST: 0   CTEST: 0   STRTEST: 0
STOP  LAPW0 END
STOP  LAPW1 END
STOP  LAPW2 END
STOP  CORE  END
STOP DSTART ENDS
STOP  MIXER END
ec cc fc and str_conv 0 1 1 1
...
in cycle 7    ETEST: .002435275000   CTEST: .0096356 STRTEST: 0
STOP  LAPW0 END
STOP  LAPW1 END
STOP  LAPW2 END
STOP  CORE  END
STOP DSTART ENDS
STOP  MIXER END
ec cc fc and str_conv 0 1 1 1
in cycle 8    ETEST: .00069865   CTEST: .0065417 STRTEST: 0
STOP  LAPW0 END
STOP  LAPW1 END
STOP  LAPW2 END
STOP  CORE  END
STOP DSTART ENDS
STOP  MIXER END
ec cc fc and str_conv 1 1 1 1

>   stop

On 6/13/2024 10:32 PM, Chithra M Mathew wrote:

@Fecher, Gerhard

On Tue, 11 Jun 2024 at 20:13, Fecher, Gerhard  wrote:

you have never shown your case.struct file !!!

your NEC01: is realy strange

I was recently running ZnO with wurtzide structure and had no problems.

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 Physics
Johannes Gutenberg - University
55099 Mainz

Von: Wien [wien-boun...@zeus.theochem.tuwien.ac.at] im Auftrag von Chithra M 
Mathew [chithr...@nirmalagiricollege.ac.in]
Gesendet: Dienstag, 11. 

Re: [Wien] ERROR Iin using LDA

[Gavin Abo]

I think I found the cause of the runtime gfortran compiled lapw0 error 
given in the previous post below.


In SRC_lapw0/lapw0.F of WIEN2k 23.2 on line 2645, there is:

IF(GGA_SWITCH .eqv. .TRUE.) allocate( CFFT_STR_GGA(iff1,iff2,iff3,1:9) )

Also, on line 2651, there is:

IF(GGA_SWITCH .eqv. .TRUE.) allocate( CFFT_STR_GGA(1,1,1,1:9) )

One of the above two allocates CFFT_STR_GGA which should explain why 
there is no issue when its a GGA calculation.


However, where the error seems to be happening with LDA is on line 2655 
having:


CFFT_STR_GGA = ZEROC

The cause seems to be CFFT_STR_GGA being used without being allocated in 
the LDA case (or more broadly when its not a GGA case).  The  error goes 
away if the line 2655 is changed to:


IF(GGA_SWITCH .eqv. .TRUE.) CFFT_STR_GGA = ZEROC

Could another person confirm that as a solution or see a better fix for it?

Thanks,

Gavin
WIEN2k user

On 5/25/2024 8:16 AM, 夏宇阳 wrote:

Dear all,
I cannot use the Vxc option LDA to calculate any struct(i have tried different 
materials). Everything is fine when doing init, but there is an error in scf.

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0  0x7c1f5223960 in ???
#1  0x7c1f5222ac5 in ???
#2  0x7c1f4e4251f in ???
at ./signal/../sysdeps/unix/sysv/linux/x86_64/libc_sigaction.c:0
#3  0x7c1f4fa1082 in ???
at ../sysdeps/x86_64/multiarch/memset-vec-unaligned-erms.S:394
#4  0x58fced8efc47 in ???
#5  0x58fced88680e in ???
#6  0x7c1f4e29d8f in __libc_start_call_main
at ../sysdeps/nptl/libc_start_call_main.h:58
#7  0x7c1f4e29e3f in __libc_start_main_impl
at ../csu/libc-start.c:392
#8  0x58fced886834 in ???
#9  0x in ???
Segmentation fault (core dumped)
grep: No match.
grep: No match.
grep: No match.
grep: No match.
grep: No match.
grep: No match.
grep: No match.
grep: No match.
grep: No match.
grep: No match.
grep: No match.

My system is Ubuntu 22.04. And the complier is gfortran. i followed the step on 
the pdf files provided by Gavin Abo to install wien2k.

And Other options have no problem.

Is there anyone have the same problem? How can i solve it?

Looking forward to your reply.

Best wishes!

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Re: [Wien] unit of eval in case.in2

[Gavin Abo]

To find the answer to your question, it might help to look at the WIEN2k 
23.2 source code.


In SRC_lapw2/fermi.F, lines 108 and 109 should have:

 IF(myid.EQ.0) write(21,'(//,27h   TEMP.-SMEARING WITH 
,f10.5,4h Ry )')  &

  etemp

In x_lapw, line 979 should have:

21,'$file.scf2$sc$hf$updn','unknown','formatted',0

From the above, it looks like the file unit 21 would be a calculation 
case file having the file extension .scf2*, where * could be hf for 
.scf2hf for example depending on the type of calculation being ran.


I would suggest setting eval as 0.0018 in case.in2, then check the 
case.scf2* file(s) after lapw2 finishes running to see if it prints


TEMP.-SMEARING WITH 0.0018 Ry

Then, do it again but with 0 in case.in2, then check the case.scf2* 
file(s) to see if it prints


TEMP.-SMEARING WITH 0 Ry

or if it instead prints

TEMP.-SMEARING WITH 0.0018 Ry

The WIEN2k 23.1 (or 23.2) userguide [1] on page 160 has

eval when efmod is set to TEMP(S) (eval=0 will lead to room 
temperature broadening, 0.0018 Ry ...


If I interpreted the userguide correctly, by setting eval to 0, the 
program uses that as a shorter way to set 0.0018 for room temperature 
broadening in units of Rydberg (Ry) such that in the case.scf2* file you 
will likely find


TEMP.-SMEARING WITH 0.0018 Ry

In summary, if you inspect the case.scf2* output file, it looks like you 
could determine what the program is correctly using compared to the eval 
value you set.


[1] http://wien2k.at/reg_user/textbooks/usersguide.pdf

Hopefully that helps and kind regards,

Gavin
WIEN2k user

On 5/9/2024 8:20 AM, shamik chakrabarti wrote:
Is it that we have to use either 0 or 0.0018 for room temperature 
broadening?


On Thu, 9 May 2024, 17:40 shamik chakrabarti, 
 wrote:


sorry the query should be eval to 0.00 or 0.0018?

On Thu, 9 May 2024 at 17:39, shamik chakrabarti
 wrote:

Dear Wien2k users,

    I have a query. What is the unit of eval in
case.in2. I want to change TETRA to TEMP in case.in2. Should I
change the eval to 0.018 or kept it to 0 ?

Looking forward to your response in this regard.

with regards,

-- 
Dr. Shamik Chakrabarti

Research Fellow
Department of Physics
Indian Institute of Technology Patna
Bihta-801103
Patna
Bihar, India



-- 
Dr. Shamik Chakrabarti

Research Fellow
Department of Physics
Indian Institute of Technology Patna
Bihta-801103
Patna
Bihar, India
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Re: [Wien] error in x wplot -wf

[Gavin Abo]

What WIEN2k version?  If you're using a version older than WIEN2k 23.2, 
MAT_TOL could be set as 1e-10_DPk.  It may need relaxed to 1e-8_DPk or 
1e-6_DPk.  Refer to [1].


[1] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19093.html


On 4/28/2024 9:14 PM, 夏宇阳 wrote:

Dear all,

When i use 'x wplot -wf 1' in wien2wannier, an error came out:

Local rotation matrix not orthogonal

i use the template, case.inwplot. what should i edit it?

Looking for your reply.

With regards!

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Re: [Wien] Query regarding wien2k_scratch directory

[Gavin Abo]

 have also checked /var. there are log files as
mentioned in your reference [1]. In this regard, which files
should I remove to recover the lost spaces?

with regards,

On Sat, 27 Apr 2024 at 17:42, Gavin Abo 
wrote:

If your WIEN2k cases are located somewhere under the
/home directory, is this the directory you are seeing the
space increase in?

If your looking at the space of the entire storage drive
before and after the calculation, another possibility is
the increase could be due to normal usage logging by the
operating system.  So, if its the /var you are seeing
increase after the calculation, it could potentially be
due to that as log files could be stored there as seen
for example at [1].

[1]

https://ubuntu.com/tutorials/viewing-and-monitoring-log-files#2-log-files-locations

Kind Regards,

Gavin
WIEN2k user

On 4/26/2024 10:52 PM, shamik chakrabarti wrote:

In that case, after deleting the case directory, the
space in hd of Linux should be recovered. But the space
is decreasing every time, I ran some calculations and
after copying delete the whole directory.

On Sat, 27 Apr 2024, 01:48 Tomas Kana, 
wrote:

The dot and slash ./ means your current directory


Dear Sir,

  After echo $SCRATCH the output is:   ./


Any comments



On Fri, 26 Apr 2024 at 22:14, Peter Blaha
 wrote:







    During   userconfig  you have specified a
SCRATCH directory. Only
      you can know what you did there.

    PS:   echo $SCRATCH   will tell you, what you
specified.





    Am 26.04.2024 um 13:30 schrieb shamik
      chakrabarti:






        Dear Wien2k users,





         After running
calculations I am saving
          the data in external hdd while deleting
the same from linux.
          However, at each time, after deleting
data, I have found that
          some amount of spaces are not recovered.
Wien2k is saving some
          files in Linux which I am not able to delete.

        My query is where are those extra files are
stored? Whether
          there is some directory called as _scratch
but then I am not
          able to find it either?





        Any response is eagerly awaited.





        with regards,
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Re: [Wien] Rhombhohedral coordinates needed in simulation of LiNiO2

[Gavin Abo]

Sorry, missed a word, that should read "not an error message"

On 4/28/2024 9:47 AM, Gavin Abo wrote:


As far as I know, w2web is not able to automatically detect yet if you 
have entered the atomic positions correctly for space group 166.  So, 
the "positions must be specified in rhombohedral coordinates!" is NOT 
an error message but a reminder text that will always be there whether 
you enter position correctly or incorrectly.  Thus, you have to 
carefully check for yourself that you have entered the position correctly.


As you might recall from the post at [1], WIEN2k is a bit unusual in 
that for the struct file it needs hexagonal lattice constants but 
rhombohedral for the atomic positions for an R lattice space group 
such as 166 R-3m.


For LiNIO2, you should double check, but I believe the both lattice 
constants and atomic positions in the hexagonal setting are:


Initial Setting: R-3m:h (No. 166)

166
5.404616 5.404616 26.569550 90 90 120 <= This is the hexagonal lattice 
parameters needed for the struct file of WIEN2k

3
Li    1    3a    0.00    0.00    0.00 <= These are the 
hexagonal atomic positions, which would be incorrect to use for WIEN2k

Ni    1    3b    0.00    0.00    0.50
O    1    6c    0.00    0.00    0.240984

Using SETSTRU [2], its equivalent in the rhombohedral setting should be:


Final Setting: R-3m:r (No. 166)

166 #R-3m:r
9.3901 9.3901 9.3901 33.45 33.45 33.45 <= These are the rhombohedral 
lattice parameters, which would be incorrect to use for WIEN2k

3
Li    1    -    0.00    0.00    0.00 <= These are the 
rhomboderal atomic positions needed for the struct file of WIEN2k

Ni    1    -    0.50    0.50    0.50
O    1    -    0.240984    0.240984    0.240984


In your LiNiO2_opt.struct, I see:

a = 5.404616 bohr in hexagonal setting

b = 5.404616 bohr in hexagonal setting

c = 26.569550 bohr in hexagonal setting

alpha = 90.00 deg in hexagonal setting

beta = 90.00 deg in hexagonal setting

beta = 120.00 deg in hexagonal setting

Li x=0. y=0. z=0. in rhombohedral setting

Ni z=0.5000 y=0.5000 z=0.5000 in rhombohedral setting

O x=0.24098400 y=0.24098400 z=0.24098400 in rhombohedral setting

[1] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg05554.html


[2] https://www.cryst.ehu.es/cryst/setstru.html


On 4/28/2024 8:00 AM, shamik chakrabarti wrote:

Dear Wien2k users,

   I want to simulate properties of LiNiO2. However, adopting 
the structure (file attached) by bringing it into rhombohedral axis 
in Vesta, when I copy the cif file into the working directory & 
converting it into a struct file, after save structure, it complains 
about


" positions must be specified in rhombohedral coordinates!"

Please guide.

with regards,

--
Dr. Shamik Chakrabarti
Research Fellow
Department of Physics
Indian Institute of Technology Patna
Bihta-801103
Patna
Bihar, India___
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Re: [Wien] Rhombhohedral coordinates needed in simulation of LiNiO2

[Gavin Abo]

As far as I know, w2web is not able to automatically detect yet if you 
have entered the atomic positions correctly for space group 166.  So, 
the "positions must be specified in rhombohedral coordinates!" is an 
error message but a reminder text that will always be there whether you 
enter position correctly or incorrectly.  Thus, you have to carefully 
check for yourself that you have entered the position correctly.


As you might recall from the post at [1], WIEN2k is a bit unusual in 
that for the struct file it needs hexagonal lattice constants but 
rhombohedral for the atomic positions for an R lattice space group such 
as 166 R-3m.


For LiNIO2, you should double check, but I believe the both lattice 
constants and atomic positions in the hexagonal setting are:


Initial Setting: R-3m:h (No. 166)

166
5.404616 5.404616 26.569550 90 90 120 <= This is the hexagonal lattice 
parameters needed for the struct file of WIEN2k

3
Li    1    3a    0.00    0.00    0.00 <= These are the 
hexagonal atomic positions, which would be incorrect to use for WIEN2k

Ni    1    3b    0.00    0.00    0.50
O    1    6c    0.00    0.00    0.240984

Using SETSTRU [2], its equivalent in the rhombohedral setting should be:


Final Setting: R-3m:r (No. 166)

166 #R-3m:r
9.3901 9.3901 9.3901 33.45 33.45 33.45 <= These are the rhombohedral 
lattice parameters, which would be incorrect to use for WIEN2k

3
Li    1    -    0.00    0.00    0.00 <= These are the 
rhomboderal atomic positions needed for the struct file of WIEN2k

Ni    1    -    0.50    0.50    0.50
O    1    -    0.240984    0.240984    0.240984


In your LiNiO2_opt.struct, I see:

a = 5.404616 bohr in hexagonal setting

b = 5.404616 bohr in hexagonal setting

c = 26.569550 bohr in hexagonal setting

alpha = 90.00 deg in hexagonal setting

beta = 90.00 deg in hexagonal setting

beta = 120.00 deg in hexagonal setting

Li x=0. y=0. z=0. in rhombohedral setting

Ni z=0.5000 y=0.5000 z=0.5000 in rhombohedral setting

O x=0.24098400 y=0.24098400 z=0.24098400 in rhombohedral setting

[1] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg05554.html


[2] https://www.cryst.ehu.es/cryst/setstru.html


On 4/28/2024 8:00 AM, shamik chakrabarti wrote:

Dear Wien2k users,

   I want to simulate properties of LiNiO2. However, adopting 
the structure (file attached) by bringing it into rhombohedral axis in 
Vesta, when I copy the cif file into the working directory & 
converting it into a struct file, after save structure, it complains 
about


" positions must be specified in rhombohedral coordinates!"

Please guide.

with regards,

--
Dr. Shamik Chakrabarti
Research Fellow
Department of Physics
Indian Institute of Technology Patna
Bihta-801103
Patna
Bihar, India___
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Re: [Wien] Query regarding wien2k_scratch directory

[Gavin Abo]

If your WIEN2k cases are located somewhere under the /home directory, is 
this the directory you are seeing the space increase in?


If your looking at the space of the entire storage drive before and 
after the calculation, another possibility is the increase could be due 
to normal usage logging by the operating system.  So, if its the /var 
you are seeing increase after the calculation, it could potentially be 
due to that as log files could be stored there as seen for example at [1].


[1] 
https://ubuntu.com/tutorials/viewing-and-monitoring-log-files#2-log-files-locations


Kind Regards,

Gavin
WIEN2k user

On 4/26/2024 10:52 PM, shamik chakrabarti wrote:
In that case, after deleting the case directory, the space in hd of 
Linux should be recovered. But the space is decreasing every time, I 
ran some calculations and after copying delete the whole directory.


On Sat, 27 Apr 2024, 01:48 Tomas Kana,  wrote:

The dot and slash ./ means your current directory


Dear Sir,

  After echo $SCRATCH the output is:   ./


Any comments



On Fri, 26 Apr 2024 at 22:14, Peter Blaha
 wrote:







    During   userconfig  you have specified a SCRATCH directory. Only
      you can know what you did there.

    PS:   echo $SCRATCH   will tell you, what you specified.





    Am 26.04.2024 um 13:30 schrieb shamik
      chakrabarti:






        Dear Wien2k users,





         After running calculations I am saving
          the data in external hdd while deleting the same from linux.
          However, at each time, after deleting data, I have found
that
          some amount of spaces are not recovered. Wien2k is
saving some
          files in Linux which I am not able to delete.

        My query is where are those extra files are stored? Whether
          there is some directory called as _scratch but then I am not
          able to find it either?





        Any response is eagerly awaited.





        with regards,





        --








                      Dr. Shamik
                        Chakrabarti

                      Research Fellow

                      Department of Physics

                      Indian Institute of
                        Technology Patna

                      Bihta-801103

                      Patna

                      Bihar, India





















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    --
---
Peter Blaha,  Inst. f. Materials Chemistry, TU Vienna, A-1060 Vienna
Phone: +43-158801165300
Email: peter.bl...@tuwien.ac.at
WWW: http://www.imc.tuwien.ac.at     WIEN2k: http://www.wien2k.at
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-- 
Dr. Shamik Chakrabarti

Research Fellow
Department of Physics
Indian Institute of Technology Patna
Bihta-801103
Patna
Bihar, India
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Re: [Wien] w2web xcrysden problem

[Gavin Abo]

What WIEN2k version are you using?

Could you provide what XCRYSDEN_TOPDIR is?

It looks like the Perl code in WIEN2k 23.2 is implemented differently 
between that of "view structure" and that of the "Calculate density with 
XCrysDen" and "View density with XCrysDen" in w2web.


For "view structure", in SRC_w2web/htdocs/util/viewxcrys.pl, it looks 
like XCRYSDEN_TOPDIR runs through some regular expressions [1] before 
getting stored in the XCRYSDENDIR variable before it executes the 
XCrysDen command:


${XCRYSDENDIR}xcrysden --wien_struct $DIR

On the other hand, "Calculate density with XCrysDen" and "View density 
with XCrysDen" in SRC_w2web/htdocs/util/rhoxcrys.pl executes XCrysDen 
commands, respectively, as:


xcrysden --wien_density $DIR

xcrysden --wien_renderdensity $DIR

Since the above two calls work fine on your computer system, you could 
maybe find "${XCRYSDENDIR}xcrysden --wien_struct $DIR" in viewxcrys.pl 
and try removing the ${XCRYSDENDIR} to make the XCrysDen command similar:


xcrysden --wien_struct $DIR"

[1] https://en.wikipedia.org/wiki/Regular_expression

Kind Regards,
Gavin
WIEN2k user

On 4/23/2024 9:35 AM, Straus, Daniel B wrote:


I am having a problem where only some of the xcrysden functionality 
works in w2web.


Executionàview structure does not work. The following message is printed:

*View structure with XCrysDen*

Requires X-Windows system ...

However, if I go to TasksàEl. Dens. and click either the Calculate 
density with XCrysDen or View density with XCrysDen, xcrysden opens 
and works fine.


The XCRYSDEN_TOPDIR environment variable is set correctly.

Any suggestions?

Thank you!

Daniel Straus

Assistant Professor

Department of Chemistry

Tulane University

5088 Percival Stern Hall

6400 Freret Street

New Orleans, LA 70118

(504) 862-3585

http://straus.tulane.edu/ 
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Re: [Wien] Requesting your help in "running qtl in parallel mode"

[Gavin Abo]

The WIEN2k version 21.1 has "x qtl -p" bugs.  I used to have a temporary 
qtlpara_lapw.patch and x_lapw.patch for that.  However, the patches have 
been replaced by the latest WIEN2k (version 23.2) having the permanent 
fixes.


On the WIEN2k updates page [1], you should see the descriptions about 
the qtl parallel calculation bug fixes:


*VERSION_23.2*: 8.3.2023:

qtlpara_lapw: missing label "single" defined

*VERSION_23*: 19.1.2023:

qtlpara_lapw: set so added

x_lapw:

 * x qtl runs automatically "x lapw2 -fermi" first

[1] http://www.wien2k.at/reg_user/updates/

Kind Regards,

Gavin
WIEN2k user

On 3/10/2024 7:11 AM, Pranjal Nandi wrote:


Dear WIEN2K Community,

It would be helpful if someone could please help me with the following 
as I am using up too much time in doing serial calculation as the 
TELNES is not working in parallel mode. In serial mode, everything is 
working fine.


In parallel mode, SCF runs well, Optic package runs well (version 
21.1). But when I run x qtl -p -telnes (from w2web), I get the 
following error


running QTL in parallel mode

calculating QTL's from parallel vectors

so: Undefined variable.

0.035u 0.043s 0:00.09 77.7% 0+0k 0+24io 0pf+0w

error: command /home/WIEN2k/WIEN2k/qtlpara qtl.def   failed

I checked the forum too and found the following suitable threads. 
Looks like everything is fine with my files (maybe something I am 
unable to spot)


http://zeus.theochem.tuwien.ac.at/pipermail/wien/2021-May/031757.html 
(the thread looks incomplete)


https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg21125.html 
(I should check set so in the qtlpara_lapw and also run x lapw2 -fermi 
(-p)? I am asking because I use the w2web and in that there is no x 
lapw2 -fermi (-p) in the TELNES pack, there is one in Optics, which 
once I tried first and then ran TELNES but the same error happened)


https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg20660.html 
(vec2old_lapw -p -local $so -$updn is already mentioned in the 
qtlpara_lapw file in the root folder)


I have attached some of the relevant files. Please let me know if you 
need more information.


It would be helpful if you could kindly guide me on the right track.

Thank you and with regards,

Pranjal Nandi



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Re: [Wien] Error in optimization

[Gavin Abo]

It failed during the nn step from the error message.  Although, there is 
not enough information for specifically determining how to resolve it.


You would need to check for example the data in case.outputnn and 
analyze it for what went wrong.


In general, one potential cause of the error could be overlapping RMT 
spheres.  If the structure change of -10 is too much, one solution might 
be to use a smaller structure change than that.


Another possibility is that if you had used for example a setrmt_lapw 
reduction value of 0 %, then you could follow the advice in section "3.6 
Creating the “master input“ file case.struct" of the WIEN2k 23.1 
usersguide [1] to change that to around the often times good value of 
about 3 % for structure optimization where it states:


/Choose a reduction of 3 % so that we can later optimize the lattice 
parameter./


Also, search the mailing list archive [2] as you might find other advice 
that could help with this error.  For example, see [3].


[1] http://susi.theochem.tuwien.ac.at/reg_user/textbooks/usersguide.pdf
[2] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/maillist.html
[3] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg15309.html


Kind Regards,

Gavin
WIEN2k user

On 3/4/2024 11:00 AM, Neetu Malik wrote:

Dears,

During volume optimization getting below error.

Please help me to resolve this issue.

ERROR status in Sr2CoWO6_coa__-10.00
>   stop error

grep: lapw2*.error: No such file or directory
grep: lapw2*.error: No such file or directory
grep: lapw2*.error: No such file or directory
grep: lapw2*.error: No such file or directory
grep: lapw2*.error: No such file or directory
grep: lapw2*.error: No such file or directory
NN - Error
  LAPW0 END
clmextrapol_lapw has generated a new Sr2CoWO6.clmsum
0.043u 0.000s 0:00.04 100.0%0+0k 0+2960io 0pf+0w
1.105u 0.007s 0:00.32 343.7%0+0k 0+2976io 0pf+0w
DSTART ENDS
  C  T F
running dstart in single mode
1.100u 0.022s 0:00.34 329.4%0+0k 0+2984io 0pf+0w
DSTART ENDS
  C  T F
running dstart in single mode

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Re: [Wien] BoltzTrap-electronic thermal conductivity

[Gavin Abo]

Your understanding is correct.  The BoltzTraP code solves an 
approximation of the electronic Boltzmann transport equation that 
outputs electronic thermal conductivity per relaxation time (ke/τ).


On the other hand, the phonon Boltzmann transport equation for example 
has to be solved to get the lattice thermal conductivity (kl). almaBTE 
is a code for VASP [1] and phono3py is a code for Quantum Espresso (QE) 
[2]. Unfortunately, I have yet to find one that supports WIEN2k.


If you're referring to the unsupported user contributed 
add_boltz2_to_w2web that hasn't been maintained to work with the latest 
bug fixed [3] WIEN2k version, then that add_boltz2_to_w2web package did 
output an incorrect ZT value assuming kl =0 in its calculation.


For example, the LaFe3CoSb12 experimental zT value at 300 K is 0.14 in 
Table I of the paper titled "Seebeck Coefficient and the Thermoelectric 
Figure of Merit in Semiconductors and Conducting Polymers" by B. F. 
Howell et al at [4].


If kl is ignored, ZT is computed as 0.54 which is far from the 
experimental value of 0.14.


ZT ≈ σS^2T/ke = {6.3860e+04 1/(ohm*m)}*{1.0090e-04 V/K}^2*{300 K}/{0.36 
W/(K*m)} = 0.54


On the other hand, when kl is included, the computed value of 0.12 is 
close to the experimental value of 0.14.


ZT ≈ σS^2T/(ke + kl) = {6.3860e+04 1/(ohm*m)}*{1.0090e-04 V/K}^2*{300 
K}/{0.36 W/(K*m) + 1.26 W/(K*m) } = 0.12


[1] https://almabte.bitbucket.io/
[2] https://phonopy.github.io/phono3py/
[3] http://www.wien2k.at/reg_user/updates/
[4] Accession Number ADA327846 at: https://ntrl.ntis.gov/NTRL/

Kind Regards,

Gavin
WIEN2k user

On 2/15/2024 2:14 AM, Bara abujafar via Wien wrote:
I would like to inquire about the BoltzTraP code implemented in the 
WIEN2k package. I am uncertain whether it neglects lattice thermal 
conductivity, as there are conflicting claims suggesting that 
BoltzTrap may only focus on electronic thermal conductivity. Your 
feedback on this matter would be greatly appreciated.

With best regards
Mohammed Abu-Jafar___
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Re: [Wien] Error-Missing Header

[Gavin Abo]

In the past, we saw that error happen when the SRC_w2web directory got 
corrupted (or maybe it could be caused by a file permission issue).  
Installing a fresh copy of fresh copy of SRC_w2web solved the issue for 
a user previously. [1]


[1] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg11735.html


On 2/8/2024 6:07 AM, evren görkem özdemir wrote:

Dear Wien2k users,
When I want to connect to localhost, I encounter the following 
problem. "*Error-Missing Header*
Modification of a read-only value attempted at ../../libs/w2web.pl 
 line 110."
Is it possible to solve this problem without destroying my ongoing 
calculations?


Thank you.
Best regards.

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Re: [Wien] lapw1.def failed

[Gavin Abo]

A possible cause of the "Killed" message is the operating system 
terminating the program.  For example, the user or queue system might 
have initiated a kill to the operating system for the job while it was 
still in the process of running.  The operating system might also 
automatically kill the running process if all memory (or queue system 
memory limit [1]) on the system has been exhausted.


You might want to check the system log.  Refer to [2].

[1] https://doc.hpc.iter.es/2023.08/en/slurm/slurm_memory_limits/
[2] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19703.html


Kind Regards,

Gavin
WIEN2k user

On 12/17/2023 6:11 AM, shamik chakrabarti wrote:

Dear Madam & Sir,
                         The error appeared at the first cycle itself 
with the following error;

STOP  LAPW0 END
Killed
grep: lapw2*.error: No such file or directory

>   stop error

What could be the remedy?

Looking forward to your reply.

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Re: [Wien] WIENncm installation error

[Gavin Abo]

Thanks for reporting that the error was caused by the 2013 version of 
the Intel compiler.


In the article titled "WIEN2k: An APW+lo program for calculating the 
properties of solids" by P. Blaha et al. [1], there is the sentence:


/The setup and execution of WIENNCM is as in WIEN2k; however .../

With the execution being the same, I would expect that the Band 
Structure would use "x spaghetti" and that the DOS would still use "x 
tetra".


[1] https://doi.org/10.1063/1.5143061

Kind Regards,

Gavin
WIEN2k user

On 12/14/2023 12:17 PM, Safikul Islam wrote:

Dear Sir,

                The problem has been sorted out. The error is due to 
the 2013 Intel compiler. I am now trying to calculate band structure 
and dos using WIENncm. But I am not finding any source. In the paper 
titled " Ab initio electronic structure of metallized NiS2 in the 
noncollinear magnetic phase"  the band structure has been calculated 
using WIENncm.  I am not finding any commands for the band structure 
calculation in the WIENncm manual.



                  Sir, how should I solve this problem? Looking for 
our suggestions eagerly.


Kind Regards,
Safikul Islam







On Thu, Dec 14, 2023 at 5:02 PM Safikul Islam 
 wrote:


Dear Sir,

               I am writing to you regarding the calculations of
WIENncm examples. I am trying to do a test run of the given
examples (febcc,uo2_2k,uo2_3k,Mn3Sn). For example febcc it is
working fine but for other examples I am getting errors while
running WIENncm. The error is as follows.

Error:
runncm with  /home/safikul_akd/WIENNCM/WIENNCM
in cycle 1    ETEST: 0   CTEST: 0
 LAPW0 END
*** glibc detected *** /home/safikul_akd/WIENNCM/WIENNCM/lapw1c:
free(): invalid pointer: 0x02ad6d90 ***
=== Backtrace: =
/lib64/libc.so.6[0x3ae0675e5e]
/lib64/libc.so.6[0x3ae0678cad]
/home/safikul_akd/WIENNCM/WIENNCM/lapw1c[0x488e5c]
/home/safikul_akd/WIENNCM/WIENNCM/lapw1c[0x435b4b]
/home/safikul_akd/WIENNCM/WIENNCM/lapw1c[0x441788]
/home/safikul_akd/WIENNCM/WIENNCM/lapw1c[0x43036a]
/home/safikul_akd/WIENNCM/WIENNCM/lapw1c[0x403906]
/lib64/libc.so.6(__libc_start_main+0x100)[0x3ae061ed20]
/home/safikul_akd/WIENNCM/WIENNCM/lapw1c[0x4037d9]
=== Memory map: 
0040-00552000 r-xp  08:11 194416842
/home/safikul_akd/WIENNCM/WIENNCM/lapw1c
00752000-0075d000 rw-p 00152000 08:11 194416842
/home/safikul_akd/WIENNCM/WIENNCM/lapw1c
0075d000-00893000 rw-p  00:00 0
0277c000-03334000 rw-p  00:00 0                   [heap]
3ae020-3ae022 r-xp  08:02 6029314                
  /lib64/ld-2.12.so 
3ae042-3ae0421000 r--p 0002 08:02 6029314                
  /lib64/ld-2.12.so 
3ae0421000-3ae0422000 rw-p 00021000 08:02 6029314                
  /lib64/ld-2.12.so 
3ae0422000-3ae0423000 rw-p  00:00 0
3ae060-3ae078b000 r-xp  08:02 6045824                
  /lib64/libc-2.12.so 
3ae078b000-3ae098a000 ---p 0018b000 08:02 6045824                
  /lib64/libc-2.12.so 
3ae098a000-3ae098e000 r--p 0018a000 08:02 6045824                
  /lib64/libc-2.12.so 
3ae098e000-3ae099 rw-p 0018e000 08:02 6045824                
  /lib64/libc-2.12.so 
3ae099-3ae0994000 rw-p  00:00 0
3ae0a0-3ae0a02000 r-xp  08:02 6029381                
  /lib64/libdl-2.12.so 
3ae0a02000-3ae0c02000 ---p 2000 08:02 6029381                
  /lib64/libdl-2.12.so 
3ae0c02000-3ae0c03000 r--p 2000 08:02 6029381                
  /lib64/libdl-2.12.so 
3ae0c03000-3ae0c04000 rw-p 3000 08:02 6029381                
  /lib64/libdl-2.12.so 
3ae120-3ae1283000 r-xp  08:02 6045825                
  /lib64/libm-2.12.so 
3ae1283000-3ae1482000 ---p 00083000 08:02 6045825                
  /lib64/libm-2.12.so 
3ae1482000-3ae1483000 r--p 00082000 08:02 6045825                
  /lib64/libm-2.12.so 
3ae1483000-3ae1484000 rw-p 00083000 08:02 6045825                
  /lib64/libm-2.12.so 
3ae620-3ae6216000 r-xp  08:02 6045828                
  /lib64/libgcc_s-4.4.7-20120601.so.1
3ae6216000-3ae6415000 ---p 00016000 08:02 6045828                
  /lib64/libgcc_s-4.4.7-20120601.so.1
3ae6415000-3ae6416000 rw-p 00015000 08:02 6045828                
  /lib64/libgcc_s-4.4.7-20120601.so.1
3d6aa0-3d6aa17000 r-xp  08:02 6029317                
  /lib64/libpthread-2.12.so 
3d6aa17000-3d6ac17000 ---p 

Re: [Wien] WIENncm invalid pointer error

[Gavin Abo]

That's an error message type that might not have a simple fix.

I don't recall ever pinpointing the exact version that WIENncm was based 
on, but I found in my past post at [1] that I had narrowed it down to 
about the 2006 release of WIEN2k version 6.4 or prior.


We used to have memory errors like that in the older versions of 
WIEN2k.  There is a good chance that the latest version of WIEN2k 
contains source code that would probably fix that if is being caused by 
a source code bug.  Another possibility is that error could be caused by 
the compiler.  The 2013 Intel compiler you are using wouldn't have 
existed back in 2006.  Some of the WIEN2k source code I think had to be 
changed to work more smoothly with newer versions of the Intel compilers 
[2].


Unfortunately, I don't think we have found someone in the WIEN2k mailing 
list yet that has been willing and able to take on the major effort that 
would be needed to bring WIENncm up to the same base of the latest 
WIEN2k version.  The last mention about that might have been in the post 
at [3].  You might recall that the WIENncm page at [4] states that 
"support is very limited" and the above can hopefully provide some 
insight on why that is.


[1] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg16337.html
[2] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg16588.html
[3] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg20643.html

[4] http://www.wien2k.at/reg_user/ncm/

Respectively,

Gavin
WIEN2k user


On 12/14/2023 4:32 AM, Safikul Islam wrote:

Dear Sir,

               I am writing to you regarding the calculations of 
WIENncm examples. I am trying to do a test run of the given examples 
(febcc,uo2_2k,uo2_3k,Mn3Sn). For example febcc it is working fine but 
for other examples I am getting errors while running WIENncm. The 
error is as follows.


Error:
runncm with  /home/safikul_akd/WIENNCM/WIENNCM
in cycle 1    ETEST: 0   CTEST: 0
 LAPW0 END
*** glibc detected *** /home/safikul_akd/WIENNCM/WIENNCM/lapw1c: 
free(): invalid pointer: 0x02ad6d90 ***

=== Backtrace: =
/lib64/libc.so.6[0x3ae0675e5e]
/lib64/libc.so.6[0x3ae0678cad]
/home/safikul_akd/WIENNCM/WIENNCM/lapw1c[0x488e5c]
/home/safikul_akd/WIENNCM/WIENNCM/lapw1c[0x435b4b]
/home/safikul_akd/WIENNCM/WIENNCM/lapw1c[0x441788]
/home/safikul_akd/WIENNCM/WIENNCM/lapw1c[0x43036a]
/home/safikul_akd/WIENNCM/WIENNCM/lapw1c[0x403906]
/lib64/libc.so.6(__libc_start_main+0x100)[0x3ae061ed20]
/home/safikul_akd/WIENNCM/WIENNCM/lapw1c[0x4037d9]
=== Memory map: 
0040-00552000 r-xp  08:11 194416842             
/home/safikul_akd/WIENNCM/WIENNCM/lapw1c
00752000-0075d000 rw-p 00152000 08:11 194416842             
/home/safikul_akd/WIENNCM/WIENNCM/lapw1c

0075d000-00893000 rw-p  00:00 0
0277c000-03334000 rw-p  00:00 0             [heap]
3ae020-3ae022 r-xp  08:02 6029314             
/lib64/ld-2.12.so 
3ae042-3ae0421000 r--p 0002 08:02 6029314             
/lib64/ld-2.12.so 
3ae0421000-3ae0422000 rw-p 00021000 08:02 6029314             
/lib64/ld-2.12.so 

3ae0422000-3ae0423000 rw-p  00:00 0
3ae060-3ae078b000 r-xp  08:02 6045824             
/lib64/libc-2.12.so 
3ae078b000-3ae098a000 ---p 0018b000 08:02 6045824             
/lib64/libc-2.12.so 
3ae098a000-3ae098e000 r--p 0018a000 08:02 6045824             
/lib64/libc-2.12.so 
3ae098e000-3ae099 rw-p 0018e000 08:02 6045824             
/lib64/libc-2.12.so 

3ae099-3ae0994000 rw-p  00:00 0
3ae0a0-3ae0a02000 r-xp  08:02 6029381             
/lib64/libdl-2.12.so 
3ae0a02000-3ae0c02000 ---p 2000 08:02 6029381             
/lib64/libdl-2.12.so 
3ae0c02000-3ae0c03000 r--p 2000 08:02 6029381             
/lib64/libdl-2.12.so 
3ae0c03000-3ae0c04000 rw-p 3000 08:02 6029381             
/lib64/libdl-2.12.so 
3ae120-3ae1283000 r-xp  08:02 6045825             
/lib64/libm-2.12.so 
3ae1283000-3ae1482000 ---p 00083000 08:02 6045825             
/lib64/libm-2.12.so 
3ae1482000-3ae1483000 r--p 00082000 08:02 6045825             
/lib64/libm-2.12.so 
3ae1483000-3ae1484000 rw-p 00083000 08:02 6045825             
/lib64/libm-2.12.so 
3ae620-3ae6216000 r-xp  08:02 6045828             
/lib64/libgcc_s-4.4.7-20120601.so.1
3ae6216000-3ae6415000 ---p 00016000 08:02 6045828             
/lib64/libgcc_s-4.4.7-20120601.so.1
3ae6415000-3ae6416000 rw-p 00015000 08:02 6045828             
/lib64/libgcc_s-4.4.7-20120601.so.1
3d6aa0-3d6aa17000 r-xp  08:02 6029317             
/lib64/libpthread-2.12.so 

Re: [Wien] WIENncm installation error

[Gavin Abo]

Your bashrc block looks fine.  There is likely something else I'm not 
seeing.


In a terminal, enter the command: echo $WIENROOT

Does that output:

/scratch/19ph92r03/safikul/WIENNCM/WIENNCM

Previously, one of your errors was:

/scratch/19ph92r03/safikul/WIENNCM/WIENNCM/lapw0: Command not found.

Did you put your compiled lapw0 file in that directory?

Enter the terminal command: ls -la $WIENROOT | grep lapw0

Does the non-empty lapw0 file show up as being there as you would expect 
in the output?


On 11/18/2023 10:14 PM, Safikul Islam wrote:

Dear Sir,

               Even though I have added the path for WIENncm the error 
persists. Here is my bashrc file. How will I add the path of  WEIN2k 
and WIENncm simultaneously?

..
# added by WIEN2k: BEGIN
# 
alias lsi="ls -aslp *.in*"
alias lso="ls -aslp *.output*"
alias lsd="ls -aslp *.def"
alias lsc="ls -aslp *.clm*"
alias lss="ls -aslp *.scf* */*.scf"
alias lse="ls -aslp *.error"
alias LS="ls -aslp | grep /"
alias pslapw="ps -ef |grep "lapw""
alias cdw="cd /home/19ph92r03/WIEN2k"
export OMP_NUM_THREADS=1
#export LD_LIBRARY_PATH=.
export EDITOR="gedit"
export SCRATCH=./
#export WIENROOT=/scratch/19ph92r03/safikul/wien2k
export WIENROOT=/scratch/19ph92r03/safikul/WIENNCM/WIENNCM
export W2WEB_CASE_BASEDIR=/home/19ph92r03/WIEN2k
export STRUCTEDIT_PATH=$WIENROOT/SRC_structeditor/bin
export PDFREADER=acroread
export 
PATH=$WIENROOT:$STRUCTEDIT_PATH:$WIENROOT/SRC_IRelast/script-elastic:$PATH:.

export OCTAVE_EXEC_PATH=${PATH}::
export OCTAVE_PATH=${STRUCTEDIT_PATH}::

export PATH=$PATH:$WIENROOT:.
ulimit -s unlimited
alias octave="octave -p $OCTAVE_PATH"
# --- BERRYPI START ---
export BERRYPI_PATH=$WIENROOT/SRC_BerryPI/BerryPI
export BERRYPI_PYTHON=/usr/bin/python2.7
alias berrypi="${BERRYPI_PYTHON} ${BERRYPI_PATH}/berrypi"
# --- BERRYPI END ---
# 
# added by WIEN2k: 
END...



with kind regards,
Safikul Islam








--
*SAFIKUL ISLAM*
[Ph.D Research Scholar]
---
Department of Physics.
Indian Institute of Technology,
Kharagpur.
West Bengal, India.
_Pin Code_:- 721302.
---
_Contact_:- 9832979985___
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Re: [Wien] WIENncm installation error

[Gavin Abo]

In .bashrc, the "export WIENROOT=/home/username/WIEN2k" line can be 
replaced by:


export WIENROOT=/home/username/WIENNCM

The "/home/username/WIENNCM" would have to be changed if you installed 
WIENncm in a different directory on your system.  Also, remember to 
restart the computer (or close and open a new terminal) after saving the 
changes to .bashrc so that the changes go into affect.


On 11/18/2023 1:29 PM, Safikul Islam wrote:

Dear Sir,

              I am trying to do  a testrun for the example febcc but 
getting the following errors. The compilation was okay. After the 
compilation I have done ./userconfig_lapw. But it is adding the paths 
for WIEN2k in bashrc file. Sir there is no userconfig_lapw in WEINncm 
directory. Then how will I add the executables of the WIENncm in the 
bashrc file?

..
Errror
(base) [19ph92r03@login06 febcc]$ runncm
runncm with  /scratch/19ph92r03/safikul/WIENNCM/WIENNCM
in cycle 1    ETEST: 0   CTEST: 0
/scratch/19ph92r03/safikul/WIENNCM/WIENNCM/lapw0: Command not found.
/scratch/19ph92r03/safikul/WIENNCM/WIENNCM/lapw1c: Command not found.
/scratch/19ph92r03/safikul/WIENNCM/WIENNCM/lapw2c: Command not found.
CORE - Error
...

             Sir I eanestly request  you to please help me to sort out 
this issue.


Kind Regards,
Safikul Islam

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Re: [Wien] Problem in All compilation

[Gavin Abo]

It looks like it tells you exactly what is wrong as it has:


SRC_3ddens/compile.msg:Fatal Error: Cannot open included file ‘fftw3.f03’


That error is likely from a file permissions problem.  Typically, both 
fftw3 and WIEN2k are installed as a user.  It could be caused by 
fftw-3.3.10.tar.gz [1] being installed as root or superuser instead of 
as a user with WIEN2k being install as a user.



On the other hand, if you installed fftw3 in Ubuntu 23.10 using the 
package manager [2] (e.g., sudo apt-get install -y fftw3 [3]), it is 
hard to say what is causing the opening of the fftw3.f03 file to fail.



Ubuntu 23.10 is unstable which is why it is quite common to the use the 
stable LTS version that is currently Ubuntu 22.04.3 [4]. Ubuntu 22.04.2 
(or 22.04.3 LTS) is what I have installed WIEN2k on before [5].



If the failure of reading the fftw3.f03 from your fftw3 installation is 
from a file permission problem, then the chmod command [6] would be 
needed to fix it.



[1] https://www.fftw.org/download.html

[2] https://launchpad.net/ubuntu/+source/fftw3

[3] https://zoomadmin.com/HowToInstall/UbuntuPackage/fftw3

[4] https://ubuntu.com/download/desktop

[5] 
https://github.com/gsabo/WIEN2k-Docs/blob/main/WIEN2k23.2_Ubuntu22.04_Install_with_gfortran.pdf


[6] https://en.wikipedia.org/wiki/Chmod


Kind Regards,

Gavin

WIEN2k user


On 11/15/2023 6:52 PM, Shahid Mahmood Chaudhry via Wien wrote:


Dear Sir

Where is the problem and how to solve it


Ubuntu 23.1

Wien2k 23.2

Libxc

Openblas

fftw3

gfortran compiler


Compile time errors (if any) were:
SRC_3ddens/compile.msg:Fatal Error: Cannot open included file ‘fftw3.f03’
SRC_3ddens/compile.msg:make: *** [Makefile:84: fft_modules.o] Error 1
SRC_afmsim/compile.msg:collect2: error: ld returned 1 exit status
SRC_afmsim/compile.msg:make: *** [Makefile:68: afmsim] Error 1
SRC_aim/compile.msg:collect2: error: ld returned 1 exit status
SRC_aim/compile.msg:make[1]: *** [Makefile:93: aim] Error 1
SRC_aim/compile.msg:make: *** [Makefile:85: real] Error 2
SRC_aim/compile.msg:collect2: error: ld returned 1 exit status
SRC_aim/compile.msg:make[1]: *** [Makefile:96: aimc] Error 1
SRC_aim/compile.msg:make: *** [Makefile:88: complex] Error 2
SRC_clminter/compile.msg:collect2: error: ld returned 1 exit status
SRC_clminter/compile.msg:make: *** [Makefile:52: clminter] Error 1
SRC_dipan/compile.msg:collect2: error: ld returned 1 exit status
SRC_dipan/compile.msg:make: *** [Makefile:68: dipan] Error 1
SRC_dstart/compile.msg:collect2: error: ld returned 1 exit status
SRC_dstart/compile.msg:make[1]: *** [Makefile:99: dstart] Error 1
SRC_dstart/compile.msg:make: *** [Makefile:90: seq] Error 2
SRC_eosfit6/compile.msg:collect2: error: ld returned 1 exit status
SRC_eosfit6/compile.msg:make: *** [Makefile:36: eosfit6] Error 1
SRC_filtvec/compile.msg:collect2: error: ld returned 1 exit status
SRC_filtvec/compile.msg:make[1]: *** [Makefile:82: filtvec] Error 1
SRC_filtvec/compile.msg:make: *** [Makefile:72: real] Error 2

Thanks






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Re: [Wien] semicore band ranges too large error: for MoSi2N4

[Gavin Abo]

I suppose the modified l2main.F to SRC_lapw2 for WIEN2k 23.2 won't 
affect this particular case, but if one wants to try it out to know for 
sure, I have posted the patch file for it today at [1] or put the link 
in the README at [1] that directs to the mailing list post with the 
l2main.F.gz file if preferred instead.


I think I got a WIEN2k 23.2 patch file at [1] for those reported so far 
except for fixes to the ELF [2] and NMR [3] that looked planned for a 
future WIEN2k release.


[1] https://github.com/gsabo/WIEN2k-Patches/tree/master/23.2
[2] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg22070.html
[3] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg22468.html


Kind Regards,

Gavin
WIEN2k user

On 11/14/2023 1:00 AM, Peter Blaha wrote:
As I wrote before: I cannot reproduce this. For me it converges fine 
even with RKmax=7. No errors. Thus, I don't know how to help you.


Are you using WIEN2k_23.2 ??


Am 13.11.2023 um 15:39 schrieb hajar.nejatipoor--- via Wien:

Dear Dr. Blaha
I act as you said, but the problem "LAPW2' - semicore band-ranges too 
large, ghostbands" exists again!!
LO for N-2s orbitals in case.in1c were removed, but it worked just 
for rkm=6 (with or without LO for N).

I tried your way with changing rmt of atoms but the problem remained.

I tried a normal scf with RKm=7, from the beginning, at a different 
directory, but nothing was changed. Just, crashing LAPW2 is postponed 
in some more cycles.
On Sunday, November 12, 2023 at 08:42:25 PM GMT+3:30, Peter Blaha 
 wrote:



I tried your struct file, converged with RKM=6, saved, increased RKMax
to 7 and continued with run_lapw.
No problem. As expected with your RMTs rather small change from 6 to 7
and quick convergence.

You must have changed something else, like mixing a density with
different RMTs,  


Am 12.11.2023 um 07:30 schrieb hajar.nejatipoor--- via Wien:
 > Dear Dr. Blaha
 > The way you proposed, just worked for RKm=6, and the error below
 > appeared for the case of RKm=7:
 >   'SELECT' - no energy limits found for atom   1  L= 0
 >   'SELECT' - E-bottom -520.0   E-top -520.0
 >
 > It is worth to mention that since for Si-muffin tin radius 1.68, 
there

 > is a huge charge leak out, I set the muffin tin raddii as:
 >
 >    1  42.0  2.12  2.2
 >    2  14.0  1.68  2.1
 >    3  7.0  1.61  1.2
 >    4  7.0  1.60  1.2
 >
 > On Saturday, November 11, 2023 at 10:43:42 PM GMT+3:30, Peter Blaha
 > mailto:peter.bl...@tuwien.ac.at>> wrote:
 >
 >
 > First of all,  setrmt  gives:
 >    1  42.0  2.12  2.12
 >    2  14.0  1.68  1.68
 >    3  7.0  1.61  1.60
 >    4  7.0  1.60  1.60
 >
 > So the N radii are much larger and Si and Mo smaller.
 >
 > It might be that the ghostband comes from N-2s, as the small RMT 
may not

 > allow for 2 radial functions. You could try to remove the LO for N-s
 > (only keep:
 >    0.30    2  0      (GLOBAL E-PARAMETER WITH n OTHER CHOICES, global
 > APW/LAPW)
 >    0  -1.07    0.0010 CONT 1
 >    1    0.30    0. CONT 1
 > for the N atoms (maybe use instead a HDLO).
 >
 >
 > Am 11.11.2023 um 19:26 schrieb hajar.nejatipoor--- via Wien:
 >  > MoSi2N4
 >  > H   LATTICE,NONEQUIV.ATOMS:  4 187_P-6m2
 >  > MODE OF CALC=RELA unit=bohr
 >  >    5.502431  5.502431 38.534460 90.00 90.00120.00
 >  > ATOM  -1: X=0. Y=0. Z=0.
 >  >            MULT= 1          ISPLIT= 4
 >  > Mo1        NPT=  781  R0=0.1000 RMT=    2.2000  Z: 42.000
 >  > 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. Y=0.3334 Z=0.14710600
 >  >            MULT= 2          ISPLIT= 4
 >  >        -2: X=0.6668 Y=0.3334 Z=0.85289400
 >  > Si1        NPT=  781  R0=0.0001 RMT=    2.1000  Z: 14.000
 >  > 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=0.6667 Z=0.82807700
 >  >            MULT= 2          ISPLIT= 4
 >  >        -3: X=0.3334 Y=0.6667 Z=0.17192300
 >  > N 1        NPT=  781  R0=0.0001 RMT=    1.2000  Z:  7.000
 >  > LOCAL ROT MATRIX:    1.000 0.000 0.000
 >  >                       0.000 1.000 0.000
 >  >                       0.000 0.000 1.000
 >  > ATOM  -4: X=0. Y=0.3334 Z=0.93855400
 >  >            MULT= 2          ISPLIT= 4
 >  >        -4: X=0.6668 Y=0.3334 Z=0.06144600
 >  > N 2        NPT=  781  R0=0.0001 RMT=    1.2000  Z:  7.000
 >  > LOCAL ROT MATRIX:    1.000 0.000 0.000
 >  >                       0.000 1.000 0.000
 >  >                       0.000 0.000 1.000
 >
 > --
 > 
--

 > Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
 > 

Re: [Wien] How to get "klist file" for orthorhombic P structure

[Gavin Abo]

You likely need to describe further what the problem is.

Take for example the attached SnS.struct having space group 62_Pnma.

1. In a Linux terminal on a system with XCrySDen version 1.6.2, enter: 
xcrysden


2. Click File -> Open WIEN2k -> Select k-path

3. Select the particular k-path that you want, then click OK

4. Type in how many "total number of k-points along the path" that you 
want, for example: 100


5. Click OK

6. Type in a File name, for example: SnS.klist_path

7. Click Save

8. Click Close

9.  If successful, a SnS.klist_path file is generated

For the above, see if you can view the animated gif at [1].

[1] https://drive.google.com/file/d/1frAafWmawB0GoLvl6OapoFxKz-LpWGFv/view

Kind Regards,
Gavin
WIEN2k user

On 8/23/2023 9:32 AM, Chang, Hong Young wrote:


Dear Wien2k users,

I am trying to calculate Band Structure for an Orthorhombic Crystal 
structure (# of space group: 62, Pnma).


Because Wien2k/SRC_templates/klist provides for 4 klist files ( fcc, 
bcc, hcp, and simple cubic), I have tried to get K-meshes of Brillouin 
zone from “XCRYSDEN” software. But, it is not possible to make 
“xcrysden.klist” from XCRYSDEN (1.6 version) for Wien2k.


Maybe, XCRYSDEN (1.6 version) does not provide the function of “Save 
K-Path” for Wien2k.  Please, let me know how to generate a klist file 
for the Orthorhombic P structure.


In advance, I appreciate your interest in my question.

Sincerely,
SnS
P   LATTICE,NONEQUIV.ATOMS:  2 62_Pnma 
MODE OF CALC=RELA unit=bohr
 21.127138  7.524889  8.180624 90.00 90.00 90.00
ATOM  -1: X=0.3507 Y=0.2500 Z=0.0201
  MULT= 4  ISPLIT= 8
  -1: X=0.6493 Y=0.7500 Z=0.9799
  -1: X=0.8507 Y=0.2500 Z=0.4799
  -1: X=0.1493 Y=0.7500 Z=0.5201
S  NPT=  781  R0=0.0001 RMT=2.2800   Z: 16.000 
LOCAL ROT MATRIX:0.000 1.000 0.000
 0.000 0.000 1.000
 1.000 0.000 0.000
ATOM  -2: X=0.61937000 Y=0.2500 Z=0.3806
  MULT= 4  ISPLIT= 8
  -2: X=0.38063000 Y=0.7500 Z=0.6194
  -2: X=0.11937000 Y=0.2500 Z=0.1194
  -2: X=0.88063000 Y=0.7500 Z=0.8806
Sn NPT=  781  R0=0.1000 RMT=2.5000   Z: 50.000 
LOCAL ROT MATRIX:0.000 1.000 0.000
 0.000 0.000 1.000
 1.000 0.000 0.000
   8  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
-1 0 0 0.5000
 0-1 0 0.
 0 0 1 0.5000
   3
-1 0 0-0.
 0 1 0 0.5000
 0 0-1-0.
   4
-1 0 0 0.5000
 0 1 0 0.5000
 0 0 1 0.5000
   5
 1 0 0 0.5000
 0-1 0 0.5000
 0 0-1 0.5000
   6
 1 0 0 0.
 0-1 0 0.5000
 0 0 1-0.
   7
 1 0 0 0.5000
 0 1 0-0.
 0 0-1 0.5000
   8
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Re: [Wien] Speeding up calculations in parallel mose

[Gavin Abo]

Sometimes it can be better to have a cheap computer if you can remote 
connect to a high performance computing (hpc) [1] cluster.


There can be quite a bit of difference in the computing resources that a 
thousand dollar desktop computer provides compared at a million dollar 
hpc [2].


If your in academia, there are usually more options available for 
getting access to a hpc such as use your own university's or 
department's one if available, use a research center if there is one 
nearby, collaborate with a professor at another university that has one, 
get a research grant to pay to use a commercial one (e.g., Amazon Cloud 
[3]), and so on.  If in industry, it might be harder to get access to 
one unless you work at a large corporation that has one.


Desktop computers used to ship with 100 Mbps cards.   However, in new 
computers nowadays, you will likely find them to have 1 Gbps cards.  A 
Gigabit switch used to be expensive, but they have probably come down in 
price now.


If you can find some buddies (aka fellow researchers) at your local site 
and can connect them up to a Gigabit switch, while not as good as a hpc 
with InfiniBand [4], you may be able to Beowulf cluster [5] them to be 
better than a single desktop computer.


You might recall reading, since it has been in the archive and has been 
re-posted a few times, the post at [6] about how a Gigabit network of 
computers with i7 processors worked relatively well.


[1] https://en.wikipedia.org/wiki/High-performance_computing
[2] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg22676.html

[3] https://aws.amazon.com/education/
[4] https://en.wikipedia.org/wiki/InfiniBand
[5] https://en.wikipedia.org/wiki/Beowulf_cluster
[6] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg09334.html


Kind Regards,

Gavin
WIEN2k user

On 8/22/2023 11:48 PM, Victor Zenou wrote:

Dear Laurie and Pavel,
Thanks for your answer
1. In fact I'm using RKMAX 5.4 and 125 kpts
0.01 cc and 0.001 ec


2. About my boss, it took me more than one year to get a new computer. 
Please define "fast"!

Victor


‫בתאריך יום ג׳, 22 באוג׳ 2023 ב-14:35 מאת ‪Laurence Marks‬‏ 
<‪laurence.ma...@gmail.com‬‏>:‬


Beyond what Pavel said, you are still talking weeks for a
calculation. A critical issue is whether you are using sensible
parameters. Many people have used RKMAX 7 and 1000 kpts assuming
that those are "right" -- they are not. If your H and He have
small RMTs then RKMAX should also be smaller. Also, what is needed
is a k-point density, so the number of k-points is less for a
supercell.

I suggest that you copy your case.struct file to a new directory
then do init_lapw in that directory. 23.2 will pick appropriate
values for you, and you can then copy them over.

Beyond that, get your boss to buy you a faster computer.

--
Professor Laurence Marks (Laurie)
Walter P Murphy Professor Emeritus
Department of Materials Science and Engineering, Northwestern
University
www.numis.northwestern.edu 
"Research is to see what everybody else has seen, and to think
what nobody else has thought" Albert Szent-Györgyi

On Tue, Aug 22, 2023, 04:32 Victor Zenou  wrote:

Dear Wien2k users!

I’m investigating a 54 tungsten atoms supercell , with 1
helium atom and 1 hydrogen atom (primitive cell) at different
interstitial sites. It takes ~ 46 hr per calculation cycle,
and half of it (~23 hr) in parallel mode. The Wien2k version
23.2 was installed on Ubuntu 22.04.2 LTS. using gfortran and I
set OMP_NUM_THREADS to 1, and used 2 parallel_jobs in the
current work. The computer is build from i7-10700 processor @
2.90GHz (8 cores; 16 Threads), 32 GB memory and 500 GB SSD.
In the past using the same computer , it took me ~ 14 hr per
cycle for the same calculations, meaning 2-4 times faster than
today. The wien2k version was 21.1, bur I can’t remember if
the calculations were done in parallel, probably yes (I think
the number of parallel jobs was chosen automatically), and I
think I set OMP_NUM_THREADS to 4, but again I’m not sure.
How can I speed up my calculations using the same computer?
Best regards, Victor

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Re: [Wien] Volume optimization and Eloss function.

[Gavin Abo]

ion and run 
scf with the minimum energy struct file obtained in the earlier 
optimisation and don’t change the structure suggested by sgroup and 
again repeat the optimisation on this struct file so that I can check 
if loweing the volume more than -20 can minimise the energy (I will 
start with -10 to 0 as the existing structure is already -20). /


//

/However, now I am getting the error 'NN' - overlapping spheres, which 
I will try to fix it (if free you may comment on this too but I guess 
I may find a thread addressed to this error). /


//

/*But my question is that am I going in the right direction with the 
optimisation procedure?*/**


Thank you for your help once again.

With warm regards,

Pranjal

*From:*Wien  *On Behalf Of 
*Gavin Abo

*Sent:* Friday, August 18, 2023 5:06 AM
*To:* wien@zeus.theochem.tuwien.ac.at
*Subject:* Re: [Wien] Volume optimization and Eloss function.

If the structure is still hexagonal after the substitution, the 
starting point could be section "5.3 Structure optimization" on 
lattice parameter optimization starting on page 87 in the WIEN2k 23.1 
(or 23.2) usersguide [1].


There you should see that you may select between two different packages.

If using *optimize*, there is:

[5] VARY A and C (2D-case) (tetragonal or hexagonal lattice)

Or if using *optimize_abc_lapw*, there is:

optimize_abc -t 2

After that, if the structure contains any free positions for atomic 
position optimization, then there is section "5.3.2 Minimization of 
internal parameters" on page 91 of the usersguide [1].


Yes, case.eloss is for the loss function [2].  On slide 9 in [3], it 
looks to be showing that case.epsilon contains the real and imaginary 
parts for the complex dielectric tensor and case.sigmak contains the 
real and imaginary parts for the optical conductivity.


[1] 
http://www.wien2k.at/reg_user/textbooks/usersguide.pdfhttp://www.wien2k.at/reg_user/textbooks/usersguide.pdf 
<http://www.wien2k.at/reg_user/textbooks/usersguide.pdfhttp:/www.wien2k.at/reg_user/textbooks/usersguide.pdf>
[2] Slide 22: 
http://www.wien2k.at/events/ws2006/Optics_Vienna_April_2006.pdf
[3] 
http://www.wien2k.at/reg_user/textbooks/WIEN2k_lecture-notes_2013/optic_handout.pdf


On 8/17/2023 11:23 AM, Pranjal Nandi wrote:

Dear All,

I have an issue with 2 different parts (not related to each
other). They are as follows.

 1. I am having a hard time in getting a hcp structure of HfO0.7
(or Hf605 which is close to 0.7). Therefore, what I have done
is that I have downloaded the hcp structure of HfPo and
substituted the Po with Oxygen.

Now, I want to do the structural and volumetric relaxation so
that I have the stable relaxed structure of HfO0.7. I did read
the guidebook but I need guidance on what should be the
correct order of optimisation (I am lost as I can’t understand
from which optimisation I should start).


 2. In the eloss programme, which part of the function does the
eloss, epsilon and sigmak correspond to ? I guess eloss =
energy loss function, epsilon = real part of the dielectric
function , sigmaK = imaginary part of the dielectric function.
Am I right?

Looking forward to your kind guidance.

Thank you.

With warm regards,

Pranjal



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Re: [Wien] Volume optimization and Eloss function.

[Gavin Abo]

If the structure is still hexagonal after the substitution, the starting 
point could be section "5.3 Structure optimization" on lattice parameter 
optimization starting on page 87 in the WIEN2k 23.1 (or 23.2) usersguide 
[1].


There you should see that you may select between two different packages.

If using *optimize*, there is:

[5] VARY A and C (2D-case) (tetragonal or hexagonal lattice)

Or if using *optimize_abc_lapw*, there is:

optimize_abc -t 2

After that, if the structure contains any free positions for atomic 
position optimization, then there is section "5.3.2 Minimization of 
internal parameters" on page 91 of the usersguide [1].


Yes, case.eloss is for the loss function [2].  On slide 9 in [3], it 
looks to be showing that case.epsilon contains the real and imaginary 
parts for the complex dielectric tensor and case.sigmak contains the 
real and imaginary parts for the optical conductivity.


[1] 
http://www.wien2k.at/reg_user/textbooks/usersguide.pdfhttp://www.wien2k.at/reg_user/textbooks/usersguide.pdf
[2] Slide 22: 
http://www.wien2k.at/events/ws2006/Optics_Vienna_April_2006.pdf
[3] 
http://www.wien2k.at/reg_user/textbooks/WIEN2k_lecture-notes_2013/optic_handout.pdf



On 8/17/2023 11:23 AM, Pranjal Nandi wrote:


Dear All,

I have an issue with 2 different parts (not related to each other). 
They are as follows.


 1. I am having a hard time in getting a hcp structure of HfO0.7 (or
Hf605 which is close to 0.7). Therefore, what I have done is that
I have downloaded the hcp structure of HfPo and substituted the Po
with Oxygen.

Now, I want to do the structural and volumetric relaxation so that
I have the stable relaxed structure of HfO0.7. I did read the
guidebook but I need guidance on what should be the correct order
of optimisation (I am lost as I can’t understand from which
optimisation I should start).

 2. In the eloss programme, which part of the function does the eloss,
epsilon and sigmak correspond to ? I guess eloss = energy loss
function, epsilon = real part of the dielectric function , sigmaK
= imaginary part of the dielectric function. Am I right?

Looking forward to your kind guidance.

Thank you.

With warm regards,

Pranjal



Aquest missatge, i els fitxers adjunts que hi pugui haver, pot 
contenir informació confidencial o protegida legalment i s’adreça 
exclusivament a la persona o entitat destinatària. Si no consteu com a 
destinatari final o no teniu l’encàrrec de rebre’l, no esteu 
autoritzat a llegir-lo, retenir-lo, modificar-lo, distribuir-lo, 
copiar-lo ni a revelar-ne el contingut. Si l’heu rebut per error, 
informeu-ne el remitent i elimineu del sistema tant el missatge com 
els fitxers adjunts que hi pugui haver.


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recibirlo, no está autorizado a leerlo, retenerlo, modificarlo, 
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Re: [Wien] SOC value \zeta

[Gavin Abo]

Should it helpful to you, below is something I came across when 
searching in some of my old notes on WIEN2k.



*5/7/2016 WIEN2k Notes*

WIEN2k articles on the 'artificial' adjustment of the spin orbit 
coupling strength, xi, using the speed of light, c (i.e., xi ∝ c^-2):


C. Zeng, et al., "Linear magnetization dependence of the intrinsic 
anomalous Hall effect", http://arxiv.org/abs/cond-mat/0606354v1
Y. Yao, et al., "First Principles Calculation of Anomalous Hall 
Conductivity in Ferromagnetic bcc Fe", 
http://arxiv.org/abs/cond-mat/0307337v2


Hso = xi*(S dot L)

where

xi = hbar/(2*M*c^2)*1/r*dV/dr [ 
http://www.wien2k.at/reg_user/textbooks/novak_lecture_on_spinorbit.pdf 
(equation 28) ]


Spin orbit coupling strength is not an external WIEN2k input [ 
http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg06559.html 
] or output parameter [ 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg09672.html 
].


Hack Method 1: 
https://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg08972.html
Hack Method 2: 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg12321.html



Kind Regards,

Gavin

WIEN2k user


On 8/16/2023 3:20 PM, Samolyuk, German D. via Wien wrote:

Dear colleagues,

I'm running wien2k version WIEN2K_19_LI on linux cluster. The goal is 
to analyze magnetic anisotropy energy in YCo_5 intermetallic.


As it was explained in few presentation discussing SOC implementation 
in wien2K it's added in following form


\zeta ({\vec \sigma}{\vec l}), where \zeta = 1/(2Mc^2) 1/r^2 dV/dr.

Question: is it possible to output value \zeta for each atom, orbital 
moment?


I cant find it in output files and was not able to find following  
discussion in archive.


Thank you,

German

Dr. German D Samolyuk
Materials Theory Group
Materials Science & Technology Division
Oak Ridge National Laboratory
Post Office Box 2008
Oak Ridge, TN 37831-6138
(865) 241-5394
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Re: [Wien] lapw0.def failed

[Gavin Abo]

If you're building fftw3 from source with gfortran and are following my 
steps, the fftw3.f03 is installed in the ~/fftw-3.3.10/include directory 
as seen in step 4 of [1].


If you're using ifort instead of gfortran, fftw3 can also be built from 
source and the fftw3.f03 can be installed in the ~/fftw-3.3.10/include 
directory as seen in step 2 of [2].


If you are instead using fftw3 from the Ubuntu 22.04.2 LTS package, 
which likely only works when using gfortran, the library header file 
fftw3.f03 gets installed in the /usr/include/ directory as seen below:


username@computername:~/Desktop$ lsb_release -a
No LSB modules are available.
Distributor ID:    Ubuntu
Description:    Ubuntu 22.04.2 LTS
Release:    22.04
Codename:    jammy
username@computername:~/Desktop$ ls /usr/include/fftw3*
ls: cannot access '/usr/include/fftw3*': No such file or directory
username@computername:~/Desktop$ sudo apt install libfftw3-dev
...
username@computername:~/Desktop$ ls /usr/include/fftw3*
/usr/include/fftw3.f    /usr/include/fftw3.h /usr/include/fftw3q.f03
/usr/include/fftw3.f03  /usr/include/fftw3l.f03

Of note, the fftw3 library files (libfftw3.a and libfftw3.so), from the 
Ubuntu 22.04.2 LTS package get installed in the 
/usr/lib/x86_64-linux-gnu/ directory:


username@computername:~/Desktop$ ls /usr/lib/x86_64-linux-gnu/libfftw3.*
/usr/lib/x86_64-linux-gnu/libfftw3.a
/usr/lib/x86_64-linux-gnu/libfftw3.so
/usr/lib/x86_64-linux-gnu/libfftw3.so.3
/usr/lib/x86_64-linux-gnu/libfftw3.so.3.5.8

Depending on the install approach that you use for fftw3, you have to 
adjust the FFTW options and FFTW-LIBS in siteconfig appropriately.


[1] 
https://github.com/gsabo/WIEN2k-Docs/blob/main/WIEN2k23.2_Ubuntu22.04_Install_with_gfortran.pdf
[2] 
https://github.com/gsabo/WIEN2k-Docs/blob/main/WIEN2k23.2_Ubuntu22.04_Install_with_OneAPI(ifort).pdf


Kind Regards,

Gavin
WIEN2k user

On 7/21/2023 9:31 AM, Laurence Marks wrote:

They are all the same error, associated with fftw3.f03 not being found.

What you need to do is ls $WIENROOT/SRC_lapw0/fftw3.f03 (it is 
probably not there, but just checking.)


Then look at the few lines above the first error (you don't need them 
all). This will give you the compilation options. There should be 
something that starts with a -I where your FFTW3 library include 
files are. This is wrong on your system. To see what you currently 
have you can do

grep "-- fftw" $WIENROOT/SRC_lapw0/Makefile -A10

I cannot say exactly what is wrong as I dont know how you 
configured fftw (not part of Wien2k). Something with them, which is 
also in $WIENROOT/WIEN2k_OPTIONS for entries with FFTW in them



On Fri, Jul 21, 2023 at 9:53 AM Brik Hamida  wrote:

hmd@hmd-host:~/wien2k23$ grep -i "error" */compile.msg | grep -v
-e arguments -e xerror |grep -v know

SRC_3ddens/compile.msg:fft_modules.F:174: Error: Can't open
included file 'fftw3.f03'


--
Professor Laurence Marks (Laurie)
Department of Materials Science and Engineering
Northwestern University
www.numis.northwestern.edu 
"Research is to see what everybody else has seen, and to think what 
nobody else has thought", Albert Szent-Györgyi___
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Re: [Wien] System Error....Couldn't write to/.

[Gavin Abo]

That output file, case.outputd, as far as I know is not used an input to 
another calculation process. Thus, it seems safe to click the "initlapw 
without saving" button which would be another way to get around the 
"Couldn't write to /." error from "Save and initlapw" in this case.  
Although, if you are clicking the "initlapw without saving" or "Save and 
initlapw" button too quickly, you might have missed viewing the 
case.outputd to check if the condition gmax > gmin was meet.  Proceeding 
with a gmin value less then gmax could affect your results.


You didn't give the different file sizes of the case.outputd files for 
the BP, ZnSiP2 and other.  I suspect the file sizes are smaller than the 
case.outptud files produced for the C24H72N8In2Br14 and C16H20O7.


The TiC example in the usersguide [1] produces a case.outputd with a 
file size of about 21.8 kB.  That is a small unit cell and one of the 
calculation cases when the error is not observed.  The C16H20O7 has a 
relatively large unit cell [2] in comparison to that of TiC 
corresponding with the MB size case.outputd versus the kB one, respectively.


Whether you get the error "Couldn't write to /." or not with C16H20O7 
seems to also depend on the type of computer system(s) you are using 
(laptop, desktop, hpc? amount of RAM? SSD or HDD? how may CPU cores? 
using a virtual machine or not? Etc.).


For running calculation with WIEN2k, you have probably noticed how a 
single desktop computer is good for small unit cells but when moving to 
large structures such as slabs it can push researchers into using a hpc 
(e.g., the Roadrunner [3]).


At [4], you can probably see how there is quite a bit of difference in 
the computing ability and the computer resources between say a $1,700 
desktop and a $101,000,000 Roadrunner computer system.


[1] http://susi.theochem.tuwien.ac.at/reg_user/textbooks/usersguide.pdf
[2] https://doi.org/10.1007/s00894-022-05340-3
[3] https://en.wikipedia.org/wiki/Roadrunner_(supercomputer)
[4] 
https://insidehpc.com/2012/03/supercomputers-vs-your-computer-a-bang-for-the-buck-battle/ 




On 7/20/2023 10:23 PM, karina Khan wrote:
Thank you for your response. I want to ask you that if I complete the 
process by clicking continue initlapw without saving will it affect my 
results as doing so I didn't find any error in scf convergence.


One more thing this " System ErrorCouldn't write to/." didn't 
observe in other molecules like BP, ZnSiP2 and other.


On Fri, 21 Jul, 2023, 8:14 AM Gavin Abo,  wrote:

On an older, slower computer system, I was able to reproduce the
error displayed in w2web as:

*System Error*

Couldn't write to /.

_back to last page_

To produce the error, what I did in w2web was 1) I clicked the
"view case.outputd and cp case.in0_std case.in0" button, 2) paused
about 5 seconds, and 3) clicked the "Save and initlapw" button.

The file size of the case.outputd is 43.6 MB.  I suspect the error
results because my computer is slow in opening the case.outputd
file where I clicked on the save button before the file got opened up.

When I clicked "view case.klist" followed by clicking as fast as
possible "Save and initlapw", I do not encounter the same error. 
The file size of case.klist, however, is only 101 bytes.

I also 1) clicked the "view case.outputd and cp case.in0_std
case.in0" button, 2) paused about 1 minute, and 3) clicked the
"Save and initlapw" button.  When doing that, the error did not occur.

I put the 43.6 MB case.outputd on a new faster computer system
clicking the "Save and initlapw" button immediately after having
clicked the "view case.outputd and cp case.in0_std case.in0"
button and the error do not appear.

From that, it seems to be a computer system resource limitation
that is causing the error.

Kind Regards,

Gavin
WIEN2k user

On 7/14/2023 4:59 AM, karina Khan wrote:

Ok I will keep this thing in my mind for future
This command works well with different systems like Cs2AgInBr6,
BP but not with system having molecular formula C24H72N8In2Br14
and C16H20O7

On Thu, 13 Jul, 2023, 8:34 PM Peter Blaha,
 wrote:

I cannot reproduce this. It works perfectly fine with me.

Please try again in another case. Or use the recommended fast
mode. This will set automatically good parameters in
case.in0/1/2 and klist, and not the "stupid" defaults of the
step by step initialization.

PS: You cannot send large images to the mailing list. There
is a limit of 40 kB per message.


Am 13.07.2023 um 11:48 schrieb karina Khan:

Dear Wien2k users,
                       During initialisation, I stuck up in
the step *view 

Re: [Wien] lapw0.def failed

[Gavin Abo]

Another user was tackling the same error.  Thus, the following post 
might help:


https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg22648.html

On 7/20/2023 4:27 PM, Brik Hamida wrote:

Dear

There is no such lapw0 in the directory : home/hmd/wien2k23
but there are  lapw0para and  lapw0para_lapw  ( the same for lapw2 )
What should I do ?
Thanks

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Re: [Wien] System Error....Couldn't write to/.

[Gavin Abo]

On an older, slower computer system, I was able to reproduce the error 
displayed in w2web as:


*System Error*

Couldn't write to /.

_back to last page_

To produce the error, what I did in w2web was 1) I clicked the "view 
case.outputd and cp case.in0_std case.in0" button, 2) paused about 5 
seconds, and 3) clicked the "Save and initlapw" button.


The file size of the case.outputd is 43.6 MB.  I suspect the error 
results because my computer is slow in opening the case.outputd file 
where I clicked on the save button before the file got opened up.


When I clicked "view case.klist" followed by clicking as fast as 
possible "Save and initlapw", I do not encounter the same error. The 
file size of case.klist, however, is only 101 bytes.


I also 1) clicked the "view case.outputd and cp case.in0_std case.in0" 
button, 2) paused about 1 minute, and 3) clicked the "Save and initlapw" 
button.  When doing that, the error did not occur.


I put the 43.6 MB case.outputd on a new faster computer system clicking 
the "Save and initlapw" button immediately after having clicked the 
"view case.outputd and cp case.in0_std case.in0" button and the error do 
not appear.


From that, it seems to be a computer system resource limitation that is 
causing the error.


Kind Regards,

Gavin
WIEN2k user

On 7/14/2023 4:59 AM, karina Khan wrote:

Ok I will keep this thing in my mind for future
This command works well with different systems like Cs2AgInBr6, BP but 
not with system having molecular formula C24H72N8In2Br14 and C16H20O7


On Thu, 13 Jul, 2023, 8:34 PM Peter Blaha,  
wrote:


I cannot reproduce this. It works perfectly fine with me.

Please try again in another case. Or use the recommended fast
mode. This will set automatically good parameters in case.in0/1/2
and klist, and not the "stupid" defaults of the step by step
initialization.

PS: You cannot send large images to the mailing list. There is a
limit of 40 kB per message.


Am 13.07.2023 um 11:48 schrieb karina Khan:

Dear Wien2k users,
                       During initialisation, I stuck up in the
step *view case.outpd and cp case.in0_std case.in0, *when I click
on the step save and initlapw, I get a *System Error couldn't
write to/. * back to last page.
However this step is working for the other sample but not for
this new sample having 32 atoms.
Looking for your suggestions
*Thanks & Regards*
*Karina Khan*


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-- 
---

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Phone: +43-158801165300
Email:peter.bl...@tuwien.ac.at   
WWW:http://www.imc.tuwien.ac.at   WIEN2k:http://www.wien2k.at

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Re: [Wien] lapw0.def failed

[Gavin Abo]

In your post below, it looks like you only provided a part of the 
case.dayfile.


What about stdout and the error files, were there any additional 
information in them?


You will probably have different messages, but an example with TiC is 
shown below.  The TiC.struct parameters were taken from the table under 
chapter 3.6 in the WIEN2k 13.1 usersguide currently on the website 
(which is also used for WIEN2k 23.2) [ 
http://susi.theochem.tuwien.ac.at/reg_user/textbooks/usersguide.pdf ].


username@computername:~/wiendata/TiC$ ls
TiC.struct
username@computername:~/wiendata/TiC$ init_lapw -b
...
  init_lapw finished ok
username@computername:~/wiendata/TiC$ cat *.in0
TOT  XC_PBE (XC_LDA,XC_PBESOL,XC_WC,XC_MBJ,XC_SCAN)
NR2V  IFFT  (R2V)
   45   45   45    2.00  1 NCON 9  # min IFFT-parameters, enhancement 
factor, iprint, NCON n

username@computername:~/wiendata/TiC$ gedit TiC.in0
username@computername:~/wiendata/TiC$ run_lapw &> stdout
username@computername:~/wiendata/TiC$ cat *.dayfile

Calculating TiC in /home/username/wiendata/TiC
on computername with PID 215842
using WIEN2k_23.2 (Release 9/3/2022) in /home/username/WIEN2k


    start     (Thu Jul 20 12:12:47 AM MDT 2023) with lapw0 (40/99 to go)

    cycle 1     (Thu Jul 20 12:12:47 AM MDT 2023)     (40/99 to go)

>   lapw0  (00:12:47) 0.020u 0.036s 0:00.05 100.0% 0+0k 0+24io 
1pf+0w


> stop error

username@computername:~/wiendata/TiC$ cat *.error
 'LAPW0' - Invalid XC_SWITCH set. Please choose a valid potential option!
username@computername:~/wiendata/TiC$ cat stdout
Invalid potential option chosen (check lapw0.error)
grep: *scf1*: No such file or directory
grep: lapw2*.error: No such file or directory
grep: lapw2*.error: No such file or directory
grep: lapw2*.error: No such file or directory
grep: lapw2*.error: No such file or directory
grep: lapw2*.error: No such file or directory
grep: lapw2*.error: No such file or directory
grep: lapw1*.error: No such file or directory
grep: lapw1*.error: No such file or directory

> stop error
username@computername:~/wiendata/TiC$ cat *.in0
TOT  XC_PB (XC_LDA,XC_PBESOL,XC_WC,XC_MBJ,XC_SCAN)
NR2V  IFFT  (R2V)
   45   45   45    2.00  1 NCON 9  # min IFFT-parameters, enhancement 
factor, iprint, NCON n


The cause of the above error is because during the "gedit TiC.in0" step, 
while viewing the TiC.in0 file, the "E" in "XC_PBE" accidentally got 
removed and saved as "XC_PB".


On 7/19/2023 5:24 PM, Brik Hamida wrote:

Dear,

I installed wien2k_23.2 using this video : 
https://www.youtube.com/watch?v=wXCbK2WuZVw


When I do the run_lapw command in terminal or start SCF cycle , I have 
this problem :

 start  (20 جويلية, 2023 CET 12:13:45 ص) with lapw0 (40/99 to go)

 cycle 1(20 جويلية, 2023 CET 12:13:45 ص) (40/99 to go)

>   lapw0(00:13:45) 0.000u 0.000s 0:00.00 0.0%   0+0k 0+0io 0pf+0w
error: command   /home/hmd/wien2k23/lapw0 lapw0.def   failed

>   stop error


Please can someone help me.Thanks

Best regards
Brik___
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Re: [Wien] System Error....Couldn't write to/.

[Gavin Abo]

For C16H20O7, did you happen to use the cif from [1]?

If so, I suppose you viewed it in xcrysden:

username@computername:~/wiendata/1503927$ ls -l
total 12
-rw-r--r-- 1 username username 10283 Jul 13 23:38 1503927.cif
username@computername:~/wiendata/1503927$ cif2struct 1503927.cif
 T monoclinic
username@computername:~/wiendata/1503927$ xcrysden --wien_struct 
1503927.struct


As you might have read in the mailing list archive such as at [2] and 
[3], you cannot have partial occupancies or overlapping atoms/spheres, 
respectively.


For the overlapping spheres of C seen in xcrysden [4], how did you 
address that?  Did you find and use a structure having different 
structure parameters?  Did you change the structure into a supercell [5,6]?


[1] http://crystallography.net/cod/1503927.html
[2] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg05079.html
[3] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg02997.html
[4] 
https://drive.google.com/file/d/1eJnD8IYS5tlygaFpVBB5ZgYpZOnBvi77/view?usp=drive_link
[5] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg05007.html
[6] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg00226.html


On 7/14/2023 4:59 AM, karina Khan wrote:

Ok I will keep this thing in my mind for future
This command works well with different systems like Cs2AgInBr6, BP but 
not with system having molecular formula C24H72N8In2Br14 and C16H20O7


On Thu, 13 Jul, 2023, 8:34 PM Peter Blaha,  
wrote:


I cannot reproduce this. It works perfectly fine with me.

Please try again in another case. Or use the recommended fast
mode. This will set automatically good parameters in case.in0/1/2
and klist, and not the "stupid" defaults of the step by step
initialization.

PS: You cannot send large images to the mailing list. There is a
limit of 40 kB per message.


Am 13.07.2023 um 11:48 schrieb karina Khan:

Dear Wien2k users,
                       During initialisation, I stuck up in the
step *view case.outpd and cp case.in0_std case.in0, *when I click
on the step save and initlapw, I get a *System Error couldn't
write to/. * back to last page.
However this step is working for the other sample but not for
this new sample having 32 atoms.
Looking for your suggestions
*Thanks & Regards*
*Karina Khan*


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-- 
---

Peter Blaha,  Inst. f. Materials Chemistry, TU Vienna, A-1060 Vienna
Phone: +43-158801165300
Email:peter.bl...@tuwien.ac.at   
WWW:http://www.imc.tuwien.ac.at   WIEN2k:http://www.wien2k.at

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Re: [Wien] some error occur during scf calculation

[Gavin Abo]

/home/shruti/wien2k/lapw0: Command not found. <= As your error message 
says, it cannot find the lapw0 file in your directory /home/shruti/wien2k.


Run siteconfig again and check if it compiled correctly.  It looks like 
the following on my system with WIEN2k 23.2, but it should look similar 
on your computer:


username@computername:~$ cd $WIENROOT
username@computername:~/WIEN2k$ ls -l lapw0
ls: cannot access 'lapw0': No such file or directory <= This means the 
lapw0 file does not exist yet.

username@computername:~/WIEN2k$ ./siteconfig
...
  Selection: R
...
 Selection: S
   Which program to recompile? lapw0
...
ifort -o ./lapw0 cputim.o modules.o libxc_mod.o W2kinit.o fft_modules.o 
reallocate.o acggac.o ainv.o ak13.o am05_xscss.o b88.o br89.o brj.o 
cap.o charge.o chfac.o chslv.o corgga.o corpbe_revtpss.o corpbe_tpss.o 
cub_xc_back.o corlsd.o dergl.o dfxhpbe.o dfxrevtpss.o dfxtpss.o dfundr.o 
dylm.o efg.o energy.o epot1.o eramps.o errclr.o errflg.o ev92.o ev92ex.o 
exch.o fxhpbe.o fx_revtpss.o fx_tpss.o gbass.o gbj.o gcor.o getff1.o 
getfft.o gpoint.o gpointL.o gpointm.o grans.o gtfnam.o hcthc.o hcthx.o 
hjs.o htbs.o id_func_get.o ifflim.o inputpars.o kcis.o lapw0.o latgen.o 
lb94.o libxc.o lyp.o mbeefx.o mgga_ms.o multfc.o multsu.o mvsx.o 
optb86b.o optb88.o outerr.o pbea.o pbec.o pbeint.o pbex.o poissn.o 
potfac.o pwxad4.o pwxad5.o readstruct.o rean_direct_fft.o rean0.o 
rean3.o rean4.o rge2.o rhopw.o rotate.o rotdef.o rpbe.o rscanc.o 
rscanx.o r2scanc.o r2scanx.o scanc.o scanx.o setff0.o setff1.o setfft.o 
setff2.o sortag.o sg4c.o sg4x.o sicpbe.o sicpbe_revtpss.o sicpbe_tm.o 
sicpbe_tpss.o sphbes.o spline.o srolyl.o stern.o sumfac.o suml.o 
SymmRot.o tmx.o vpw91.o vresp.o vs98.o vwn5.o vxclm2.o vxcpw2.o 
vx_screened.o wc05.o workf1.o W2kutils.o xcener.o xcpot.o xcpot1.o 
xcpot1Q.o xcpot3.o ykav.o ylm.o coulint.o c_alpha_m.o gaunt.o notri.o 
t3j0.o t3j.o ph.o finl_elect_str.o kahan_summ_gxyz.o stress_gga.o -O -FR 
-mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -traceback -assume 
buffered_io -I/opt/intel/oneapi/mkl/2022.1.0/include  -DFFTW3 
-I/home/username/fftw-3.3.10/include  -qopenmp 
-L/opt/intel/oneapi/mkl/2022.1.0/lib/ -lpthread -lm -ldl -liomp5 
-L/home/username/fftw-3.3.10/lib -lfftw3  -lmkl_intel_lp64 
-lmkl_intel_thread -lmkl_core

make[1]: Leaving directory '/home/username/WIEN2k/SRC_lapw0'
if [ -f /include/xc_funcs.h ]; then cp /include/xc_funcs.h .; fi
make: *** No rule to make target 'complex'.  Stop.
Copying programs
  SRC_lapw0/lapw0
  SRC_lapw0/lapw0_mpi

done.

Compile time errors (if any) were:
grep: No match. <= You should get this message or it should be blank if 
it compiled lapw0 without errors.  Else, you should get a error message 
here it if failed that you will have to resolve.

grep: No match.


Check file   compile.msg   in the corresponding SRC_* directory for the
compilation log and more info on any compilation problem.

 Press RETURN to continue
...
  Selection: Q
username@computername:~/WIEN2k$ ls -l lapw0
-rwxrwxr-x 1 username username 4457752 Jul 13 22:58 lapw0 <= If 
successful, you should know have a lapw0 file that was generated by 
siteconfig.


Kind Regards,

Gavin
WIEN2k user

On 7/13/2023 10:25 PM, Rao Shruti Arya wrote:

Respected sir
when i do scf calculation then following error comes out
>   stop error

grep: lapw1*.error: No such file or directory
grep: lapw1*.error: No such file or directory
grep: lapw2*.error: No such file or directory
grep: lapw2*.error: No such file or directory
grep: lapw2*.error: No such file or directory
grep: lapw2*.error: No such file or directory
grep: lapw2*.error: No such file or directory
grep: lapw2*.error: No such file or directory
grep: *scf1*: No such file or directory
/home/shruti/wien2k/lapw0: Command not found.___
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Re: [Wien] WARNING elpa_setup during lapw1_mpi

[Gavin Abo]

That might be an issue worth asking about over in the Spack Community [1].


Not sure if I'm interpreting the message correctly, but if I am, the 
"@1.5.4:2" in the message from spack info I believe is indicating that 
thread_multiple will be disabled unless OpenMPI version 1.5.4 [2] to 2 
[3] is being used.



In the Spack source code of its current latest version 0.20.0 [4], the 
openmpi/package.py file has on lines 662-668:



 # thread_multiple
    if version in spack.version.ver("1.5.4:2"):
    match = re.search(r"MPI_THREAD_MULTIPLE: (\S+?),?", output)
    if match and is_enabled(match.group(1)):
    variants.append("+thread_multiple")
    else:
    variants.append("~thread_multiple")


Since you are using OpenMPI 4.1.5, I suspect line 663 might need changed 
for example to "if version in spack.version.ver("1.5.4:4.1.5"):".  
Perhaps there are other changes a Spark developer would know about that 
might also be needed for the MPI_THREAD_MULTIPLE to work with Spack when 
using OpenMPI 4.1.5.



[1] https://github.com/spack/spack/blob/develop/README.md#community

[2] https://www.open-mpi.org/software/ompi/v1.5/

[3] https://www.open-mpi.org/software/ompi/v2.0/

[4] 
https://github.com/spack/spack/blob/v0.20.0/var/spack/repos/builtin/packages/openmpi/package.py



Gavin

WIEN2k user


On 7/4/2023 11:59 AM, Ilias, Miroslav wrote:


Hello,


sorry for hidden link;


the point is that  the "|ompi_info -a | grep THREAD|" says 
|MPI_THREAD_MULTIPLE: yes|,



but  "spack info openmpi@4.1.5" gives "thread_multiple [off] 
[@1.5.4:2] on, off Enable MPI_THREAD_MULTIPLE support"



Maybe this is the case of the ELPA  "WARNING elpa_setup: MPI threading 
level MPI_THREAD_SERALIZED or MPI_THREAD_MULTIPLE required but your 
implementation does not support this! The number of OpenMP threads 
within ELPA will be limited to 1"



I will investigate it deeper, as I need Wien2k parallel as fast as 
possible.


Intel MPI will come later, again, I need ELPA built with Intel. I 
guess that IntelMPI+MKL  Wien2k is faster than OpenMPI+Openblas ?


Best, Miro


*From:* Wien  on behalf of 
Laurence Marks 

*Sent:* 04 July 2023 18:02
*To:* A Mailing list for WIEN2k users
*Subject:* Re: [Wien] WARNING elpa_setup during lapw1_mpi
That is a private site, do I cannot read anything.

All I can suggest is doing a Google search on "missing  
MPI_THREAD_MULTIPLE". It looks as if you have to enable this in 
openmpi configure, although there might be some bugs. There could also 
be some environmental parameters that need to be set.


Or use Intel mpi. While it does not have everything that some sysadmin 
want, if you are using mkl & ifort (both free) it integrates 
trivially. I personally dislike openmpi as it keeps changing and is 
not always user friendly.


--
Professor Laurence Marks (Laurie)
Department of Materials Science and Engineering, Northwestern University
www.numis.northwestern.edu 
"Research is to see what everybody else has seen, and to think what 
nobody else has thought" Albert Szent-Györgyi


On Tue, Jul 4, 2023, 09:33 Ilias, Miroslav  wrote:

Dear Professor Marks,


concerning
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg22621.html  
:



I am trying to find out why is ELPA module complaining of missing
MPI_THREAD_MULTIPLE .


We have a debate on this
https://git.gsi.de/SDEGroup/SIR/-/issues/85#note_55392


If you somebody could comment on this topic as I would like to
investigate deeply. Can somebody advice me a short ELPA testing
program for this ?


Best, Miro








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Re: [Wien] hf error -monolayer

[Gavin Abo]

When installing WIEN2k 23.2, what were the issue(s) or error 
message(s)?  Would need to know that to try to help.


If installing using the ifort compiler, the pdf might help that should 
be at:


https://github.com/gsabo/WIEN2k-Docs/blob/main/WIEN2k23.2_Ubuntu22.04_Install_with_OneAPI(ifort).pdf

IF installing using the gfortran compiler, the pdf might help that 
should be at:


https://github.com/gsabo/WIEN2k-Docs/blob/main/WIEN2k23.2_Ubuntu22.04_Install_with_gfortran.pdf

The WIEN2k 23.1 usersguide (which is the same usersguide used for WIEN2k 
23.2) can also be used as a reference for installation:


http://www.wien2k.at/reg_user/textbooks/usersguide.pdf

Kind Regards,
Gavin
WIEN2k user


On 6/24/2023 2:10 PM, Brik Hamida wrote:

I m using wien2k_18.2.

I tried to install Wien2k_23 but in vain

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Re: [Wien] hf error -monolayer

[Gavin Abo]

In your post at [1], I don't see it labeled as your case.dayfile, but I 
believe that is what it is.  There I see lapw0, lapw1, lapw2, lcore, hf  
-mode1 -redklist, and


error: command   /home/hmd/wien18/hf hf.def   failed

The wien18 in the path.  Does that mean you are using either WIEN2k 18.1 
or 18.2?


As you know from the WIEN2k updates page [2], there have been bug fixes 
and improvements made to WIEN2k.  For example, changes in source code 
have been made to lapw0 corresponding to SRC_lapw0 and to hf (SRC_hf and 
run_kgenhf_lapw).


Have you tried the calculation using the latest WIEN2k version to check 
that the problem is not just caused by a bug in the old version?


Also, I don't recall if you posted about your standard output for the 
calculation.  As sometimes error messages are printed in the standard 
output.  If using a terminal, the standard output is displayed there.  
In w2web, I think there was a link that had to be clicked on to view it 
but I don't recall the name of the link. If using a computer system with 
a job scheduler, the error messages are often times written to a 
standard error log.


[1] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg22594.html

[2] http://susi.theochem.tuwien.ac.at/reg_user/updates/

Kind Regards,

Gavin
WIEN2k user

On 6/22/2023 12:02 PM, Brik Hamida wrote:

Dears,

*1) All files you indicated are already generated.:* case.klist_fbz, 
case.klist_ibz, case.kgen_ibz and case.outputkgenhf

*
*
*2) For the number of 'nbands' : I set nband_occ +1.*
For my case , I set : 14   ( I also tried with 16 or 17 , the error 
still).

  Insulator, EF-inconsistency corrected
:GAP (global)   :  0.157470 Ry = 2.142 eV (accurate value if proper k-mesh)
  Bandranges (emin - emax) and occupancy:
:BAN3:   3   -2.835841   -2.824643  2.
:BAN4:   4   -2.833211   -2.824643  2.
:BAN5:   5   -1.280319   -1.145577  2.
:BAN6:   6   -1.185292   -1.129622  2.
:BAN7:   7   -0.668293   -0.611429  2.
:BAN8:   8   -0.605711   -0.438976  2.
:BAN9:   9   -0.544477   -0.438976  2.
:BAN00010:  10   -0.482979   -0.376093  2.
:BAN00011:  11   -0.459595   -0.359116  2.
:BAN00012:  12   -0.367030   -0.320697  2.
:BAN00013:  13   -0.299789   -0.246051  2.
:BAN00014:  14   -0.088581   -0.045169  0.
:BAN00015:  15   -0.075909   -0.042077  0.
:BAN00016:  16   -0.0349310.036604  0.
:BAN00017:  17   -0.0280400.089279  0.
:BAN00018:  180.1483860.303402  0.
 Energy to separate low and high energystates:   -0.71829

:NOE  : NUMBER OF ELECTRONS  =  26.000

:FER  : F E R M I - ENERGY(TETRAH.M.)=  -0.2460508540
:GMA  : POTENTIAL AND CHARGE CUT-OFF  12.00 Ry**.5

*3) For case.inhf  is the following : ( I also tried with alpha equal 
to 0.2  and increase gmax but error still)

*
*
*
0.25         alpha
T            screened (T) or unscreened (F)
0.165        lambda
14          nband
6            gmax
3            lmaxe
3            lmaxv
1d-3         tolu
*
*
*
*
*4)  the content of   hf.error  :  error in hf (only this message is 
written in hf.error file) *___
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Re: [Wien] ** testerror: Error in Parallel LAPW

[Gavin Abo]

The "Host key verification failed" is an error from ssh [1].


Thus, it seems like you need to fix your ssh so that WIEN2k can connect 
to your remote node (in your case below, it looks like the remote node 
is lxbk1177).



It looks like there is an ssh example on slide 10 of the WIEN2k 
presentation at [2].



I believe it is common to use ssh-keygen to create a key pair (private 
and public key) on the head node and then use ssh-copy-id to put the 
public key on each of the remote nodes.  However, ssh can be uniquely 
configured for a computer system.  So, you might want to search online 
for different examples on how ssh has been configured.  One example that 
might be helpful should be at [3].



[1] 
https://askubuntu.com/questions/45679/ssh-connection-problem-with-host-key-verification-failed-error


[2] 
https://www.bc.edu/content/dam/bc1/schools/mcas/physics/pdf/wien2k/PB-installation.pdf


[3] 
https://www.digitalocean.com/community/tutorials/ssh-essentials-working-with-ssh-servers-clients-and-keys



Kind Regards,

Gavin

WIEN2k user


On 6/20/2023 3:25 PM, Ilias Miroslav, doc. RNDr., PhD. wrote:

Dear Professor Blaha,

thanks, I used PATH variable extension instead of linking;

it  crashed with the message  "Host key verification failed. "

Herethe content of file 
/lustre/ukt/milias/scratch/Wien2k_23.2_job.main.N1.n4.jid3009460/LvO2onQg/.machines:

1:lxbk1177
1:lxbk1177
1:lxbk1177
1:lxbk1177
1:lxbk1177
1:lxbk1177
1:lxbk1177
1:lxbk1177

Job is running on lxbk1177, with 8 cpus allocated;

and this is from log :

running x dstart :
starting parallel dstart at Tue 20 Jun 2023 05:16:21 PM CEST
 .machine0 : processors
running dstart in single mode
STOP DSTART ENDS
10.249u 0.322s 0:11.19 94.3%    0+0k 158496+101160io 437pf+0w

running 'run_lapw -p -ec 0.0001 -NI'
STOP  LAPW0 END
Host key verification failed.
[1]  + Done  ( ( $remote $machine[$p] "cd 
$PWD;$set_OMP_NUM_THREADS;$t $taskset0 $exe ${def}_$loop.def ;fixerr
or_lapw ${def}_$loop"; rm -f .lock_$lockfile[$p] ) >& .stdout1_$loop; 
if ( -f .stdout1_$loop ) bashtime2csh.pl_lapw .stdout1_$loop > .
temp1_$loop; grep \% .temp1_$loop >> .time1_$loop; grep -v \% 
.temp1_$loop | perl -e "print stderr " )

Host key verification failed.
[1]  + Done  ( ( $remote $machine[$p] "cd 
$PWD;$set_OMP_NUM_THREADS;$t $taskset0 $exe ${def}_$loop.def 
;fixerror_lapw ${def}_$loop"; rm -f .lock_$lockfile[$p] ) >& .stdo
ut1_$loop; if ( -f .stdout1_$loop ) bashtime2csh.pl_lapw 
.stdout1_$loop > .temp1_$loop; grep \% .temp1_$loop >> .time1_$loop; 
grep -v \% .temp1_$loop | perl -e "print stderr " )

Host key verification failed.
[1]  + Done  ( ( $remote $machine[$p] "cd 
$PWD;$set_OMP_NUM_THREADS;$t $taskset0 $exe ${def}_$loop.def 
;fixerror_lapw ${def}_$loop"; rm -f .lock_$lockfile[$p] ) >& .stdo
ut1_$loop; if ( -f .stdout1_$loop ) bashtime2csh.pl_lapw 
.stdout1_$loop > .temp1_$loop; grep \% .temp1_$loop >> .time1_$loop; 
grep -v \% .temp1_$loop | perl -e "print stderr " )

Host key verification failed.
[1]  + Done  ( ( $remote $machine[$p] "cd 
$PWD;$set_OMP_NUM_THREADS;$t $taskset0 $exe ${def}_$loop.def 
;fixerror_lapw ${def}_$loop"; rm -f .lock_$lockfile[$p] ) >& .stdo
ut1_$loop; if ( -f .stdout1_$loop ) bashtime2csh.pl_lapw 
.stdout1_$loop > .temp1_$loop; grep \% .temp1_$loop >> .time1_$loop; 
grep -v \% .temp1_$loop | perl -e "print stderr " )

Host key verification failed.
[1]  + Done  ( ( $remote $machine[$p] "cd 
$PWD;$set_OMP_NUM_THREADS;$t $taskset0 $exe ${def}_$loop.def 
;fixerror_lapw ${def}_$loop"; rm -f .lock_$lockfile[$p] ) >& .stdo
ut1_$loop; if ( -f .stdout1_$loop ) bashtime2csh.pl_lapw 
.stdout1_$loop > .temp1_$loop; grep \% .temp1_$loop >> .time1_$loop; 
grep -v \% .temp1_$loop | perl -e "print stderr " )

Host key verification failed.
[1]  + Done  ( ( $remote $machine[$p] "cd 
$PWD;$set_OMP_NUM_THREADS;$t $taskset0 $exe ${def}_$loop.def 
;fixerror_lapw ${def}_$loop"; rm -f .lock_$lockfile[$p] ) >& .stdo
ut1_$loop; if ( -f .stdout1_$loop ) bashtime2csh.pl_lapw 
.stdout1_$loop > .temp1_$loop; grep \% .temp1_$loop >> .time1_$loop; 
grep -v \% .temp1_$loop | perl -e "print stderr " )

Host key verification failed.
[1]  + Done  ( ( $remote $machine[$p] "cd 
$PWD;$set_OMP_NUM_THREADS;$t $taskset0 $exe ${def}_$loop.def 
;fixerror_lapw ${def}_$loop"; rm -f .lock_$lockfile[$p] ) >& .stdo
ut1_$loop; if ( -f .stdout1_$loop ) bashtime2csh.pl_lapw 
.stdout1_$loop > .temp1_$loop; grep \% .temp1_$loop >> .time1_$loop; 
grep -v \% .temp1_$loop | perl -e "print stderr " )

Host key verification failed.
[1]    Done  ( ( $remote $machine[$p] "cd 
$PWD;$set_OMP_NUM_THREADS;$t $taskset0 $exe ${def}_$loop.def 
;fixerror_lapw ${def}_$loop"; rm -f .lock_$lockfile[$p] ) >& .stdo
ut1_$loop; if ( -f .stdout1_$loop ) bashtime2csh.pl_lapw 
.stdout1_$loop > .temp1_$loop; grep \% 

Re: [Wien] FFTW compiling

[Gavin Abo]

I don't think you can use libfftw3_threads.a.


For libfftw3_mpi.a, you need to get FFTW 3.3.10 at [1] and build it.  
During building it, the --enable-mpi flag [2] must be used during the 
configure step for being able to get libfftw3_mpi.a.



I'm not sure, but it might also be possible to get libfftw3_mpi.a by 
installing an operating system package as an alternative solution. 
However, it seems like you would need to choose the correct package 
based on the mpi version that your are using.  For Intel MPI, it might 
be the fftw334-gcc-impi-devel package [3] that is needed.  For OpenMPI, 
it might be the fftw-openmpi-devel package [4] that is needed.



However, as you know from [5], the mpi is not needed on a single 
computer and becomes useful if you are installing on a HPC (high 
performance computing) cluster.  Since clusters are unique and complex, 
typically a user does not install FFTW on their own. They usually have 
to talk to the cluster administrator that was hired with specialized 
training who can setup the fftw to work with the mpi flavor installed on 
the cluster server as well as have it play nicely with the queue system 
(such as slurm [6]) installed.  The queue system also needs job scripts 
[7] for running the WIEN2k calculations.  The cluster administrator or 
help desk should have instructions on how to access the needed fftw 
version (which can be loading of a particular module; for example, like 
the "module load" that should be seen at [8]).



[1] https://www.fftw.org/download.html

[2] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg20507.html


[3] 
https://rhel.pkgs.org/7/springdale-computational-x86_64/fftw334-gcc-impi-devel-3.3.4-5.sdl7.x86_64.rpm.html


[4] 
https://rhel.pkgs.org/8/okey-x86_64/fftw-openmpi-devel-3.3.5-11.el8.x86_64.rpm.html


[5] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg22427.html


[6] https://en.wikipedia.org/wiki/Slurm_Workload_Manager

[7] http://susi.theochem.tuwien.ac.at/reg_user/faq/pbs.html

[8] https://wiki.cse.ucdavis.edu/support/hpc/software/wien2k


Kind Regards,

Gavin

WIEN2k user


On 6/4/2023 7:31 AM, Ilias Miroslav, doc. RNDr., PhD. wrote:

Hello,

ad: 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18799.html


I have CentOS 7, but the elpa rpm packages do not contain the 
libfftw3_mpi.a file,  only /usr/lib64/libfftw3_threads.a


Can the libfftw3_threads.a  file  be instead of libfftw3_mpi.a ?

Miro


PS:  List of all fftw library files:
ls /usr/lib64/libfftw*
/usr/lib64/libfftw.a /usr/lib64/libfftw3_omp.so.3.3.2* 
 /usr/lib64/libfftw3f_omp.so.3@    /usr/lib64/libfftw3l_omp.so@
/usr/lib64/libfftw.so@   /usr/lib64/libfftw3_threads.a   
 /usr/lib64/libfftw3f_omp.so.3.3.2*  /usr/lib64/libfftw3l_omp.so.3@
/usr/lib64/libfftw.so.2@ /usr/lib64/libfftw3_threads.so@ 
 /usr/lib64/libfftw3f_threads.a    /usr/lib64/libfftw3l_omp.so.3.3.2*
/usr/lib64/libfftw.so.2.0.7* /usr/lib64/libfftw3_threads.so.3@ 
 /usr/lib64/libfftw3f_threads.so@    /usr/lib64/libfftw3l_threads.a
/usr/lib64/libfftw3.a    /usr/lib64/libfftw3_threads.so.3.3.2* 
 /usr/lib64/libfftw3f_threads.so.3@  /usr/lib64/libfftw3l_threads.so@
/usr/lib64/libfftw3.so@  /usr/lib64/libfftw3f.a    
 /usr/lib64/libfftw3f_threads.so.3.3.2* 
 /usr/lib64/libfftw3l_threads.so.3@
/usr/lib64/libfftw3.so.3@  /usr/lib64/libfftw3f.so@    
 /usr/lib64/libfftw3l.a  /usr/lib64/libfftw3l_threads.so.3.3.2*
/usr/lib64/libfftw3.so.3.3.2*  /usr/lib64/libfftw3f.so.3@    
 /usr/lib64/libfftw3l.so@  /usr/lib64/libfftw_threads.a
/usr/lib64/libfftw3_omp.a  /usr/lib64/libfftw3f.so.3.3.2*  
 /usr/lib64/libfftw3l.so.3@  /usr/lib64/libfftw_threads.so@
/usr/lib64/libfftw3_omp.so@  /usr/lib64/libfftw3f_omp.a    
 /usr/lib64/libfftw3l.so.3.3.2*    /usr/lib64/libfftw_threads.so.2@
/usr/lib64/libfftw3_omp.so.3@  /usr/lib64/libfftw3f_omp.so@  
 /usr/lib64/libfftw3l_omp.a  /usr/lib64/libfftw_threads.so.2.0.7*



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Re: [Wien] Issues with ifort and MKL while installing on Red Hat

[Gavin Abo]

Not sure if it helps or not:

I saw that you said you used setvars.sh.  I might have missed it, but 
did you also say you used "setvars.h intel64" like what is shown on page 
3 in:


https://github.com/gsabo/WIEN2k-Docs/blob/main/WIEN2k23.2_Ubuntu22.04_Install_with_OneAPI(ifort).pdf

I think the default gfortran settings may have worked with old version 
of that compiler, but I believe I had to adjust them to work with more 
recent compilers.  Perhaps the same setting I used in Ubuntu will also 
work in RHEL.  See:


https://github.com/gsabo/WIEN2k-Docs/blob/main/WIEN2k23.2_Ubuntu22.04_Install_with_gfortran.pdf

With RHEL, I suspect the main different might be having to install 
operating system packages with yum instead of the apt that Ubuntu uses.


Kind Regards,

Gavin
WIEN2k user

On 6/2/2023 5:43 PM, Brandon Gunn via Wien wrote:

Hi Laurence,

Thank you for your response, the gfortran route sounds promising. When 
I run ./siteconfig_lapw, I do select the LG gfortran+gcc+OpenBlas 
option and, on the following prompts, I do set the compilers to 
gfortran and gcc, which led to the errors I posted. Do I need to 
manually change to gfortran via a text editor and, if so, do I need to 
modify siteconfig or siteconfig_lapw?


Thank you,
Brandon

On Fri, Jun 2, 2023 at 1:51 PM Laurence Marks 
 wrote:


Your last problem is easy: you need to change in site_config to
use gfortran, as all the compiler options are different.

It is hard to know exactly what the earlier issues are, beyond
that your PATH variable is being messed up. All I wonder is
whether $MKLPATH, $MKLROOT etc were properly sourced/set before
you run site_config, they probably were not. For certain this is
not a Wien2k problem, it is something in your OS/configuration, sorry.

On Fri, Jun 2, 2023 at 3:25 PM Brandon Gunn via Wien
 wrote:

Also, if I try to install using gfortran + gcc, it gives
errors like this when compiling:

rm  -f *.o *.list *.prj ../libblas_lapw.a
gfortran -c  -O -FR -mp1 -w -prec_div -pc80 -pad -ip
-DINTEL_VML -traceback -assume buffered_io -I/include blas_lapw1.f
gfortran: error: unrecognized command-line option ‘-assume’
make: *** [Makefile:86: ../libblas_lapw.a(blas_lapw1.o)] Error 1
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-- 
Professor Laurence Marks (Laurie)

Department of Materials Science and Engineering
Northwestern University
www.numis.northwestern.edu


"Research is to see what everybody else has seen, and to think
what nobody else has thought", Albert Szent-Györgyi
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Re: [Wien] Install boltztrap1.2.5

[Gavin Abo]

That is a question that should be asked in the BoltzTraP Google group [1].

[1] https://groups.google.com/forum/#!forum/boltztrap

On 6/1/2023 10:39 PM, عبدالرزاق خيرالدين wrote:
Hi, I trying to install boltztrap, but I get an error: "make: *** 
[makefile: 72: gmlib2.o] error 127" when using ifort with gedit 
makefile "FC = ifort" and:
"make: *** [makefile: 42: c3fft.o] error 1" when using gfortran with 
gedit makefile "FC = gfortran". Please, I need help.

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Re: [Wien] relinking the code, keeping compiled object files

[Gavin Abo]

Yes, you may link to the 2 documents.


Yeah, I use those installation steps to get me quickly up and running, 
but I do run siteconfig again to make adjustments as needed whether that 
be adjusting NMATMAX per the "Site configuration for WIEN2k" of the 
WIEN2k usersguide, for linking in ELPA, adjusting the mpi remote 
configuration, and so on.



[1] http://susi.theochem.tuwien.ac.at/reg_user/textbooks/usersguide.pdf


Gavin

WIEN2k user


On 5/30/2023 3:23 AM, Peter Blaha wrote:


Dear Gavin

Thank you very much for the detailed istallation descriptions. It 
should be very useful for new users.


If you allow, I'll make a link at the installation page to these 2 
documents.



I've only one comment: You also installed the mpi version of the code 
but you did not install ELPA.


Without ELPA the lapw1mpi code is quite slow and thus of limited use.


I very much recommend to install ELPA if you want also the mpi version 
of the code. Note, that this mpi-compilation is only useful if you 
have a cluster with infiniband network or at least a very powerful 
multicore workstation (probably min 16 cores).



Best regards

Peter Blaha


Am 28.05.2023 um 20:10 schrieb Gavin Abo:


I was able to compile and link without any build errors a fresh 
install of WIEN2k 23.2 using gfortran 11.3.0 in Ubuntu 22.04.2 LTS 
today.  Should it be of interest to anyone installing the 23.2 
version of WIEN2k, the PDF in which I recorded the steps should be at:



https://github.com/gsabo/WIEN2k-Docs/blob/main/WIEN2k23.2_Ubuntu22.04_Install_with_gfortran.pdf


Kind Regards,

Gavin

WIEN2k user


On 5/28/2023 9:57 AM, Ilias Miroslav, doc. RNDr., PhD. wrote:

Hello,

after lenghty compilation of Wien2k the linking step crashed. It 
there a quick way just to fix the linking command and relink the 
code for getting final executables ?


Wien2k setup offers only recompilation of the whole bunch, without 
checking if files were previously compiled.


Best, Miro


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Email:peter.bl...@tuwien.ac.at   
WWW:http://www.imc.tuwien.ac.at   WIEN2k:http://www.wien2k.at

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Re: [Wien] Installation of wien2k in compact clusters.

[Gavin Abo]

I installed OneAPI (ifort 2021.9.0) on a computer today.  With it, I was 
able to compile and link without any build errors a fresh install of 
WIEN2k 23.2 in Ubuntu 22.04.2 LTS.


The installation seemed simpler with OneAPI as it took me 11 steps 
instead of the 14 it took me with gfortran.


Should it be of interest to anyone installing the 23.2 version of WIEN2k 
with OneAPI, the PDF in which I recorded the steps should be at:


https://github.com/gsabo/WIEN2k-Docs/blob/main/WIEN2k23.2_Ubuntu22.04_Install_with_OneAPI(ifort).pdf

If interested in knowing the installation differences between OneAPI and 
gfortran, you may compare the OneAPI steps with those for gfortran.  The 
link to gfortran PDF is in the past post at:


https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg22450.html

Kind Regards,

Gavin
WIEN2k user

On 5/29/2023 11:59 AM, Gavin Abo wrote:


OneAPI likely can still be installed following the post at:

https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg21942.html

Looks like someone made a WIEN2k 23.2 install YouTube video here:

https://youtu.be/_Gms-iie3Jo

Since there is too many remote access (ssh, VPN) programs, I cannot 
help with that as usage of each of them are different.  I suggest you 
talk to your IT department at your organization as each organization 
usually should have webpages with usage information, program 
documentation for the particular cluster computer being used, and/or a 
help desk that assists with usage.


Kind Regards,

Gavin
WIEN2k user

On 5/29/2023 4:09 AM, Burhan Ahmed wrote:


Dear experts, I am having a compact cluster with 100gb RAM, 36 cores 
and 12 TB SATA hard disk. I want to install wien2k_23.1 version in my 
system with intel oneapi compiler, such that I can do the parallel 
calculation and also can do the remote access from outside the lab. 
Is there any installation tutorial available ( video will be helpful) 
apart from the wien2k user guide one.


Regards

Burhan Ahmed

*Research Scholar, AUS *
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Re: [Wien] Installation of wien2k in compact clusters.

[Gavin Abo]

OneAPI likely can still be installed following the post at:

https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg21942.html

Looks like someone made a WIEN2k 23.2 install YouTube video here:

https://youtu.be/_Gms-iie3Jo

Since there is too many remote access (ssh, VPN) programs, I cannot help 
with that as usage of each of them are different.  I suggest you talk to 
your IT department at your organization as each organization usually 
should have webpages with usage information, program documentation for 
the particular cluster computer being used, and/or a help desk that 
assists with usage.


Kind Regards,

Gavin
WIEN2k user

On 5/29/2023 4:09 AM, Burhan Ahmed wrote:


Dear experts, I am having a compact cluster with 100gb RAM, 36 cores 
and 12 TB SATA hard disk. I want to install wien2k_23.1 version in my 
system with intel oneapi compiler, such that I can do the parallel 
calculation and also can do the remote access from outside the lab. Is 
there any installation tutorial available ( video will be helpful) 
apart from the wien2k user guide one.


Regards

Burhan Ahmed

*Research Scholar, AUS *
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Re: [Wien] relinking the code, keeping compiled object files

[Gavin Abo]

I was able to compile and link without any build errors a fresh install 
of WIEN2k 23.2 using gfortran 11.3.0 in Ubuntu 22.04.2 LTS today.  
Should it be of interest to anyone installing the 23.2 version of 
WIEN2k, the PDF in which I recorded the steps should be at:



https://github.com/gsabo/WIEN2k-Docs/blob/main/WIEN2k23.2_Ubuntu22.04_Install_with_gfortran.pdf


Kind Regards,

Gavin

WIEN2k user


On 5/28/2023 9:57 AM, Ilias Miroslav, doc. RNDr., PhD. wrote:

Hello,

after lenghty compilation of Wien2k the linking step crashed. It there 
a quick way just to fix the linking command and relink the code for 
getting final executables ?


Wien2k setup offers only recompilation of the whole bunch, without 
checking if files were previously compiled.


Best, Miro___
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Re: [Wien] relinking the code, keeping compiled object files

[Gavin Abo]

Is it just a few of the modules that have failed to build?  If so, in 
siteconfig, you can recompile individual packages.



Kind Regards,

Gavin

WIEN2k user


On 5/28/2023 9:57 AM, Ilias Miroslav, doc. RNDr., PhD. wrote:

Hello,

after lenghty compilation of Wien2k the linking step crashed. It there 
a quick way just to fix the linking command and relink the code for 
getting final executables ?


Wien2k setup offers only recompilation of the whole bunch, without 
checking if files were previously compiled.


Best, Miro___
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Re: [Wien] problem in uploading cif file

[Gavin Abo]

Have you tried installing the perl CGI package?

For example,

Fedora [1]: yum install perl-CGI

Ubuntu [2]: sudo apt install libcgi-pm-perl

[1] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg09575.html


[2] https://finisky.github.io/2020/09/01/perlcgi.en/

On 5/18/2023 11:38 PM, Neetu Malik wrote:
Dear team, when i try to upload cif file for structure generation, 
getting this error. Can you please tell me anything need to get 
installed.Thankyou

Can't locate CGI.pm in @INC (you may need to install the CGI module) (@INC contains: 
/etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.34.0 /usr/local/share/perl/5.34.0 
/usr/lib/x86_64-linux-gnu/perl5/5.34 /usr/share/perl5 
/usr/lib/x86_64-linux-gnu/perl-base /usr/lib/x86_64-linux-gnu/perl/5.34 
/usr/share/perl/5.34 /usr/local/lib/site_perl) at 
/home/neetu/Desktop/wien/SRC_w2web/htdocs/util/upload2.pl    
line 3.
BEGIN failed--compilation aborted at 
/home/neetu/Desktop/wien/SRC_w2web/htdocs/util/upload2.pl    
line 3.
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Re: [Wien] Problem running fold2bloch interface with wien2k_17

[Gavin Abo]

Dear Oleg,

The tutorial 1 at:

https://github.com/rubel75/fold2Bloch-Wien2k/wiki/Tutorial-1:-Lattice-of-Hydrogen-atoms

It has:

~/fold2Bloch/fold2Bloch -c 6-atom2D.vector "''1 0 0:0 2 0:0 0 3''"

Cannot remember for sure but that might not have worked starting with 
(double quote)(single quote)(single quote).  I think it needed to be 
(double quote)(single quote).  Similarly ending with (single 
quote)(double quote).


The ubs_dot.m link seems to be broken pointing to:

https://github.com/rubel75/fold2Bloch/blob/master/Utils/ubs_dots.m

The working link now appears to be:

https://github.com/rubel75/fold2Bloch-Wien2k/blob/master/utils/ubs_dots.m

It might just be me, but instead of the matlab script, I like using the 
octave script at:


https://github.com/rubel75/fold2Bloch-Wien2k/blob/master/utils/ubs_dots_w2k_octave.m

However, if I recall correctly, the script failed to run right.

The ubs_dots.m has line 43:

roundOffErrK = 0.01; % this is the round off error 1/3 = 0.33 + err

and it has lines 70-72:

epsk = [roundOffErrK roundOffErrK roundOffErrK]; % k rounding error
epsk = coordTransform(epsk,G); % transform to Cart. coords
epsk = sqrt(dot(epsk,epsk)); % get magnitude of the vector

I believe I had to add line 43 after line 54 and lines 70-72 between 
lines 72 and 73 in the current ubs_dots_w2k_octave.m for it to work.


Regarding Tutorial 2 at:

https://github.com/rubel75/fold2Bloch-Wien2k/wiki/Tutorial-2:-Bismuth-in-GaAs

It has:

~/fold2Bloch/fold2Bloch -c Ga8As7Bi1.vector 2:2:2

According to your post below, that needs to be:

~/fold2Bloch/fold2Bloch -c 6-atom2D.vector "'2 0 0:0 2 0:0 0 2'"

The link to ubs_dot.m for Ga8As7Bi1.unfolded for reproducing the 
tutorial 2 plot seems to be broken (for me it leads me to a github page 
with a 404  error).


Thanks,

Gavin
WIEN2k user

On 4/18/2023 11:16 AM, Rubel, Oleg wrote:

Dear Dibya,

thanks for sharing the error. It is a nice case when the error message is 
helpful and tells you exactly what went wrong and how to fix (please read) 

The input arguments were changed (around Aug 2022) to accommodate a full 3x3 
transformation matrix P (not just multipliers for each lattice vector). Your matrix will, 
probably, be "'2 0 0:0 2 0:0 0 2'". Watch out for double quotes! It is strange, 
but I found them needed to pass the argument as a whole string. (Does anyone have better 
suggestion?)

If you need more insight, please check fold2Bloch 
Guide:https://github.com/rubel75/fold2Bloch-Wien2k/wiki/fold2Bloch-Guide
The ultimate level of details can be found in this 
manuscript:https://arxiv.org/abs/2301.02696

Good luck
Oleg

P.S. Please let me where you got the old format "~/fold2Bloch/fold2Bloch -c 
Ga8As7Bi1.vector 2:2:2", so we can go back and change the documentation where 
possible.


-Original Message-
From: Wien  On Behalf Of
DibyaR Prakash
Sent: Tuesday, April 18, 2023 10:29 AM
To:wien@zeus.theochem.tuwien.ac.at
Subject: [Wien] Problem running fold2bloch interface with wien2k_17

Dear Wien2K users,

I have a problem running fold2boch command . I install fold2bloch program
using make command.
fold2bloch excitable is generated.
However when I run the tutorial.
# ~/fold2Bloch/fold2Bloch -c Ga8As7Bi1.vector 2:2:2 I got the following error,


  **
  ** fold2Bloch   **
  ** version Jul 12, 2022 **
  **
Detected 3 input arguments
Checking prerequisite files...
Ga8As7Bi1.vector  vector file found
  Unable to read the Dp2s(1,:) matrix
  Relevant input line = 2:2:1
  Parsed input section = 2
  while expected 3 numerical values separated by space.
ERROR: Unable to recognize command line options. Possible options are:
fold2Bloch -h # get help
fold2Bloch -r case.vector[_1] "'P11 P12 P13:P21 P22 P23:P31 P32 P33'" #
real calculation (inversion symm.) no SO fold2Bloch -c case.vector[_1] "'P11
P12 P13:P21 P22 P23:P31 P32 P33'" # complex calc. (no inv. symm.) no SO
fold2Bloch case.vector[_1] "'P11 P12 P13:P21 P22 P23:P31 P32 P33'" #
complex calc. implied no SO fold2Bloch -so case.vectorso[_1]
case.vectorsodn[_1] case.normsoup[_1] case.normsodn[_1] "'P11 P12
P13:P21 P22 P23:P31 P32 P33'" # spin-orbit without -sp fold2Bloch -so
case.vectorsoup[_1] case.vectorsodn[_1] case.normsoup[_1]
case.normsodn[_1] "'P11 P12 P13:P21 P22 P23:P31 P32 P33'" # spin-orbit
with -sp

Notes:
(1) [P] matrix (internally called Dp2s) is used to transform primitive a_p to
supercell a_s lattice vectors (same as in VESTA):
a_s(i) = sum_j a_p(j)*P(j,i)  i,j = 1, 2, 3
(2) Use quotations to input the [P] matrix _exactly_ as shown in this help
(3) Tutorials can be found athttps://github.com/rubel75/fold2Bloch-
Wien2k/wiki


The log file is attached.


Thank you in advance.


Dibya Prakash Rai
-

Assistant Professor

Physical Sciences Research Center(PSRC)

Pachhunga University College

Aizawl,Mizoram

India-796001

Mobile:8132832252
-

Re: [Wien] DMFT

[Gavin Abo]

Since the webpage at [1] shows Python (version 2) as a required package 
for DFT+ embedded DMFT (eDMFT), have you tried using that instead of 
Python3?



Most recent Linux distributions probably still have a Python2 package.


Take Ubuntu jammy 22.04 LTS as an example.  It has a Python2 package 
[2].  It can be installed according to [3] using:



sudo apt install python2


At [1] it has:


python setup.py


In old Linux distributions that would run Python2, but in new 
distribution might run Python3.



To tell it use Python2 in Ubuntu 22.04 LTS, reference [4] shows that 
command could be changed to:



python2 setup.py


Another approach might be to instead install conda [5] and setup conda 
environment [6] that only has Python2 installed which would likely allow 
the original "python setup.py" command to be used.



[1] http://hauleweb.rutgers.edu/tutorials/Installation.html

[2] https://packages.ubuntu.com/jammy/python2

[3] 
https://linuxconfig.org/install-python-2-on-ubuntu-22-04-jammy-jellyfish-linux


[4] 
https://www.fosslinux.com/39384/switching-between-python-2-and-3-versions-on-ubuntu-20-04.htm


[5] 
https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html


[6] 
https://docs.conda.io/projects/conda/en/latest/user-guide/getting-started.html#managing-environments



Kind Regards,

Gavin

WIEN2k user


On 4/17/2023 12:16 PM, delamora via Wien wrote:
I tried the DFT+eDMFT but it seems that it is no longer compatible 
with Python3

This is what Kristjan Haule commented;
Unfortunately DFT+eDMFT is not yet available with Python3.
   Kristjan

So, are other options apart from TRIQS ?

Saludos

Pablo

Hi,

you can use either TRIQS as suggested before or DFT+eDMFT:
http://hauleweb.rutgers.edu/tutorials/Overview.html
For me, the DFT+eDMFT was easier to install, but it may depend on the
software you already have on the machine.

Best regards,
Sylwia



W dniu 09.07.2021 05:24, delamora napisał(a):
> Dear WIEN community;
>  I want to do a DMFT calculation.
>  My quetion is which package is good to be used with WIEN2k
>  That is, it is easy to install and easy to run.
>  I say this because I had a lot of trouble to install one package in
> the past.
>
>  Thanks
>
>  Pablo___
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Re: [Wien] XCrySDen Version: 1.6.2

[Gavin Abo]

It might not work for other Linux distributions, but should it help, the 
following is what I did to install XCrySDen 1.6.2 for Ubuntu 22.04.2 LTS 
[1].



First, I checked if my system was set to Wayland or X11 [2]:


username@computername:~/Desktop$ grep Wayland /etc/gdm3/custom.conf
#WaylandEnable=false


The above shows that Ubuntu after installation was set to Wayland.


For using sudo commands, I had to be an administrator (or I had to ask 
my administrator to do those steps).



The custom.conf file was edited [3]:


username@computername:~/Desktop$ sudo gedit /etc/gdm3/custom.conf
...

username@computername:~/Desktop$ grep Wayland /etc/gdm3/custom.conf
WaylandEnable=false


The above shows the edit to custom.conf that removed the comment (#) for 
setting Wayland to false for enabling X11.



The computer was restarted to change Wayland to X11.


XCrySDen 1.6.2 was installed using:


username@computername:~/Desktop$ sudo apt install xcrysden
...


Since I wanted to use XCrySDen in w2web, XCRYSDEN_TOPDIR variable was 
set in the .basrhc using:



username@computername:~/Desktop$ gedit ~/.bashrc
username@computername:~/Desktop$ grep XCRYSDEN ~/.bashrc
export XCRYSDEN_TOPDIR=/usr/bin
username@computername:~/Desktop$ source ~/.bashrc


The w2web was started up:


username@computername:~/Desktop$ w2web
...


Then, I navigated to and clicked "view structure" in w2web. Then, the 
struct file was displayed [4].



[1] https://ubuntu.com/download/desktop

[2] 
https://unix.stackexchange.com/questions/202891/how-to-know-whether-wayland-or-x11-is-being-used


[3] 
https://askubuntu.com/questions/1410256/how-do-i-use-x-instead-of-wayland-on-22-04 



[4] 
https://raw.githubusercontent.com/gsabo/xcrysden-Patches/main/Ubuntu%2022.04.2%20XCrySDen%201.6.2.png 




Kind Regards,

Gavin

WIEN2k user


On 3/25/2023 1:47 AM, Peter Blaha wrote:


The semishared version has most libraries included and runs on almost 
any Linux system.


For the more recent version, the  developers provide only a "shared" 
version, i.e. most libraries are NOT included, but must be present on 
your Linux system.


On their website it is mentioned what libraries you need. At least you 
miss


libfftw3.so.3

but probably also others.


PS: I still use on most computers 1.5.60, as I do not want to install 
all  the necessary libraries on all my machines.




Am 25.03.2023 um 01:31 schrieb delamora:

The only difference is
semishared => shared


*De:* Wien  en nombre de 
delamora 

*Enviado:* viernes, 24 de marzo de 2023 06:28 p. m.
*Para:* A Mailing list for WIEN2k users 
*Asunto:* [Wien] XCrySDen Version: 1.6.2
Dear WIEN2k community
I am having trouble with XCrySDen, if I use;
xcrysden-1.5.60-bin-semishared
I have no problem, but if I use
  xcrysden-1.6.2-bin-shared

+-+
|*|
|*                                     *|
|*  XCrySDen -- (X-Window) CRYstalline Structures and DENsities  *|
|*               = ===         =              ===        *|
|*---*|
|*                                     *|
|*    Anton Kokalj (tone.kok...@ijs.si)                  *|
|*    Jozef Stefan Institute, Ljubljana, Slovenia                *|
|*                                     *|
|*    Copyright (c) 1996--2019 by Anton Kokalj                   *|
|*                                     *|
|*|
+-+

  Version: 1.6.2

  Please report bugs to: tone.kok...@ijs.si


  TERMS OF USE:
  -
  XCRYSDEN is released under the GNU General Public License.

  Whenever graphics generated by XCRYSDEN are used in scientific
  publications, it shall be greatly appreciated to include an explicit
  reference. The preferred form is the following:

  [ref] A. Kokalj, J. Mol. Graph. Model., Vol. 17, pp. 176-179, 1999.
        Code available from http://www.xcrysden.org/.

XCRYSDEN_TOPDIR=/home/Programas/xcrysden-1.6.2-bin-shared
XCRYSDEN_SCRATCH=/home/pablo/xcrys_tmp

/home/Programas/xcrysden-1.6.2-bin-shared/bin/xcrys: error while 
loading shared libraries: libfftw3.so.3: cannot open shared object 
file: No such file or directory


-
For the
xcrysden-1.5.60-bin-shared
I get the same answer, except for the line
 "Version: 1.6.2"

Saludos

Pablo



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Phone: +43-158801165300

Re: [Wien] lapw1

[Gavin Abo]

When reinstalling WIEN2k, so that I don't have to change the WIENROOT 
variable in my .bashrc (or .cshrc), I move or delete the old WIEN2k 
installation directory so that it can installed again in the same location.


Also, it looks like you might have accidentally navigated to the wrong 
option in siteconfig.


It looks like you selected "U Update a package" when you probably wanted 
"R Compile/Recompile".


The "U Update a package" is for updating an individual package and 
typically not used for a full installation.


There used to be a block [1] that I thought explained that well on the 
WIEN2k updates page, but it currently is no longer there [2].  That 
block was as follows.


To update from previous versions you can either download and install the 
complete package (highly recommended when upgrading from a rather old 
version) or download and update only individual packages (the ones which 
have been changed according to the list given below):


    SRC_w2web: just expand: gunzip SRC_w2web.tar.gz;tar -xvf SRC_w2web.tar
    SRC: expand and cp the respective shell-script to $WIENROOT: gunzip 
SRC.tar.gz;tar -xvf SRC.tar;cp SRC/CORRECTED_SCRIPT_lapw .
    For all other packages (Fortran programs) use the "update" option 
of siteconfig_lapw.


[1] 
https://web.archive.org/web/20200219062310/http://susi.theochem.tuwien.ac.at/reg_user/updates/

[2] http://susi.theochem.tuwien.ac.at/reg_user/updates/

Best Regards,

Gavin
WIEN2k user

On 1/6/2023 12:53 AM, naincy Pandit wrote:

RESPECTED SIR


as you told me to install oneAPI so i did it and now it is installed 
but there is a problem with Wien2k previously I have Wien2k 19.01 and 
now I installed Wien2k 21.1.


please tell me how to uninstall the older version so that the new one 
comes into account


again there is a problem that is

/home/naincy/WIEN2k_21.1/lapw1: Command not found.
0.000u 0.000s 0:00.00 0.0%  0+0k 0+0io 0pf+0w
error: command   /home/naincy/WIEN2k_21.1/lapw1 lapw1.def   failed


 you told me to do ./siteconfig, i already did it but  this comes

* ***
   *           Update a package from its SRC_XX.tar.gz file              *
 ***

Available packages:
ls: No match.
ls: No match.
     Specify the name of the package XX (e.g. lapw1): lapw1
SRC_lapw1.tar.gz does not exist. Please check.

 ***
   *           Update a package from its SRC_XX.tar.gz file              *
 ***

Available packages:
ls: No match.
ls: No match.
     Specify the name of the package XX (e.g. lapw1): *

lapw1.tar.gz is not present only two folders *lapw1para_lapw 
*and* lapw1para_lapw*.*orig*  exists and I m not able to correct it 
please help me out.


On Wed, 4 Jan 2023 at 17:26, Laurence Marks  
wrote:


What you sent describes the issue:

/home/naincy/WIEN2k_21.1/nn: Command not found

That means you did not compile it correctly. Go back and check for
errors during the compilation when you did siteconfig. For
instance, go to /home/Nancy/WIEN_21.1, do ./siteconfig and
recompile just nn (for instance).

Look at the errors.

--
Professor Laurence Marks
Department of Materials Science and Engineering, Northwestern
University
www.numis.northwestern.edu 
"Research is to see what everybody else has seen, and to think
what nobody else has thought" Albert Szent-Györgyi

On Wed, Jan 4, 2023, 04:44 naincy Pandit
 wrote:

Dear Prof. Blaha sir and Wien2k users,


  i am working with Wien2k_21.1 version with Ubuntu 22.04 with oneAPI 
installed recently after installation i m geeting this type of error

  stop error
  
error: command   /home/naincy/WIEN2k_21.1/nn nn.def   failed

0.000u 0.000s 0:00.00 0.0%  0+0k 0+0io 0pf+0w
/home/naincy/WIEN2k_21.1/nn: Command not found.
  next is nn
fileBaZrS3.struct_setrmt   generated
atom  Z   RMT-max   RMT
Use of uninitialized value $rmt[3] in sprintf at 
/home/naincy/WIEN2k_21.1/setrmt_lapw line 249,  line 41.
Use of uninitialized value $rmt[2] in sprintf at 
/home/naincy/WIEN2k_21.1/setrmt_lapw line 249,  line 32.
Use of uninitialized value $rmt[1] in sprintf at 
/home/naincy/WIEN2k_21.1/setrmt_lapw line 249,  line 19.
Use of uninitialized value $rmt[0] in sprintf at 
/home/naincy/WIEN2k_21.1/setrmt_lapw line 249,  line 10.
readline() on closed filehandle NN at 
/home/naincy/WIEN2k_21.1/setrmt_lapw line 163.
readline() on closed filehandle NN at 
/home/naincy/WIEN2k_21.1/setrmt_lapw line 152.
error: command   /home/naincy/WIEN2k_21.1/nn nn.def   failed
0.000u 0.000s 0:00.00 0.0%  0+0k 0+0io 0pf+0w

Re: [Wien] help NaN error

[Gavin Abo]

all the compounds are having the same space group -> That's interesting 
that they are all space group 1_P1.  Do they all have the same number of 
atoms/nonequivalent positions?  If so, the compiler might not be the 
cause of the issue. Steps from when I installed oneAPI if they help are 
at [1].



Maybe it is not helpful but should it be, below are some comments and 
historical information I have with regards to the WIEN2k sum rules from 
kram.


Section "8.20 OPTIC (calculating optical properties)" and "8.12 KRAM 
(Kramers-Kronig transformation)" of the WIEN2k 21.1 usersguide [2] has 
the following.


/This [optic/kram] program was contributed by://
/

/Claudia Ambrosch-Draxl/

Section "D. Sumrules" in C. Ambrosch-Draxl and J. O. Sofo article [3] 
contains the sentence:


/Typically, in the low energy region the contribution to the intraband 
spectrum should sum up to the number of the outermost valence electrons./


If I have interpreted the above statement correctly, "1  add 
intraband contributions? yes/no: 1/0" must be set in case.inkram and low 
energy region (emin and emax [4] in case.injoint) must be selected were 
intraband contributions are dominant.


I saw that interband contributions may be a characteristic of "metals", 
slide 20 of [5]. Although as a separate note, I do recall the plasma 
frequency needing to be 0 in the case of semiconductor [6].


In your case.inkram [7], I see you have set instead "0  add 
intraband contributions? yes/no: 1/0" and "12.60   plasma frequencies  
(from joint, opt 6)".


The original WIEN2k code by C. Ambrosch-Draxl's group seemed to 
intentionally output the sum rules only when intraband contributions 
were added.  However, a user requested the sum rule output when 
intraband contributions were not added and the kram code got modified to 
print them also when there are no intraband contributions. [8]


I have always been interested to find a reference confirming and 
clarifying the validity of the sum rules also the no intraband 
contribution cases (and insulator & semiconductor cases), but don't 
recall coming across one.


When I Googled "Chalcogenide Perovskite", the article at [9] came up having:

/Chalcogenide perovskites are an unusual type of ionic semiconductor./

Thus, it might be helpful to know if all calculations that worked and 
the one that isn't if the DFT calculation (band structure/DOS) showed 
them being semiconductor (Or metal or insulator).


C. Ambrosch-Draxl and S. Sharma I think redeveloped an optic code after 
the original WIEN2k code contribution that has since gotten further 
improved, but unfortunately it didn't go into WIEN2k but it seemed to me 
that it was put to use in Elk [10].


[1] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg21942.html

[2] http://susi.theochem.tuwien.ac.at/reg_user/textbooks/usersguide.pdf
[3] https://arxiv.org/abs/cond-mat/0402523v1
[4] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg10675.html
[5] 
http://susi.theochem.tuwien.ac.at/events/ws2017/notes/Laskowski_optic-xas.pdf
[6] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg22038.html
[7] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg22184.html

[8] http://zeus.theochem.tuwien.ac.at/pipermail/wien/2009-March/012256.html
[9] https://www.azom.com/article.aspx?ArticleID=21105
[10] https://elk.sourceforge.io/#contributions

Kind Regards,

Gavin
WIEN2k user

On 1/3/2023 6:42 AM, naincy Pandit wrote:

I read your mail sir and checked the possibilities.

opticplot or J is not possible because numbers are missing from the 
table absorb and others also are having NaN


case.joint. the file is completely ok and having the numbers not NaN

as i m working on it, from the previous work my steps are okay.

as you suggest downloading one API, is it paid or free?

and sir, all the compounds are having the same space group,

sir, I'm working on it already and all my data is saved in itself 
(current system), if at this time I will change my compiler then all 
the data will erase and my work vanishes so can you please tell me if 
there is any alternative for this problem.


On Tue, 3 Jan 2023 at 19:02, Peter Blaha  wrote:

You did not read my previous email completely, or at least did not
answer it:
 >     Use opticplot and plot "J", i.e. the unbroadened eplsilon-2 in
 >     case.joint.  Is this ok or already in this file some NaNs
?
Then we
 >     know that the steps before kram are ok.

Can you plot the unbroadened eps-2 (which comes from joint) ??
Please look into case.joint. Are there NaNs ???


Am 03.01.2023 um 13:35 schrieb naincy Pandit:
> previously also i worked on it and have not faced this type
of problem
>
> and yes. i have completed this optics work for more than 4
compounds and
> completely worked
> previously case.inkram file contains this
>
>    0.1    Gamma: broadening of interband spectrum
   

Re: [Wien] help NaN error

[Gavin Abo]

It "might" be a problem caused by the compiler then.

You mentioned using Intel Fortran compiler (parallel studio) [1].

If you search the list, there were reports in the past of I/O issues 
with big data files with some older Intel Fortran compiler versions.  
One such post is [2].


Your 1_P1 (supercell) may be creating big data compared to the 4 
compounds (unit cells?) that worked fine for you.


Using a different compiler (e.g., gfortran) or using different Intel 
Fortran compiler version (e.g., oneAPI [3]) should resolve it if that is 
cause.


[1] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg22179.html
[2] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg16802.html
[3] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg21946.html


Kind Regards,
Gavin
WIEN2k user

On 1/3/2023 5:35 AM, naincy Pandit wrote:

previously also i worked on it and have not faced this type of problem

and yes. i have completed this optics work for more than 4 compounds 
and completely worked

previously case.inkram file contains this

  0.1    Gamma: broadening of interband spectrum
  0.0    energy shift (scissors operator)
  0      add intraband contributions? yes/no: 1/0
 12.60   plasma frequencies  (from joint, opt 6)
  0.20   Gammas for Drude terms

and in the folder where it did not work also have the same things

  0.1    Gamma: broadening of interband spectrum
  0.0    energy shift (scissors operator)
  0      add intraband contributions? yes/no: 1/0
 12.60   plasma frequencies  (from joint, opt 6)
  0.20   Gammas for Drude terms

both the files have same thing so how can i say my previous work or 
steps are wrong?


at this time this is not working  there is Not a number (NaN) problem.

On Tue, 3 Jan 2023 at 17:35, Peter Blaha  wrote:

We (you) have first to find out if this is the first error, or the
problem is already in previous steps.

Use opticplot and plot "J", i.e. the unbroadened eplsilon-2 in
case.joint.  Is this ok or already in this file some NaNs ?
Then we
know that the steps before kram are ok.

If this is ok, maybe your case.inkram is wrong ?

PS: Have you ever done optics for another case ? Did it work there ?
Maybe your compilation of kram is wrong.


Am 03.01.2023 um 12:05 schrieb naincy Pandit:
> D*ear Prof. Blaha Sir and Wien2k users,*
>
> i am working with Wien2k_19.1 version with Ubuntu 22.04 i need
to get some suggestions for optical properties of chalcogenide
perovskites of orthorhombic phase.
>
> i have constructed the structural file with space group p_1.
>
> the purpose of my calculation is to get optical parameters.
>
> after doing the scf calculation i started working on optical at
w2web but at the end i got this type of error mentioned below
>
> Commandline: *x kram*
> Program input is: *""*
>
>   xx
>   yy
>   zz
>    Energy units:  [eV]
>    Lorentzian broadening with gamma:   0.100      [eV]
>          2001  data points
>    ENERGY INCREMENT:   1.3609990E-002
>   losmo1 called to perform KK for Im to Re
>   losmo1 called to perform KK for Im to Re
>   losmo1 called to perform KK for Im to Re
>   sum rule 1: Int(sigma)dw                        NaN          
       NaN
>                       NaN
>   sum rule 2: Int(eloss.w)dw                      NaN          
       NaN
>                       NaN
>   sum rule 3: Int(eloss/w)dw                      NaN          
       NaN
>                       NaN
>   KK with broadening done
> 0.0u 0.0s 0:00.06 50.0% 0+0k 2120+1192io 17pf+0w
>
> Please give your valuable suggestions. How to get rid of this error.
>
> Thanks & Regards
> Naincy Pandit
>
>
> ___
> Wien mailing list
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> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
> SEARCH the MAILING-LIST at:
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-- 
--

Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
Phone: +43-1-58801-165300
Email: peter.bl...@tuwien.ac.at   WIEN2k: http://www.wien2k.at
WWW: http://www.imc.tuwien.ac.at
-
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Re: [Wien] confusion regarding band structure of Graphene

[Gavin Abo]

Your problem, where you have P1 structure but need bands represented 
back in a hexagonal system structure, sounds like something that maybe 
the fold2Bloch tool could help with.  Though, I don't know if it would 
be useful or not in your case.  Should that be something that you 
explorer further, the past posts at the following two links might be of 
interest:


https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg21356.html
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18482.html

Kind Regards,

Gavin
WIEN2k user

On 12/30/2022 7:51 AM, shamik chakrabarti wrote:

Dear Prof. Blaha,

                    I think the structure as used by me & as can be 
used by downloading Graphene CIF file from material project database 
are same with different representation. I have checked the XRD of both 
the structures in VESTA & they are providing the same XRD pattern for 
both the structures. In this regard lithiation voltage for both the 
cases should be same. However the bandstructures need special k points 
which is available for hexagonal lattice & not for this monoclinic 
lattice. However, if the voltage is accurate I will not bother for the 
band structure.


with kind regards,

On Fri, 30 Dec 2022 at 19:08, shamik chakrabarti 
 wrote:


Specially if I want LiC6 unit cell?...

On Fri, Dec 30, 2022, 18:47 shamik chakrabarti
 wrote:

Dear Prof. Blaha,
 .   .   .  .  .  .  Thank you for your reply Sir. I have a
very dumb question. Whether the voltage simulated by this
attached structure will provide the same as will be provided
by the single unit cell?

With kind regards,

On Fri, Dec 30, 2022, 18:03 Peter Blaha
 wrote:

This is not the smallest unit cell of graphene but a 3
times larger
monoclinic cell.

Start with graphite, remove the atoms at the second z=0.75
layer and
eventually add some vacuum along z.


Am 29.12.2022 um 18:34 schrieb shamik chakrabarti:
> The structure of monolayer Graphenbe as I have used is
attached for your
> reference.
>
> On Thu, 29 Dec 2022 at 18:32, shamik chakrabarti
> mailto:shamik15041...@gmail.com>> wrote:
>
>     Dear Wien2k users,
>
>                              I have simulated a
structure of Graphene
>     monolayer with primitive cell. I am getting DOS &
voltage
>     accurately. However, while plotting band structure I
am facing a
>     problem. In hexagonal Graphene the band structure
can be obtained
>     with Gamma-M-K-Gamma, where K is the dirac point.
However, in my
>     primitive cell I am getting a Brillouin Zone of
reciprocal lattice &
>     not able to detect the Dirac point.
>
>     The purpose of taking a primitive cell of monolayer
Graphene lies on
>     the fact that I need control over all the C atoms.
>
>     Looking forward to hearing from you.
>
>     --
>     Dr. Shamik Chakrabarti
>     Research Fellow
>     Department of Physics
>     Indian Institute of Technology Patna
>     Bihta-801103
>     Patna
>     Bihar, India
>
>
>
> --
> Dr. Shamik Chakrabarti
> Research Fellow
> Department of Physics
> Indian Institute of Technology Patna
> Bihta-801103
> Patna
> Bihar, India
>
> ___
> Wien mailing list
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> 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

-- 
--

Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna,
A-1060 Vienna
Phone: +43-1-58801-165300
Email: peter.bl...@tuwien.ac.at   WIEN2k: http://www.wien2k.at
WWW: http://www.imc.tuwien.ac.at

-
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--
Dr. Shamik Chakrabarti

Re: [Wien] budget CPU and Linux system for precompiled binaries

[Gavin Abo]

For the solid state drive (SSD), from among the different types [1], I 
do recommend trying to get the M.2 PCIe NVMe [2,3] if it fits within 
your computer configuration and budget.


[1] 
https://www.onlogic.com/company/io-hub/internal-computer-storage-types-pros-and-cons/

[2] https://www.seagate.com/blog/what-is-an-nvme-ssd/
[3] 
https://www.intel.com/content/www/us/en/gaming/resources/what-is-pcie-4-and-why-does-it-matter.html


Kind Regards,
Gavin
WIEN2k user

On 12/16/2022 1:03 AM, pluto via Wien wrote:

Dear All,

I am considering to build a simple Linux PC for WIEN2k, price range 
between ca. 500-2000 EUR. It would be used to run band-structure 
calculations.


I will run precompiled WIEN2k executables on this. Is there a 
preferred CPU and Linux system that would ensure good compatibility?


I suppose this question is asked quite a lot, but hardware changes 
quickly. Any comments on a particular CPU/mainboard configuration, RAM 
amount, type of SSD etc. would be appreciated.


Best,
Lukasz

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Re: [Wien] Error during compilation

[Gavin Abo]

That's not enough information. You would need to look for additional 
information inside the SRC_hf/compile.msg file for troubleshooting the 
error.


It might also help to upgrade to WIEN2k 21.1.

On the updates page [1], it has written the following were it looks like 
WIEN2k 21.1 fixed significant hf bugs that WIEN2k 19.1 had.***

*

*SRC_hf:* Fix for "spin-polarized calc. + SO and no inversion symmetry 
(never really "active"),atoms up to ZZ=118


[1] http://susi.theochem.tuwien.ac.at/reg_user/updates/

Kind Regards,

Gavin
WIEN2k user

On 12/1/2022 3:11 AM, shamik chakrabarti wrote:

Dear Wien2k users,

                        I have tried to install wien2k 19.1 in a 
workstation in which Ubantu is installed. Compilation progresses with 
an error at SRC_hf as follows;


make[1]: *** [Makefile:273: read_uc.o] Error 1
make[1]: Leaving directory '/usr/local/Wien2k/SRC_hf'
make: *** [Makefile:183: complex] Error 2
"compile.msg" 393L, 37610C

Please suggest.

with regards,

--
Dr. Shamik Chakrabarti
Research Fellow
Department of Physics
Indian Institute of Technology Patna
Bihta-801103
Patna
Bihar, India___
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Re: [Wien] Error in parabolfit_lapw for 4D optimization of monoclinic structure

[Gavin Abo]

From the error message, it looks like the program (eosfit6) encounters 
an issue reading in the energy values in your opt_bZn2V2O7_0.7GPa.ene file.


As Lyudmila has already mentioned [1], if you need additional help with 
that, you would need to provide the opt_bZn2V2O7_0.7GPa.ene file.


[1] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg22119.html


Kind Regards,
Gavin
WIEN2k user


On 11/22/2022 12:35 AM, ma.azadparvar wrote:


Dear Gavin,

Thanks for your reply. I am using WIEN2k 21.1.

The command << parabolfit_lapw -t 4 -f case -g >> is correct and 
generates case.ene  and case.latparam.


Unfortunately, I have faced another error:

opt_bZn2V2O7_0.7GPa.ene and opt_bZn2V2O7_0.7GPa.latparam generated

  Enter dimension of fit (number of variable lattice parameters, 1-6):

4  fitcase 15  parameter

forrtl: severe (59): list-directed I/O syntax error, unit 10, file 
/home/path/opt_bZn2V2O7_0.7GPa/opt_bZn2V2O7_0.7GPa.ene


Image PC Routine Line Source

eosfit6 0047B87B Unknown Unknown  Unknown

eosfit6 0044A652 Unknown Unknown  Unknown

eosfit6 0044907C Unknown Unknown  Unknown

eosfit6 00403EED MAIN__ 67  eosfit6.f

eosfit6 00403822 Unknown Unknown  Unknown

libc.so.6 14D41DC01D90 Unknown Unknown  Unknown

libc.so.6 14D41DC01E40 __libc_start_main Unknown  Unknown

eosfit6 00403725 Unknown Unknown  Unknown

0.000u 0.012s 0:00.01 100.0%    0+0k 0+0io 0pf+0w

error: command   /home/path/wien2k/eosfit6 eosfit6.def   failed

I have checked case.ene and case.scf files related to the pointed line 
(67) but I could not find any bad numbers or any errors.


Please let me know how to fix it.

Best regards.

*Maliheh Azadparvar*___
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Re: [Wien] Error in parabolfit_lapw for 4D optimization of monoclinic structure

[Gavin Abo]

What version of WIEN2k are you using?


In the Linux terminal, try entering the command:

parabolfit_lapw -h

If the WIEN2k version you are using has the old buggy script, it should 
return:


parabolfit_lapw [ -t 2/3/4 ]  [ -f FILEHEAD ] [ -scf '*xxx*.scf' ]

If it is using the new WIEN2k 21.1 script, it should return the new -g 
option:


parabolfit_lapw [ -t 2/3/4 ]  [ -f FILEHEAD ] [ -scf '*xxx*.scf' ] [-a/b/g]


If I recall correctly, another user got a monoclinic calculation work in 
WIEN2k 21.1 using commands similar to:



cd case

parabolfit_lapw -t 4 -f case -g


For your calculation, that would likely  be:


cd opt_bZn2V2O7_0.7GPa

parabolfit_lapw -t 4 -f opt_bZn2V2O7_0.7GPa -g


I don't have monoclinc files to test it, but "-t 2/3/4" in the command 
of your email below instead of "-t 4" could maybe lead to errors.



Kind Regards,

Gavin

WIEN2k user


On 11/21/2022 5:46 PM, ma.azadparvar wrote:


Dear prof. Blaha,


Thank you for your reply. “Case” is not a real name. I wrote  “case” 
to avoid writing a long name.


The folder name is opt_bZn2V2O7_0.7GPa and the automatic name of the 
SCF files is opt_bZn2V2O7_0.7GPa_mon___number of structure_defult.scf. 
Maybe it's not correct?!


Anyway, I repeat “parabolfit_lapw “ without (-f FILEHEAD) and that 
error exists.


Also, I changed the parabolfit script to “echo $type | x_lapw -f $file 
eosfit6” and the error exists too.


I cannot solve this problem. Please guide me to solve it.

*Maliheh Azadparvar*


*From:* Wien  on behalf of 
Peter Blaha 

*Sent:* Sunday, November 20, 2022 6:32:35 PM
*To:* wien@zeus.theochem.tuwien.ac.at
*Subject:* Re: [Wien] Error in parabolfit_lapw for 4D optimization of 
monoclinic structure

CAUTION: This email originated from outside the organization.

Are your files   "Case*"  or "case*"  ?
What is the name of your directory ?

The capital letter makes a big difference.

Otherwise, I believe you used   -f FILEHEAD   in a wrong way (and this
option may even not work).

If our directory is called "case" and all your files also start with
"case", you should not use   -f filehead.   This option is only used
when the files are named differently than the directory.

I suggest you repeat parabolfit without this option.


Otherwise it could be that you should edit the following line in 
parabolfit:


echo $type | x_lapw  eosfit6
change to:
echo $type | x_lapw -f $file eosfit6


Am 20.11.2022 um 10:22 schrieb ma.azadparvar:
> Dear Wien2k users,
>
> I have optimized a monoclinic structure with option 7 "vary A, B, C ,
> and gamma (4D-case) monoclinic lattice". After optimization without any
> error (using 7 81 1%), I want to obtain lattice parameters. So by
> running the “parabolfit_lapw”:
>
>parabolfit_lapw -t 2/3/4   -f FILEHEAD -scf '*case*.scf'  -g
>
> After running, I have faced with following  error:
>
> /bin/ls:no match.
>
> The following scf files were used for analysis:
>
> Case_1_defult.scf
>
> .
>
> .
>
> .
>
> Case_81_defult.scf
>
> FILEHEAD.ene and FILEHEAD.latparam generated
>
> ERROR IN OPENING UNIT: 10
>
> FILE NAME:
>
> Case.ene
>
> STATUS:old
>
> FORM:formatted
>
> OPEN FAILED
>
> 0.008u   0.004s    0:00.01   0.0%  0+0k 0+0io   0pf+0w
>
>
> Please let me know how to solve this problem?
>
> Thank you in advance.
>
>
>
> *Maliheh Azadparvar*
>
>
> ___
> Wien mailing list
> Wien@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


--
--
Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
Phone: +43-1-58801-165300
Email: peter.bl...@tuwien.ac.at    WIEN2k: http://www.wien2k.at
WWW: http://www.imc.tuwien.ac.at
-___
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Re: [Wien] contradictory band gap in case.scf and band.agr

[Gavin Abo]

I have probably overlooked in your conversion when you mentioned whether 
you were using a shifted or non-shifted k-mesh; If you happened to have 
used a shifted k-mesh in yourperovskites calculation, then you might try 
the calculation again with a non-shifted k-mesh during "x kgen":


https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg15445.html
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19427.html
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg15445.html

Kind Regards,

Gavin
WIEN2k user

On 9/10/2022 4:20 AM, Dr. K. C. Bhamu wrote:

Thanks Prof. Marks for your suggestions.

My system is non-sp and non-SO type.

I didn't do any mistake with k-path as Its a cubic system and its 
brillouin zone is very simple.


I do agree with the k-mesh as with very fine mesh narrow band gap 
systems may show metallic character.

In one of my case it is happening.


But in a separate case where I didn't change the k-mesh after SCF for 
band structure calculation, the band structure should show the same 
band gap as I am getting with the grep command. No?


Thanks
Bhamu

On Sat, Sep 10, 2022, 3:11 PM Laurence Marks 
 wrote:


I can think this can occur in numerous ways, all a minor mistake:

1. You forgot to include -orb when you did the bands.
2. You had too small a k-mesh for the scf, the fine one for the
bands shows a metal.
3. Your grep showed just the "up" spin, not both.
4. You did not fully converge.
5. You forgot -so in the band.
6. You have a mistake in your k-mesh for the bands.
7. Something else similar.

Just my guesses, I suggest you check carefully. Number 7 is most
likely.

--
Professor Laurence Marks
Department of Materials Science and Engineering, Northwestern
University
www.numis.northwestern.edu 
"Research is to see what everybody else has seen, and to think
what nobody else has thought" Albert Szent-Györgyi

On Fri, Sep 9, 2022, 10:45 PM Dr. K. C. Bhamu
 wrote:

Dear Users

Greetings,

I am trying to compute the band structure of some ABX3
perovskites systems with Wien2k_19.2 compiled with intel
compilers.
When I grep the band gap from case.scf, I am getting some
values (~0.7eV) while when I plot the band structure, the VBM
is significantly crossing the Fermi level and the gap between
CBM and VBM is much lesser than the one I grepped from
case.scf file.
In some case, VBM and VBM are overlapping while case.scf file
is showing a clear band gap.

I have updated Fermi energy in case.insp files.

I never faced such an issue in the past.

I am wondering if you would like to help me out.

Regards
Bhamu
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Re: [Wien] Error while running IRelast - calljob_lapw

[Gavin Abo]

Thanks, I created a command_init_lapw.patch for this, which is available 
at [1].


However, to more easily apply it, I used the following three terminal 
commands:


username@computername:~$ cd $WIENROOT/SRC_IRelast/script-elastic
username@computername:~/WIEN2k/SRC_IRelast/script-elastic$ wget 
https://raw.githubusercontent.com/gsabo/WIEN2k-Patches/master/21.1/command_init_lapw.patch

...
username@computername:~/WIEN2k/SRC_IRelast/script-elastic$ patch -b 
command_init_lapw command_init_lapw.patch

patching file command_init_lapw

In addition, I encountered another small issue with the IRelast files in 
WIEN2k_21.1.tar.  The fix was simple though, just had to enter two 
terminal commands:


chmod -x $WIENROOT/SRC_IRelast/script-elastic/initIR_lapw
chmod +x $WIENROOT/initIR_lapw

I made a note of this as well in the README file at [1].

[1] https://github.com/gsabo/WIEN2k-Patches/tree/master/21.1

Kind Regards,

Gavin
WIEN2k user

On 9/7/2022 8:34 AM, Morteza Jamal via Wien wrote:

There are two ways:

1-Repeat your example again and in section Enter Data for auto initialization 
give L-max 8 otherwise 8.0

2- edit file "auto_init_lapw" and correct   L-max as:

initIR_lapw  -lmax 8

Otherwise

initIR_lapw .-lmax 8.0

With best,
Morteza___
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Re: [Wien] Error while running IRelast - calljob_lapw

[Gavin Abo]

Your TiC.in1 file has the line:


 7.0 8.0   4   ELPA pxq BL 64 (R-MT*K-MAX,MAX L IN WF,V-NMT,LIB)


However, it has to be:


 7.0 8     4   ELPA pxq BL 64 (R-MT*K-MAX,MAX L IN WF,V-NMT,LIB)


The problem is you have a float (8.0) but it must be an integer (8).


On 9/7/2022 7:40 AM, AJAY SINGH VERMA wrote:

sir,
What is to be done to rectify this and where I have done wong

*From:* AJAY SINGH VERMA 
*Sent:* Wednesday, September 7, 2022 6:35 PM
*To:* wien-requ...@zeus.theochem.tuwien.ac.at 
; wien zeus 


*Subject:* Re: Error while running IRelast - calljob_lapw
Dear Sir,

TiC.in1 is attached...

*From:* AJAY SINGH VERMA 
*Sent:* Wednesday, September 7, 2022 6:20 PM
*To:* wien-requ...@zeus.theochem.tuwien.ac.at 
; wien zeus 


*Subject:* Re: Error while running IRelast - calljob_lapw
Dear All,
After applying patch as suggested by Sir Gavin Abo, now I am getting 
this underlined error


##
Start for AUTO intialization Styp3_-2.0
##
 2 Atoms found:  with labels Ti1  C 1
generate atomic configuration for atom 1 : Ti1
generate atomic configuration for atom 2 : C 1
_SET: Command not found._
 next is setrmt
 specify nn-bondlength factor: (usually=2) [and optionally dlimit, 
dstmax (about 1.d-5, 20)]

 DSTMAX:   20.000
 iix,iiy,iiz           5           5           5 28.3378802   
     29.4945301  40.9100550

 NAMED ATOM: Ti1       Z changed to IATNR+1000 to determine equivalency
 NAMED ATOM: C 1       Z changed to IATNR+1000 to determine equivalency

    ATOM  1  Ti1        ATOM  2  C 1
 RMT(  1)=2.12000 AND RMT(  2)=1.74000
 SUMS TO 3.86000  LT.  NN-DIST= 4.09019

    ATOM  2  C 1        ATOM  1  Ti1
 RMT(  2)=1.74000 AND RMT(  1)=2.12000
 SUMS TO 3.86000  LT.  NN-DIST= 4.09019
STOP NN ENDS
0.001u 0.000s 0:00.00 0.0%0+0k 0+40io 0pf+0w
atom  Z   RMT-max   RMT
 1  22.0  2.12   2.12
 2   6.0  1.74   1.74
file    TiC.struct_setrmt   generated
 next is nn
 specify nn-bondlength factor: (usually=2) [and optionally dlimit, 
dstmax (about 1.d-5, 20)]

 DSTMAX:   20.000
 iix,iiy,iiz           5           5           5 28.3378802   
     29.4945301  40.9100550

 NAMED ATOM: Ti1       Z changed to IATNR+1000 to determine equivalency
 NAMED ATOM: C 1       Z changed to IATNR+1000 to determine equivalency

    ATOM  1  Ti1        ATOM  2  C 1
 RMT(  1)=2.12000 AND RMT(  2)=1.74000
 SUMS TO 3.86000  LT.  NN-DIST= 4.09019

    ATOM  2  C 1        ATOM  1  Ti1
 RMT(  2)=1.74000 AND RMT(  1)=2.12000
 SUMS TO 3.86000  LT.  NN-DIST= 4.09019
STOP NN ENDS
0.002u 0.000s 0:00.00 0.0%0+0k 0+16io 0pf+0w
 next is sgroup
>   sgroup  (18:16:55) 0.000u 0.000s 0:00.00 0.0% 0+0k 0+8io 0pf+0w
  Names of point group: mmm    2/m 2/m 2/m   D2h
  Names of point group: mmm    2/m 2/m 2/m   D2h
Number and name of space group: 71 (I m m m)
 next is symmery
>   symmetry  (18:16:55)  SPACE GROUP CONTAINS INVERSION
0.000u 0.001s 0:00.00 0.0%0+0k 0+32io 0pf+0w
 next is lstart
  SELECT XCPOT:
  recommended: PBE    [(13) GGA of Perdew-Burke-Ernzerhof 96]
               LDA    [( 5)]
               WC     [(11)  GGA of Wu-Cohen 2006]
               PBESOL [(19) GGA of Perdew etal. 2008]
  SELECT ENERGY to separate core and valence states:
  recommended: -6.0 Ry (check how much core charge leaks out of MT-sphere)
  ALTERNATIVELY: specify charge localization (between 0.97 and 1.0) to 
select core state

STOP LSTART ENDS
>   inputfiles prepared (18:16:55)
 inputfiles prepared
 next is kgen
  NUMBER OF K-POINTS IN WHOLE CELL: (0 allows to specify 3 divisions of G)
 length of reciprocal lattice vectors:   1.313   1.349   1.537  13.563 
 13.930  15.879

  Shift of k-mesh allowed. Do you want to shift: (0=no, 1=shift)
         427  k-points generated, ndiv=          14      14          14
STOP KGEN ENDS
 next is dstart
>   dstart  -p(18:16:55) starting parallel dstart at Wednesday 07 
September 2022 06:16:55 PM IST

 .machine0 : processors
running dstart in single mode
STOP DSTART ENDS
0.957u 0.227s 0:00.24 487.5%  0+0k 0+800io 0pf+0w

-> new TiC.in0 generated
  init_lapw finished ok
starting parallel dstart at Wednesday 07 September 2022 06:16:56 PM IST
 .machine0 : processors
running dstart in single mode
STOP DSTART ENDS
0.935u 0.247s 0:00.23 508.6%  0+0k 0+704io 0pf+0w
0.021u 0.000s 0:00.02 100.0%  0+0k 0+688io 0pf+0w
clmextrapol_lapw has generated a new TiC.clmsum
STOP  LAPW0 END
At line 393 of file inilpw.f (unit = 5, file = 'TiC.in1')
_Fortran runtime error: Bad integer for item 2 in list input_

Error termination. Backtrace:
#0  0x145928ddfae0 in ???
#1  0x145928de0659 in ???
#2  0x145928de128f in ???
#3  0x14592902b3fb in ???
#4  0x14592902e3ba in ???
#5  0x14592902f0ba in ???
#6  0x55749c1

Re: [Wien] Error while running IRelast - calljob_lapw

[Gavin Abo]

On page 138 of the WIEN2k 21.1 usersguide [1], you should see in the 
case.in1 format that MAX L IN WF is an integer (10).  However, the 
TiC.in1 you sent incorrectly has a float for that value (8.0) when it 
needs to be an integer (8).



[1] http://susi.theochem.tuwien.ac.at/reg_user/textbooks/usersguide.pdf


On 9/7/2022 7:05 AM, AJAY SINGH VERMA wrote:

Dear Sir,

TiC.in1 is attached...

*From:* AJAY SINGH VERMA 
*Sent:* Wednesday, September 7, 2022 6:20 PM
*To:* wien-requ...@zeus.theochem.tuwien.ac.at 
; wien zeus 


*Subject:* Re: Error while running IRelast - calljob_lapw
Dear All,
After applying patch as suggested by Sir Gavin Abo, now I am getting 
this underlined error


##
Start for AUTO intialization Styp3_-2.0
##
 2 Atoms found:  with labels Ti1  C 1
generate atomic configuration for atom 1 : Ti1
generate atomic configuration for atom 2 : C 1
_SET: Command not found._
 next is setrmt
 specify nn-bondlength factor: (usually=2) [and optionally dlimit, 
dstmax (about 1.d-5, 20)]

 DSTMAX:   20.000
 iix,iiy,iiz           5           5           5 28.3378802   
     29.4945301  40.9100550

 NAMED ATOM: Ti1       Z changed to IATNR+1000 to determine equivalency
 NAMED ATOM: C 1       Z changed to IATNR+1000 to determine equivalency

    ATOM  1  Ti1        ATOM  2  C 1
 RMT(  1)=2.12000 AND RMT(  2)=1.74000
 SUMS TO 3.86000  LT.  NN-DIST= 4.09019

    ATOM  2  C 1        ATOM  1  Ti1
 RMT(  2)=1.74000 AND RMT(  1)=2.12000
 SUMS TO 3.86000  LT.  NN-DIST= 4.09019
STOP NN ENDS
0.001u 0.000s 0:00.00 0.0%0+0k 0+40io 0pf+0w
atom  Z   RMT-max   RMT
 1  22.0  2.12   2.12
 2   6.0  1.74   1.74
file    TiC.struct_setrmt   generated
 next is nn
 specify nn-bondlength factor: (usually=2) [and optionally dlimit, 
dstmax (about 1.d-5, 20)]

 DSTMAX:   20.000
 iix,iiy,iiz           5           5           5 28.3378802   
     29.4945301  40.9100550

 NAMED ATOM: Ti1       Z changed to IATNR+1000 to determine equivalency
 NAMED ATOM: C 1       Z changed to IATNR+1000 to determine equivalency

    ATOM  1  Ti1        ATOM  2  C 1
 RMT(  1)=2.12000 AND RMT(  2)=1.74000
 SUMS TO 3.86000  LT.  NN-DIST= 4.09019

    ATOM  2  C 1        ATOM  1  Ti1
 RMT(  2)=1.74000 AND RMT(  1)=2.12000
 SUMS TO 3.86000  LT.  NN-DIST= 4.09019
STOP NN ENDS
0.002u 0.000s 0:00.00 0.0%0+0k 0+16io 0pf+0w
 next is sgroup
>   sgroup  (18:16:55) 0.000u 0.000s 0:00.00 0.0% 0+0k 0+8io 0pf+0w
  Names of point group: mmm    2/m 2/m 2/m   D2h
  Names of point group: mmm    2/m 2/m 2/m   D2h
Number and name of space group: 71 (I m m m)
 next is symmery
>   symmetry  (18:16:55)  SPACE GROUP CONTAINS INVERSION
0.000u 0.001s 0:00.00 0.0%0+0k 0+32io 0pf+0w
 next is lstart
  SELECT XCPOT:
  recommended: PBE    [(13) GGA of Perdew-Burke-Ernzerhof 96]
               LDA    [( 5)]
               WC     [(11)  GGA of Wu-Cohen 2006]
               PBESOL [(19) GGA of Perdew etal. 2008]
  SELECT ENERGY to separate core and valence states:
  recommended: -6.0 Ry (check how much core charge leaks out of MT-sphere)
  ALTERNATIVELY: specify charge localization (between 0.97 and 1.0) to 
select core state

STOP LSTART ENDS
>   inputfiles prepared (18:16:55)
 inputfiles prepared
 next is kgen
  NUMBER OF K-POINTS IN WHOLE CELL: (0 allows to specify 3 divisions of G)
 length of reciprocal lattice vectors:   1.313   1.349 1.537  13.563 
 13.930  15.879

  Shift of k-mesh allowed. Do you want to shift: (0=no, 1=shift)
         427  k-points generated, ndiv=          14    14          14
STOP KGEN ENDS
 next is dstart
>   dstart  -p(18:16:55) starting parallel dstart at Wednesday 07 
September 2022 06:16:55 PM IST

 .machine0 : processors
running dstart in single mode
STOP DSTART ENDS
0.957u 0.227s 0:00.24 487.5%  0+0k 0+800io 0pf+0w

-> new TiC.in0 generated
  init_lapw finished ok
starting parallel dstart at Wednesday 07 September 2022 06:16:56 PM IST
 .machine0 : processors
running dstart in single mode
STOP DSTART ENDS
0.935u 0.247s 0:00.23 508.6%  0+0k 0+704io 0pf+0w
0.021u 0.000s 0:00.02 100.0%  0+0k 0+688io 0pf+0w
clmextrapol_lapw has generated a new TiC.clmsum
STOP  LAPW0 END
At line 393 of file inilpw.f (unit = 5, file = 'TiC.in1')
_Fortran runtime error: Bad integer for item 2 in list input_

Error termination. Backtrace:
#0  0x145928ddfae0 in ???
#1  0x145928de0659 in ???
#2  0x145928de128f in ???
#3  0x14592902b3fb in ???
#4  0x14592902e3ba in ???
#5  0x14592902f0ba in ???
#6  0x55749c178436 in ???
#7  0x55749c17bd0b in ???
#8  0x55749c14f83e in ???
#9  0x14592898dd8f in __libc_start_call_main
  at ../sysdeps/nptl/libc_start_call_main.h:58
#10  0x14592898de3f in __libc_start_main_impl
  at ../csu/libc-start.c:392
#11  0x55749c14f864 in ???
#12  0x in ?

Re: [Wien] Error while running IRelast - calljob_lapw

[Gavin Abo]

The "Fortran runtime error: Bad integer for item 2 in list input" is 
likely because in TiC.in1 file the program cannot find a integer that it 
is looking for.  For example, it might be needing to read an integer 
(8), but maybe a float value (8.0) got accidentally put there instead.  
If you need further help, you would have to share the TiC.in1 file that 
is causing the error.



On 9/7/2022 6:50 AM, AJAY SINGH VERMA wrote:

Dear All,
After applying patch as suggested by Sir Gavin Abo, now I am getting 
this underlined error


##
Start for AUTO intialization Styp3_-2.0
##
 2 Atoms found:  with labels Ti1  C 1
generate atomic configuration for atom 1 : Ti1
generate atomic configuration for atom 2 : C 1
_SET: Command not found._
 next is setrmt
 specify nn-bondlength factor: (usually=2) [and optionally dlimit, 
dstmax (about 1.d-5, 20)]

 DSTMAX:   20.000
 iix,iiy,iiz           5           5           5 28.3378802   
     29.4945301  40.9100550

 NAMED ATOM: Ti1       Z changed to IATNR+1000 to determine equivalency
 NAMED ATOM: C 1       Z changed to IATNR+1000 to determine equivalency

    ATOM  1  Ti1        ATOM  2  C 1
 RMT(  1)=2.12000 AND RMT(  2)=1.74000
 SUMS TO 3.86000  LT.  NN-DIST= 4.09019

    ATOM  2  C 1        ATOM  1  Ti1
 RMT(  2)=1.74000 AND RMT(  1)=2.12000
 SUMS TO 3.86000  LT.  NN-DIST= 4.09019
STOP NN ENDS
0.001u 0.000s 0:00.00 0.0%0+0k 0+40io 0pf+0w
atom  Z   RMT-max   RMT
 1  22.0  2.12   2.12
 2   6.0  1.74   1.74
file    TiC.struct_setrmt   generated
 next is nn
 specify nn-bondlength factor: (usually=2) [and optionally dlimit, 
dstmax (about 1.d-5, 20)]

 DSTMAX:   20.000
 iix,iiy,iiz           5           5           5 28.3378802   
     29.4945301  40.9100550

 NAMED ATOM: Ti1       Z changed to IATNR+1000 to determine equivalency
 NAMED ATOM: C 1       Z changed to IATNR+1000 to determine equivalency

    ATOM  1  Ti1        ATOM  2  C 1
 RMT(  1)=2.12000 AND RMT(  2)=1.74000
 SUMS TO 3.86000  LT.  NN-DIST= 4.09019

    ATOM  2  C 1        ATOM  1  Ti1
 RMT(  2)=1.74000 AND RMT(  1)=2.12000
 SUMS TO 3.86000  LT.  NN-DIST= 4.09019
STOP NN ENDS
0.002u 0.000s 0:00.00 0.0%0+0k 0+16io 0pf+0w
 next is sgroup
>   sgroup  (18:16:55) 0.000u 0.000s 0:00.00 0.0% 0+0k 0+8io 0pf+0w
  Names of point group: mmm    2/m 2/m 2/m   D2h
  Names of point group: mmm    2/m 2/m 2/m   D2h
Number and name of space group: 71 (I m m m)
 next is symmery
>   symmetry  (18:16:55)  SPACE GROUP CONTAINS INVERSION
0.000u 0.001s 0:00.00 0.0%0+0k 0+32io 0pf+0w
 next is lstart
  SELECT XCPOT:
  recommended: PBE    [(13) GGA of Perdew-Burke-Ernzerhof 96]
               LDA    [( 5)]
               WC     [(11)  GGA of Wu-Cohen 2006]
               PBESOL [(19) GGA of Perdew etal. 2008]
  SELECT ENERGY to separate core and valence states:
  recommended: -6.0 Ry (check how much core charge leaks out of MT-sphere)
  ALTERNATIVELY: specify charge localization (between 0.97 and 1.0) to 
select core state

STOP LSTART ENDS
>   inputfiles prepared (18:16:55)
 inputfiles prepared
 next is kgen
  NUMBER OF K-POINTS IN WHOLE CELL: (0 allows to specify 3 divisions of G)
 length of reciprocal lattice vectors:   1.313   1.349 1.537  13.563 
 13.930  15.879

  Shift of k-mesh allowed. Do you want to shift: (0=no, 1=shift)
         427  k-points generated, ndiv=          14  14          14
STOP KGEN ENDS
 next is dstart
>   dstart  -p(18:16:55) starting parallel dstart at Wednesday 07 
September 2022 06:16:55 PM IST

 .machine0 : processors
running dstart in single mode
STOP DSTART ENDS
0.957u 0.227s 0:00.24 487.5%  0+0k 0+800io 0pf+0w

-> new TiC.in0 generated
  init_lapw finished ok
starting parallel dstart at Wednesday 07 September 2022 06:16:56 PM IST
 .machine0 : processors
running dstart in single mode
STOP DSTART ENDS
0.935u 0.247s 0:00.23 508.6%  0+0k 0+704io 0pf+0w
0.021u 0.000s 0:00.02 100.0%  0+0k 0+688io 0pf+0w
clmextrapol_lapw has generated a new TiC.clmsum
STOP  LAPW0 END
At line 393 of file inilpw.f (unit = 5, file = 'TiC.in1')
_Fortran runtime error: Bad integer for item 2 in list input_

Error termination. Backtrace:
#0  0x145928ddfae0 in ???
#1  0x145928de0659 in ???
#2  0x145928de128f in ???
#3  0x14592902b3fb in ???
#4  0x14592902e3ba in ???
#5  0x14592902f0ba in ???
#6  0x55749c178436 in ???
#7  0x55749c17bd0b in ???
#8  0x55749c14f83e in ???
#9  0x14592898dd8f in __libc_start_call_main
  at ../sysdeps/nptl/libc_start_call_main.h:58
#10  0x14592898de3f in __libc_start_main_impl
  at ../csu/libc-start.c:392
#11  0x55749c14f864 in ???
#12  0x in ???
_grep: lapw2*.error: No such file or directory_

_>   stop error_
-
_ERROR status in Styp3_-2.0
Wien mailing list
Wie

Re: [Wien] Error while running IRelast - calljob_lapw

[Gavin Abo]

See previous post at the following link with additional details on 
applying calLa_Pre_elast.patch:



https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg21884.html


On 9/6/2022 7:44 AM, AJAY SINGH VERMA wrote:

Dear Sir,

I am using WIEN2k 21.1 with the gfortran compiler.

For the patch work, do I need to add following
calLa_Pre_elast.patch 
 
in calLa_Pre_elast.f file of SRC_IRelast folder ?


Patch is :

310c310

< 101 format(' V0,B(GPa),BP,E0',3f15.4,f18.6)

---

> 101 format(16x,3f15.4,f18.6)

Can you please tell me so.

*From:* AJAY SINGH VERMA 
*Sent:* Tuesday, September 6, 2022 4:52 PM
*To:* wien-requ...@zeus.theochem.tuwien.ac.at 
; wien zeus 


*Subject:* Re: Error while running IRelast - calljob_lapw
Dear Sir/Mam

As per your suggestion,

the result of following commands show that initIR_lapw is executable

ls -all initIR_lapw
-rwxr-xr-x 1 rashmi rashmi 20670 Sep  5 23:06 initIR_lapw

if [ -x initIR_lapw ]; then echo "File is executable"; else echo "File 
is not executable"; fi

rely comes file is executable

what should be done next to remove error

*From:* AJAY SINGH VERMA
*Sent:* Tuesday, September 6, 2022 2:09 PM
*To:* wien-requ...@zeus.theochem.tuwien.ac.at 
; wien zeus 


*Subject:* Error while running IRelast - calljob_lapw
Dear all,

While running elastic constant of cubic TiC, this is the error 
encountered


root/Wien2k/SRC_IRelast/script-elastic/x: Command not found.
 \n stop error \n
clmextrapol_lapw did not extrapolate new density because of missing 
TiC.rsp

head: cannot open 'TiC.inm' for reading: No such file or directory
head: cannot open 'TiC.inm' for reading: No such file or directory
no TiC.clmsum(_old) file found, which is necessary for lapw0 !
grep: *scf1*: No such file or directory
grep: lapw2*.error: No such file or directory

>   stop error
-
ERROR status in Styp3_-2.0


I have tried earlier given solutions (below) but cant remove error.

 1. chmod +x *
2.
 3. "Please move (not copy) initIR_lapw from
SRC_IRelast/script-elastic to WIEN2k
directory and then run it again."
 4. giving path in initIR_lapw

Kindly help.___
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Re: [Wien] Error while running IRelast - calljob_lapw

[Gavin Abo]

Maybe you are using an old WIEN2k version, the "x: Command not found" 
happened a lot in an older WIEN2k version.



To have the least problems with IRelast, you may want to consider 
upgrading to latest WIEN2k (currently, 21.1) using Intel oneAPI for the 
compiler.  If you use WIEN2k 21.1 with the gfortran compiler, you will 
likely need the calLa_Pre_elast.patch [1].



If you are having to use an old WIEN2k version.  Some old maybe 
inaccurate notes of mine that may or may not help are:



In the WIEN2k 19.2 directory of SRC_IRelast/script-elastic, must: chmod +x *

Also in $WIENROOT must: chmod +x initIR_lapw

The SRC_IRelast/script-elastic/initIR_lapw must be renamed or moved so 
that it does not override the one in $WIENROOT.



[1] https://github.com/gsabo/WIEN2k-Patches/tree/master/21.1


Kind Regards,

Gavin

WIEN2k user


On 9/6/2022 2:39 AM, AJAY SINGH VERMA wrote:

Dear all,

While running elastic constant of cubic TiC, this is the error 
encountered


root/Wien2k/SRC_IRelast/script-elastic/x: Command not found.
 \n stop error \n
clmextrapol_lapw did not extrapolate new density because of missing 
TiC.rsp

head: cannot open 'TiC.inm' for reading: No such file or directory
head: cannot open 'TiC.inm' for reading: No such file or directory
no TiC.clmsum(_old) file found, which is necessary for lapw0 !
grep: *scf1*: No such file or directory
grep: lapw2*.error: No such file or directory

>   stop error
-
ERROR status in Styp3_-2.0


I have tried earlier given solutions (below) but cant remove error.

 1. chmod +x *
2.
 3. "Please move (not copy) initIR_lapw from
SRC_IRelast/script-elastic to WIEN2k
directory and then run it again."
 4. giving path in initIR_lapw

Kindly help.___
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Re: [Wien] Error : configure: error: could not find mpi library for --enable-mpi while installing fftw

[Gavin Abo]

I looked into this further, and below is my Ubuntu bash terminal output.


By removing mpicc from my environment, I was able to reproduce your 
reported error:



username@computername:~/fftw-3.3.10$ which mpicc

username@computername:~/fftw-3.3.10$ grep openmpi ~/.bashrc

username@computername:~/fftw-3.3.10$ ./configure FCC=gfortran CC=gcc 
MPICC=mpicc --enable-mpi --prefix=$HOME/fftw-3.3.10

...
checking for mpicc... mpicc
checking for MPI_Init... no
checking for MPI_Init in -lmpi... no
checking for MPI_Init in -lmpich... no
configure: error: could not find mpi library for --enable-mpi


To resolve it, I checked that mpicc was generated by "make all install" 
for Open MPI (in step 3 of [1]) in the bin directory:



username@computername:~/fftw-3.3.10$ ls ~/openmpi-4.1.4/bin/
aggregate_profile.pl  mpiCC    mpif77   mpirun  ompi-server 
orte-clean  orterun
mpic++    mpicxx   mpif90   ompi-clean  opal_wrapper 
orted   orte-server
mpicc mpiexec mpifort  ompi_info   ortecc    
orte-info   profile2mat.pl



Then, I added to my environment [2] mpicc:


username@computername:~/fftw-3.3.10$ gedit ~/.bashrc
username@computername:~/fftw-3.3.10$ source ~/.bashrc
username@computername:~/fftw-3.3.10$ which mpicc
/home/username/openmpi-4.1.4/bin/mpicc
username@computername:~/fftw-3.3.10$ grep openmpi ~/.bashrc
export PATH=$PATH:/home/username/openmpi-4.1.4/bin
export 
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/username/OpenBLAS:/home/username/openmpi-4.1.4/lib



Next, I ran mpicc to see what version it has:


username@computername:~/fftw-3.3.10$ mpicc --version
gcc (Ubuntu 11.2.0-19ubuntu1) 11.2.0
Copyright (C) 2021 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.


Finally, when running configure, the error had gone away and the 
MPI_Init with "no" above can be seen to have changed to "yes" below:



username@computername:~/fftw-3.3.10$ ./configure FCC=gfortran CC=gcc 
MPICC=mpicc --enable-mpi --prefix=$HOME/fftw-3.3.10

...
checking for mpicc... mpicc
checking for MPI_Init... yes
checking for mpi.h... yes
checking for mpirun... mpirun
...


Your .bashrc does look correct.  After saving the changes to .bashrc, 
maybe you didn't reload the new .bashrc settings for example by running 
"source ~/.bashrc" (Or alternatively: closing/opening a new terminal, 
logging in/out, or by restarting the computer).



[1] 
https://github.com/gsabo/WIEN2k-Docs/blob/main/WIEN2k21.1_Ubuntu22.04_Install_with_gfortran.pdf


[2] https://help.ubuntu.com/community/EnvironmentVariables


Kind Regards,

Gavin

WIEN2k user


On 9/5/2022 9:36 AM, Gavin Abo wrote:


The openmpi-4.1.4 might not be installed.  What does "which mpicc" 
return as output?



On 9/5/2022 8:52 AM, AJAY SINGH VERMA wrote:

Dear all,
I am following below pdf to install wien2k


[WIEN2k 21.1 Install with gfortran
August 1, 2022
Linux Operating System Version (lsb_release -a): Ubuntu 22.04 LTS
Fortran Compiler Version (gfortran --version): gfortran 11.2.0
WIEN2k Version (cat $WIENROOT/WIEN2k_VERSION): 21.1 (Release 14/4/2021)]



I have edited bashrc as follow for Openblas and openmpi



XCRYSDEN_TOPDIR=/usr/share/xcrysden
XCRYSDEN_LIB_BINDIR=/usr/lib/xcrysden
export XCRYSDEN_TOPDIR
export XCRYSDEN_LIB_BINDIR
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/rashmi/OpenBLAS



PATH=/home/rashmi/openmpi-4.1.4/bin:$PATH
LD_LIBRARY_PATH=/home/rashmi/OpenBLAS:/home/rashmi/openmpi-4.1.4/lib:$LD_LIBRARY_PATH
export PATH
export LD_LIBRARY_PATH



While following the commands for installing fftw-3.3.10 and giving 
this particular command


./configure FCC=gfortran CC=gcc MPICC=mpicc --enable-mpi 
--prefix=$HOME/fftw-3.3.10


I am getting error

configure: error: could not find mpi library for --enable-mpi

Kindly help.___
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Re: [Wien] Error : configure: error: could not find mpi library for --enable-mpi while installing fftw

[Gavin Abo]

The openmpi-4.1.4 might not be installed.  What does "which mpicc" 
return as output?



On 9/5/2022 8:52 AM, AJAY SINGH VERMA wrote:

Dear all,
I am following below pdf to install wien2k


[WIEN2k 21.1 Install with gfortran
August 1, 2022
Linux Operating System Version (lsb_release -a): Ubuntu 22.04 LTS
Fortran Compiler Version (gfortran --version): gfortran 11.2.0
WIEN2k Version (cat $WIENROOT/WIEN2k_VERSION): 21.1 (Release 14/4/2021)]



I have edited bashrc as follow for Openblas and openmpi



XCRYSDEN_TOPDIR=/usr/share/xcrysden
XCRYSDEN_LIB_BINDIR=/usr/lib/xcrysden
export XCRYSDEN_TOPDIR
export XCRYSDEN_LIB_BINDIR
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/rashmi/OpenBLAS



PATH=/home/rashmi/openmpi-4.1.4/bin:$PATH
LD_LIBRARY_PATH=/home/rashmi/OpenBLAS:/home/rashmi/openmpi-4.1.4/lib:$LD_LIBRARY_PATH
export PATH
export LD_LIBRARY_PATH



While following the commands for installing fftw-3.3.10 and giving 
this particular command


./configure FCC=gfortran CC=gcc MPICC=mpicc --enable-mpi 
--prefix=$HOME/fftw-3.3.10


I am getting error

configure: error: could not find mpi library for --enable-mpi

Kindly help.___
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Re: [Wien] Error in IRelast

[Gavin Abo]

Based on your post below, the -llapack_lapw in your compiler settings 
(adjustable in siteconfig) has a dash (-) in it.  However, the dash is 
missing in -llapack, which looks like it could cause that error.


Instead of "-llapack_lapw -lblas_lapw -lblas -llapack", it is noted that 
some prefer to use instead "-lopenblas" along with an operating system 
package install of the openblas library [1,2].


On the other hand, I typically use a source code install of openblas [3,4].

[1] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg21045.html
[2] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg21482.html

[3] https://www.openblas.net/
[4] 
https://github.com/gsabo/WIEN2k-Docs/blob/main/WIEN2k21.1_Ubuntu22.04_Install_with_gfortran.pdf 



Kind Regards,

Gavin

On 9/3/2022 9:17 PM, Peeyush Kumar Kamlesh wrote:

Dear sir,
After following the steps in provided solution, i am getting

gfortran -o ../C_setupc1112 C_setupc1112.o getcalljobC.o makestructC.o 
-ffree-form -O2 -ftree-vectorize -march=native -ffree-line-length-none 
-ffpe-summary=none -L../SRC_lib -llapack_lapw -lblas_lapw -lblas llapack


/usr/bin/ld: cannot find llapack: No such file or directory
collect2: error: ld returned 1 exit status
make: *** [Makefile:227: ../C_setupc1112] Error 1


Point to mention is that in my system, lapack folder is in 
Computer/usr/lib/×86_64-linux-gnu


On Sat, 3 Sept 2022, 6:03 pm Peeyush Kumar Kamlesh, 
 wrote:


Dear Users,
I am using WIEN2k 21.1. While running set_elast_lapw in IRelast of
a material of space-group 225, i am facing following error:

setup information for (c11+2c12) elastic constant calculation:

C_setupc1112: command not found

chmod: cannot access 'CUBIC.job': no such file or directory

Kindly help in resolving the issue.
Thank you!

Best Regards!


___
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Re: [Wien] Error in IRelast

[Gavin Abo]

Check the directory where your WIEN2k installation is. C_setupc1112 
should be a non-empty file there.  On my system for example, I find 
C_steupc1112 under my WIEN2k folder:


username@computername:~$ ls -l $WIENROOT/C_setupc1112
-rwxrwxr-x 1 username username 54120 Jul  5 07:09 
/home/username/WIEN2k/C_setupc1112


If the file is missing, you may have to recompile it.  Run siteconfig 
and look under "Compile time errors (if any) were:" to see if there are 
any failure messages.  If there were no failures, there will be no 
messages under it:


username@computername:~$ cd $WIENROOT
username@computername:~/WIEN2k$ ./siteconfig
...
  Selection: R
...
 Selection: S
   Which program to recompile? IRelast

SRC_IRelast ...
gfortran -o ../C_setupc1112 C_setupc1112.o getcalljobC.o makestructC.o 
-ffree-form -O2 -ftree-vectorize -march=native -ffree-line-length-none 
-ffpe-summary=none -L../SRC_lib -L/home/username/OpenBLAS -lopenblas 
-lpthread

...
gfortran -o ../stabilityJAC stabilityJAC.o  -ffree-form -O2 
-ftree-vectorize -march=native -ffree-line-length-none 
-ffpe-summary=none -L../SRC_lib -L/home/username/OpenBLAS -lopenblas 
-lpthread

Copying programs

done.

Compile time errors (if any) were:


Check file   compile.msg   in the corresponding SRC_* directory for the
compilation log and more info on any compilation problem.

 Press RETURN to continue
...
  Selection: Q

Kind Regards,

Gavin

WIEN2k user

On 9/3/2022 6:33 AM, Peeyush Kumar Kamlesh wrote:

Dear Users,
I am using WIEN2k 21.1. While running set_elast_lapw in IRelast of a 
material of space-group 225, i am facing following error:


setup information for (c11+2c12) elastic constant calculation:

C_setupc1112: command not found

chmod: cannot access 'CUBIC.job': no such file or directory

Kindly help in resolving the issue.
Thank you!

Best Regards!___
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Re: [Wien] [EXTERNAL] Re: Wien2k with oneAPI on Mac OSX (Monterey)

[Gavin Abo]

The sed may need different arguments for macOS based on webpages at the 
following two links:


https://stackoverflow.com/questions/29081799/sed-1-invalid-command-code-f

https://stackoverflow.com/questions/19456518/error-when-using-sed-with-find-command-on-os-x-invalid-command-code

WIEN2k I installed in Linux using oneAPI 2021.6.0 as described at the 
following link:


https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg21943.html

It is not shown in the above link, but the TiC example from the WIEN2k 
userguide did run and the calculation did complete the scf cycles just 
fine.


The SIGSEGV error I think is likely not related to the sed error.  I 
don't have MacOS, such that that I'm unable help troubleshot the error.


There were two links that helped me in the past with SIGSEGV errors.  So 
they might help you as well, they are:


https://www.intel.com/content/www/us/en/developer/articles/troubleshooting/determining-root-cause-of-sigsegv-or-sigbus-errors.html

http://www.democritos.it/pipermail/pw_forum/2005-March/002272.html

Kind Regards,

Gavin
WIEN2k user

On 8/4/2022 8:54 AM, Zhu, Jianxin via Wien wrote:


Dear Laurence,

I would like to respond to your N.B. on the absolute path. –

1/

After I fire up ./siteconfig_lapw, and choose “O”, and then “S” (for 
save), it displays


   ***

   *                     Changing compiler options       *

   ***

  Changing Parallel Compiler to

sed: 1: "/Users/jxzhu/wien2k.19. ...": invalid command code j

  changing Makefile in SRC_lib/blas_lapw

  changing Makefile in SRC_lib/lapack_lapw

…

Since I only want to install the non-MPI version of the code, I don’t 
understand why there is a header “Changing Parallel Compiler to”.


But maybe this block for parallel compiler is skipped, I am not so 
concerned.


2/ oneAPI on Mac has a strange way to set up on tcsh shell that I am 
using. It is advised that we do the following on an open terminal not 
placed into the login shell script file


bash-c'source /opt/intel/oneapi/setvars.sh intel64 ; exec csh'

3/

The more concerning line is:

sed: 1: "/Users/jxzhu/wien2k.19. ...": invalid command code j

Could it be the root cause for the Segment Fault error in “x lapw0”?

forrtl: severe (174): SIGSEGV, segmentation fault occurred

Image             PC                Routine            Line   Source

lapw0             00010484EE84  Unknown   Unknown  Unknown

libsystem_platfor  7FF80F4C8DFD  Unknown             Unknown  Unknown

lapw0             0001047FE935  _xcpot1_   1  xcpot1.f

lapw0             0001047BF484  _MAIN__   2308  lapw0.F

lapw0             00010472CC2E  Unknown   Unknown  Unknown

0.083u 0.110s 0:00.34 55.8% 0+0k 0+0io 949pf+0w

I am now coming back to try to understand this “sed” error.

4/ I do set a WIENROOT in the PATH of the login shell script file.

Best,

Jianxin

#
Jian-Xin Zhu, Ph.D
Theoretical Division, MS B262
Los Alamos National Laboratory
Los Alamos, New Mexico 87545
Phone: (505) 667 2363 (T-4);

(505) 667 6602 (CINT)

Fax: (505) 665 4063
Email: jxzhu.at.lanl.gov 
URL: http://cint.lanl.gov 
##

*From: *Laurence Marks 
*Reply-To: *"laurence.ma...@gmail.com" 
*Date: *Sunday, July 10, 2022 at 12:35 PM
*To: *A Mailing list for WIEN2k users 
*Cc: *Jianxin Zhu 
*Subject: *[EXTERNAL] Re: [Wien] Wien2k with oneAPI on Mac OSX (Monterey)

I only compiled on Linux, and I suspect Peter did as well. Maybe 
others have in OSX?


You should probably check the compiler options for anything specific 
to OSX, and . The errors entering xcpot1 indicates something major 
wrong with the compilation.


N.B., it may not matter but I do not understand why you have a full 
path in the parallel compiler. More normal is to setup your PATH 
variable properly, then just use the short name. Did you source the 
Intel script to set the environment (needed)?


--
Professor Laurence Marks
Department of Materials Science and Engineering, Northwestern University
www.numis.northwestern.edu 

"Research is to see what everybody else has seen, and to think what 
nobody else has thought" Albert Szent-Györgyi


On Sun, Jul 10, 2022, 1:01 PM Zhu, Jianxin via Wien 
 wrote:


Dear All,

Recently I upgraded my Mac OSX system to Monterey.
I also downloaded and installed  Intel oneAPI 2022.1.0 on the system.

1/ The compilation of  wien2k.21.1 (and wien2k.19.1) seems to be
successful.
[I only want to install the k-point coarse-grained wien2k on the
system.
After I enter "O" (Compiling Options) and then "S" (Save and
Quit), the following
comes up

 

Re: [Wien] Query regarding same structure with different symmetry

[Gavin Abo]

If you have a struct file with spacegroup B112/m [ cell choice 2 ] (No. 
12), you should be able to view it in StructGen for example then copy 
and paste the structure parameters from it into SETSTRU [1] box for 
converting it to C12/m1 [ cell choice 1 ] (No. 12).


Alternatively, you could likely open the struct file with spacegroup 
B112/m [ cell choice 2 ] (No. 12) in VESTA and export it as a cif file.  
Then, you could try loading that cif file in SETSTRU for converting it 
to C12/m1 [ cell choice 1 ] (No. 12).


In the WIEN2k 21.1 usersguide (UG) on page 231, there is section "9.24 
struct2cif" [2].  Instead of VESTA, there is struct2cif that you could try.


On the other hand, if your struct file has a P lattice type with no 
space group, then you could use "x sgroup" (refer to section "6.2 
SGROUP" on page 114 of the UG [2]).  If the P struct file does indeed 
reduce to be a structure having the B112/m [ cell choice 2 ] (No. 12), 
then you can accept the new struct file from sgroup that has spacegroup 
B112/m [ cell choice 2 ] (No. 12).  The methods described above could 
then be used to get C12/m1 [ cell choice 1 ] (No. 12) using SETSTRU.


[1] https://www.cryst.ehu.es/cryst/setstru.html
[2] http://susi.theochem.tuwien.ac.at/reg_user/textbooks/usersguide.pdf

Kind Regards,

Gavin
WIEN2k user

On 7/27/2022 7:53 AM, shamik chakrabarti wrote:

Dear Prof. Gavin,

                     I have another query. I want to transform the DFT 
converged struct file with B112/m [ cell choice 2 ] (No. 12) to the 
analogue of Experimental cif file with C12/m1 [ cell choice 1 ] (No. 
12) . But, as the struct file comes with P type, it is not able to be 
recognized as B112/m [ cell choice 2 ] (No. 12) in the link you 
have provided. Please suggest what to do?


with kind regards,

On Wed, 27 Jul 2022 at 14:46, shamik chakrabarti 
 wrote:


Dear Prof. Gavin,
 .  .  .  .  .  .  Thank you for your informative response Sir. It
is very helpful for me.

With kind regards,

    On Wed, Jul 27, 2022, 13:47 Gavin Abo  wrote:

If it is the "Transformation matrix (P,p)" that you are
looking for, you can get it as follows.

1. Go to: https://www.cryst.ehu.es/cryst/setstru.html

2. Click Browse button and select your Li3Co2SbO6_EXP_ncm.cif

3. Click Transform button

4. Select Initial C 1 2/m 1 [ cell choice 1 ]

5. Select Final B 1 1 2/m [ cell choice 2 ]

6. Click Transform button

7. Finally, you should see the following:

*Initial Setting*: C12/m1 [ cell choice 1 ] (No. 12)

12
5.2161 8.9888 5.1706 90 110.082 90

...

*Final Setting*: B112/m [ cell choice 2 ] (No. 12)

12 #B112/m:c2
5.2161 5.9516 8.9888 90.00 90.00 125.32

...

*Transformation matrix (P, p): a,-a-c,b; 0,0,0*

Matrix form:

(P, p) =

[ 1    -1 0 ] [  0]
[ 0 0 1 ] [  0]
[ 0    -1 0 ] [  0]

Kind Regards,

Gavin
WIEN2k user

References:

https://www.cryst.ehu.es/cgi-bin/cryst/programs/nph-doc-trmat


https://mattermodeling.stackexchange.com/questions/4090/rotation-of-crystal-structure-to-match-another-structure-of-the-same-compound-po

On 7/25/2022 9:46 AM, shamik chakrabarti wrote:

Dear Wien2k users,
                               Please pardon me for asking a
question which may not directly linked to wien2k. I have two
structures of Li3Co2SbO6 (attached with this mail), one from
experiment & another from DFT simulation. The experimental
structure is monoclinic with angle Beta=110.082 degree. To
simulate this monoclinic structure I have to make the
following changes using Vesta; b to c, c to b, & angle Gamma=
125.318 degree. My query is; how the value of angle different
from 90 degree changes from 110.082 degree to 125.318 degree?
Could you suggest the symmetry operation required to change
this value?

Looking forward to your reply.

with regards,

-- 
Dr. Shamik Chakrabarti

Research Fellow
Department of Physics
Indian Institute of Technology Patna
Bihta-801103
Patna
Bihar, India

___
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--
Dr. Shamik Chakrabarti
Research Fellow
Department of Physics
Indian Institute of Technology Patna
Bihta-801103
Patna
Bihar, India___
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Re: [Wien] Installing Wien2k_21.1 on Ubuntu 22.04 LTS

[Gavin Abo]

The word document I made currently available (click Download button or 
View raw link) on the webpage at:


https://github.com/gsabo/WIEN2k-Docs/blob/main/WIEN2k21.1_Ubuntu22.04_Install_with_gfortran.docx

The steps of that document use the default NUME and NMATMAX values.  You 
may of course increase those values for utilizing more of your system 
RAM for WIEN2k calculations when you have larger structures that need it 
following the WIEN2k 21.1 userguide [ 
http://www.wien2k.at/reg_user/textbooks/usersguide.pdf ] (refer to 
section 11.2.2 Site configuration for WIEN2k on page 248) or by 
referring to past mailing list posts such as those at the following 
three links:


https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg13288.html
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg16704.html
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg08136.html

Best Regards,

Gavin
WIEN2k user

On 7/26/2022 4:57 AM, Victor Zenou wrote:

Dear Gavin
Thanks a lot. I already started installing WIEN2k 21.1 using your 
"WIEN2k 21.1 Install with gfortran.pdf". Can you upload the same as a 
word document?
Right now I'm using 32 GB of RAM, and later going to add more 32 GB . 
Does that addition require any update in the Wien2k installation?

Best Regards, Victor___
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http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html

Re: [Wien] Query regarding same structure with different symmetry

[Gavin Abo]

If it is the "Transformation matrix (P,p)" that you are looking for, you 
can get it as follows.


1. Go to: https://www.cryst.ehu.es/cryst/setstru.html

2. Click Browse button and select your Li3Co2SbO6_EXP_ncm.cif

3. Click Transform button

4. Select Initial C 1 2/m 1 [ cell choice 1 ]

5. Select Final B 1 1 2/m [ cell choice 2 ]

6. Click Transform button

7. Finally, you should see the following:

*Initial Setting*: C12/m1 [ cell choice 1 ] (No. 12)

12
5.2161 8.9888 5.1706 90 110.082 90

...

*Final Setting*: B112/m [ cell choice 2 ] (No. 12)

12 #B112/m:c2
5.2161 5.9516 8.9888 90.00 90.00 125.32

...

*Transformation matrix (P, p): a,-a-c,b; 0,0,0*

Matrix form:

(P, p) =

[ 1    -1 0 ] [  0]
[ 0 0 1 ] [  0]
[ 0    -1 0 ] [  0]

Kind Regards,

Gavin
WIEN2k user

References:

https://www.cryst.ehu.es/cgi-bin/cryst/programs/nph-doc-trmat

https://mattermodeling.stackexchange.com/questions/4090/rotation-of-crystal-structure-to-match-another-structure-of-the-same-compound-po

On 7/25/2022 9:46 AM, shamik chakrabarti wrote:

Dear Wien2k users,
                               Please pardon me for asking a question 
which may not directly linked to wien2k. I have two structures of 
Li3Co2SbO6 (attached with this mail), one from experiment & another 
from DFT simulation. The experimental structure is monoclinic with 
angle Beta=110.082 degree. To simulate this monoclinic structure I 
have to make the following changes using Vesta; b to c, c to b, & 
angle Gamma= 125.318 degree. My query is; how the value of angle 
different from 90 degree changes from 110.082 degree to 125.318 
degree? Could you suggest the symmetry operation required to change 
this value?


Looking forward to your reply.

with regards,

--
Dr. Shamik Chakrabarti
Research Fellow
Department of Physics
Indian Institute of Technology Patna
Bihta-801103
Patna
Bihar, India___
Wien mailing list
Wien@zeus.theochem.tuwien.ac.at
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Re: [Wien] Installing Wien2k_21.1 on Ubuntu 22.04 LTS

[Gavin Abo]

The oneAPI is likely easier to install as it has less steps. As you 
probably saw, after setting up the Intel repo in Ubuntu, there is only 
one step "sudo apt install intel-hpckit" that will install ifort, MKL, 
and intelmpi [1].  Comparing that to gfortran where you will have 
multiple packages and steps for getting the equivalent functionality 
(gfortran, OpenBLAS, and openmpi/ScaLAPACK) [2].  The WIEN2k developers 
mostly use the Intel compilers.  Thus, the WIEN2k code tends to be bug 
free with ifort whereas gfortran has typically in the past had a few 
bugs on new releases as it is less tested by developers though those 
have been getting resolved through user bug reports.


On the other hand, the Intel compilers (e.g., Parallel Studio XE) were 
not always free to use as they are currently today with oneAPI.  The use 
of gfortan with WIEN2k gained popularity during the time the Intel 
compilers had to be paid for.  One might only hope that Intel never goes 
back to a pay model for their compilers.  Some of the old versions of 
ifort compiler were quite buggy causing WIEN2k to have memory leaks [3] 
or crash, where as WIEN2k seemed more stable (without those errors) with 
gfortran.  I haven't seen reports of similar WIEN2k issues with oneAPI 
but there might not be a large base of WIEN2k users using oneAPI yet. 
The above is just based on my observations from the mailing list posts.


Finally, I suggest you choose the compiler environment that you prefer 
and hopefully the above information can aid you in your decision.


[1] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg21942.html
[2] 
https://github.com/gsabo/WIEN2k-Docs/blob/main/WIEN2k21.1_Ubuntu22.04_Install_with_gfortran.pdf
[3] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18191.html


Best Regards,

Gavin
WIEN2k user

On 7/24/2022 11:06 PM, Victor Zenou wrote:

Thanks a lot Laurie and Gavin
Both ways, Intel ifort compiler and Intel mkl library or Fortran 
compiler and OpenBlas library, were shown by you to work fine.

Today I'm going to give it a try.
Which way, in terms of ease of installation is preferred?
Victor


‫בתאריך יום ב׳, 25 ביולי 2022 ב-2:28 מאת ‪Gavin Abo‬‏ 
<‪gabo13...@gmail.com‬‏>:‬


So after installing Ubuntu 22.04 LTS [1], installing the needed
operating system packages (perl, tcsh, ...) per section "1
Introduction" page 3 of the WIEN2k 21.1 usersguide [2], and
installing oneAPI [3], I have been able to get WIEN2k 21.1 to
compile successfully for serial calculations

Granted, I had to make some small adjustments for Intel oneAPI but
following my old Intel compiler steps [4,5] held up quite well. 
Since if you compare the steps in [4,5] to the steps below, you
should see that after tweaking the steps there are not that many
differences.

[1] https://youtu.be/oNEwEQ0uU1Y
[2] http://www.wien2k.at/reg_user/textbooks/usersguide.pdf
[3]
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg21942.html
[4]
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18663.html
[5]
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18664.html


*Install of WIEN2k 21.1 with oneAPI (ifort version 2021.6.0) in
Ubuntu 22.04 LTS*

username@computername:~/Desktop$ lsb_release -a
No LSB modules are available.
Distributor ID:    Ubuntu
Description:    Ubuntu 22.04 LTS
Release:    22.04
Codename:    jammy
username@computername:~/Desktop$ ifort -v
ifort version 2021.6.0
username@computername:~/Desktop$ cd ~
username@computername:~$ wget
http://www.tddft.org/programs/libxc/down.php?file=5.2.3/libxc-5.2.3.tar.gz
...
username@computername:~$ ls -l
down.php\?file\=5.2.3%2Flibxc-5.2.3.tar.gz
-rw-rw-r-- 1 username username 45810705 May 16 08:53
'down.php?file=5.2.3%2Flibxc-5.2.3.tar.gz'
username@computername:~$ tar xvf
down.php\?file\=5.2.3%2Flibxc-5.2.3.tar.gz
...

username@computername:~$ cd libxc-5.2.3
username@computername:~/libxc-5.2.3$ autoreconf -i --force
...
username@computername:~/libxc-5.2.3$ ./configure FC=ifort CC=icc
--prefix=$HOME/libxc-5.2.3
...
username@computername:~/libxc-5.2.3$ make
...
username@computername:~/libxc-5.2.3$ make check
...
PASS: xc-run_testsuite

Testsuite summary for libxc 5.2.3

# TOTAL: 1
# PASS:  1
# SKIP:  0
# XFAIL: 0
# FAIL:  0
# XPASS: 0
# ERROR: 0

...
username@computername:~/libxc-5.2.3$ make install
...
username@computername:~/libxc-5.2.3$ ls ~/libxc-5.2.3/lib
libxc.a  libxcf03.a libxcf03.la  libxcf90.a
libxcf90.la  

Re: [Wien] Installing Wien2k_21.1 on Ubuntu 22.04 LTS

[Gavin Abo]

So after installing Ubuntu 22.04 LTS [1], installing the needed 
operating system packages (perl, tcsh, ...) per section "1 Introduction" 
page 3 of the WIEN2k 21.1 usersguide [2], and installing oneAPI [3], I 
have been able to get WIEN2k 21.1 to compile successfully for serial 
calculations


Granted, I had to make some small adjustments for Intel oneAPI but 
following my old Intel compiler steps [4,5] held up quite well.  Since 
if you compare the steps in [4,5] to the steps below, you should see 
that after tweaking the steps there are not that many differences.


[1] https://youtu.be/oNEwEQ0uU1Y
[2] http://www.wien2k.at/reg_user/textbooks/usersguide.pdf
[3] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg21942.html
[4] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18663.html
[5] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18664.html


*Install of WIEN2k 21.1 with oneAPI (ifort version 2021.6.0) in Ubuntu 
22.04 LTS*


username@computername:~/Desktop$ lsb_release -a
No LSB modules are available.
Distributor ID:    Ubuntu
Description:    Ubuntu 22.04 LTS
Release:    22.04
Codename:    jammy
username@computername:~/Desktop$ ifort -v
ifort version 2021.6.0
username@computername:~/Desktop$ cd ~
username@computername:~$ wget 
http://www.tddft.org/programs/libxc/down.php?file=5.2.3/libxc-5.2.3.tar.gz

...
username@computername:~$ ls -l down.php\?file\=5.2.3%2Flibxc-5.2.3.tar.gz
-rw-rw-r-- 1 username username 45810705 May 16 08:53 
'down.php?file=5.2.3%2Flibxc-5.2.3.tar.gz'

username@computername:~$ tar xvf down.php\?file\=5.2.3%2Flibxc-5.2.3.tar.gz
...
username@computername:~/libxc-5.2.3$ autoreconf -i --force
...
username@computername:~/libxc-5.2.3$ ./configure FC=ifort CC=icc 
--prefix=$HOME/libxc-5.2.3

...
username@computername:~/libxc-5.2.3$ make
...
username@computername:~/libxc-5.2.3$ make check
...
PASS: xc-run_testsuite

Testsuite summary for libxc 5.2.3

# TOTAL: 1
# PASS:  1
# SKIP:  0
# XFAIL: 0
# FAIL:  0
# XPASS: 0
# ERROR: 0

...
username@computername:~/libxc-5.2.3$ make install
...
username@computername:~/libxc-5.2.3$ ls ~/libxc-5.2.3/lib
libxc.a  libxcf03.a  libxcf03.la  libxcf90.a  libxcf90.la libxc.la  
pkgconfig

username@computername:~$ wget https://www.fftw.org/fftw-3.3.10.tar.gz
...
username@computername:~$ tar xvf fftw-3.3.10.tar.gz
...
username@computername:~/fftw-3.3.10$ ./configure FCC=ifort CC=icc 
MPICC=mpiicc CFLAGS="-gcc-sys" --enable-mpi --prefix=$HOME/fftw-3.3.10

...
username@computername:~/fftw-3.3.10$ make
...
username@computername:~/fftw-3.3.10$ make install
...
username@computername:~/fftw-3.3.10$ ls -l ~/fftw-3.3.10/include 
~/fftw-3.3.10/lib

/home/username/fftw-3.3.10/include:
total 220
-rw-r--r-- 1 username username  2447 Jul 24 16:15 fftw3.f
-rw-r--r-- 1 username username 55032 Jul 24 16:15 fftw3.f03
-rw-r--r-- 1 username username 31986 Jul 24 16:15 fftw3.h
-rw-r--r-- 1 username username 27203 Jul 24 16:15 fftw3l.f03
-rw-r--r-- 1 username username 18678 Jul 24 16:15 fftw3l-mpi.f03
-rw-r--r-- 1 username username 36969 Jul 24 16:15 fftw3-mpi.f03
-rw-r--r-- 1 username username  9624 Jul 24 16:15 fftw3-mpi.h
-rw-r--r-- 1 username username 25902 Jul 24 16:15 fftw3q.f03

/home/username/fftw-3.3.10/lib:
total 2108
drwxrwxr-x 3 username username    4096 Jul 24 16:15 cmake
-rw-r--r-- 1 username username 1936856 Jul 24 16:15 libfftw3.a
-rwxr-xr-x 1 username username 904 Jul 24 16:15 libfftw3.la
-rw-r--r-- 1 username username  201560 Jul 24 16:15 libfftw3_mpi.a
-rwxr-xr-x 1 username username 959 Jul 24 16:15 libfftw3_mpi.la
drwxrwxr-x 2 username username    4096 Jul 24 16:15 pkgconfig
username@computername:~/fftw-3.3.10$ cd ~/WIEN2k
username@computername:~/WIEN2k$ ls -l
total 143680
-rw-r--r-- 1 username username 147128320 Jun 19  2021 WIEN2k_21.1.tar
username@computername:~/WIEN2k$ tar xvf WIEN2k_21.1.tar
...
username@computername:~/WIEN2k$ gunzip *.gz
username@computername:~/WIEN2k$ ./expand_lapw
WARNING: This will expand all WIEN.tar files !!!
It will overwrite all changes you have made previously in the WIEN 
subdirectories

continue (y/n)
y
...
username@computername:~/WIEN2k$ wget 
https://raw.githubusercontent.com/gsabo/WIEN2k-Patches/master/21.1/init_phonon_lapw.patch

...
username@computername:~/WIEN2k$ patch -b init_phonon_lapw 
init_phonon_lapw.patch

patching file init_phonon_lapw
Note: Apply any other patches that you want to test that are at 
https://github.com/gsabo/WIEN2k-Patches/tree/master/21.1

username@computername:~/WIEN2k$ ./siteconfig
...
  Selection: LI
...
 Your compiler: ifort
...
 Your compiler: icc
...
 Would you like to use LIBXC (usually not needed, ONLY for experts who 
want to play with different DFT options. It must have been installed 
before)? 

Re: [Wien] Installing Wien2k_21.1 on Ubuntu 22.04 LTS

[Gavin Abo]

I just installed oneAPI in Ubuntu 22.04 LTS.  As it turns out, the "sudo 
apt install intel-basekit" at [1] I did not have to use as the 
intel-basekit was automatically installed as a dependency of "sudo apt 
install intel-hpckit".  I did, however, have to setup the oneAPI 
repository in Ubuntu first by copying and pasting the commands from the 
Intel webpage [2].  A copy and paste of what was in my bash terminal 
while performing the oneAPI install is below (with some of the unneeded 
parts cut out to shorten it).  Below, you should see that ifort, icc, 
and mpiifort version 2021.6.0 are what currently get installed.


username@computername:~$ ifort -v
Command 'ifort' not found, did you mean:
  command 'fort' from deb fort-validator (1.5.3-1build1)
  command 'isort' from deb isort (5.6.4-1)
Try: sudo apt install 
username@computername:~$ wget -O- 
https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB 
\
| gpg --dearmor | sudo tee 
/usr/share/keyrings/oneapi-archive-keyring.gpg > /dev/null

...
username@computername:~$ echo "deb 
[signed-by=/usr/share/keyrings/oneapi-archive-keyring.gpg] 
https://apt.repos.intel.com/oneapi all main" | sudo tee 
/etc/apt/sources.list.d/oneAPI.list

...
username@computername:~$ sudo apt-get update
...
username@computername:~$ sudo apt install intel-hpckit
...
Do you want to continue? [Y/n] Y
username@computername:~$ echo "source /opt/intel/oneapi/setvars.sh 
intel64" >> .bashrc

username@computername:~$ grep oneapi ~/.bashrc
source /opt/intel/oneapi/setvars.sh intel64
username@computername:~$ source ~/.bashrc
...
username@computername:~$ ifort -v
ifort version 2021.6.0
username@computername:~$ icc -v
icc version 2021.6.0 (gcc version 11.2.0 compatibility)
username@computername:~$ mpiifort -v
mpiifort for the Intel(R) MPI Library 2021.6 for Linux*
Copyright Intel Corporation.
ifort version 2021.6.0

[1] https://estuarine.jp/2021/03/install-oneapi/?lang=en
[2] 
https://www.intel.com/content/www/us/en/develop/documentation/installation-guide-for-intel-oneapi-toolkits-linux/top/installation/install-using-package-managers/apt.html#apt 



Best Regards,

Gavin
WIEN2k user

On 7/24/2022 9:31 AM, Gavin Abo wrote:


The steps I use to install WIEN2k 21.1 in Ubuntu 22.04 LTS are in the 
document here:


https://github.com/gsabo/WIEN2k-Docs/blob/main/WIEN2k21.1_Ubuntu22.04_Install_with_gfortran.pdf

However, my steps use gfortran instead of oneAPI, so it might not help 
in your case.


I haven't tried the latest version of oneAPI with Ubuntu 22.04 LTS.  
For oneAPI, steps 2, 3, 5 probably have to be replaced by:


sudo apt install intel-basekit
sudo apt install intel-hpckit
username@computername:~$ gedit ~/.bashrc
...
source /opt/intel/oneapi/setvars.sh intel64
...
username@computername:~$ source ~/.bashrc

In step 11 for oneAPI,

LG would need to change to LI

gfortran would change to ifort

gcc could stay the same or change to icc

Those are likely the major step changes, but there is probably some 
other minor related step changes you would have to adjust for.


Kind Regards,

Gavin
WIEN2k user

On 7/24/2022 5:05 AM, Victor Zenou wrote:


Dear Wien2k users,

I want to install Wien2k_21.1 on Ubuntu 22.04 LTS equipped with Intel 
I7 processors.


As Intel ifort compiler is no longer standalone and also Intel® 
Parallel Studio XE is no longer available as a stand-alone product, 
one can use Intel oneAPI 2022 or Intel oneAPI 2021 instead.


Also Intel mkl library could be found under "Intel® oneAPI MKL".

Few months ago I had to struggle with these different Intel's 
names/versions, etc. I kept getting error messages.


Now that I got a new computer I'd like to ask if someone recently 
installed Wien2k_21.1 on Ubuntu 22.04 LTS and can give me some 
directions?


Yes, I looked at Wien2k's FAQ, Wien2k mailing-list archive and Intel 
websites.


Also I'm not sure what I must have to do in order to have a fully 
efficient functioning computer, as we all know that even if you got 
the best machine money can buy, and for most of us this is not true, 
one needs to "prepare" it properly.


Best regards, Victor Zenou
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Re: [Wien] Installing Wien2k_21.1 on Ubuntu 22.04 LTS

[Gavin Abo]

The steps I use to install WIEN2k 21.1 in Ubuntu 22.04 LTS are in the 
document here:


https://github.com/gsabo/WIEN2k-Docs/blob/main/WIEN2k21.1_Ubuntu22.04_Install_with_gfortran.pdf

However, my steps use gfortran instead of oneAPI, so it might not help 
in your case.


I haven't tried the latest version of oneAPI with Ubuntu 22.04 LTS.  For 
oneAPI, steps 2, 3, 5 probably have to be replaced by:


sudo apt install intel-basekit
sudo apt install intel-hpckit
username@computername:~$ gedit ~/.bashrc
...
source /opt/intel/oneapi/setvars.sh intel64
...
username@computername:~$ source ~/.bashrc

In step 11 for oneAPI,

LG would need to change to LI

gfortran would change to ifort

gcc could stay the same or change to icc

Those are likely the major step changes, but there is probably some 
other minor related step changes you would have to adjust for.


Kind Regards,

Gavin
WIEN2k user

On 7/24/2022 5:05 AM, Victor Zenou wrote:


Dear Wien2k users,

I want to install Wien2k_21.1 on Ubuntu 22.04 LTS equipped with Intel 
I7 processors.


As Intel ifort compiler is no longer standalone and also Intel® 
Parallel Studio XE is no longer available as a stand-alone product, 
one can use Intel oneAPI 2022 or Intel oneAPI 2021 instead.


Also Intel mkl library could be found under "Intel® oneAPI MKL".

Few months ago I had to struggle with these different Intel's 
names/versions, etc. I kept getting error messages.


Now that I got a new computer I'd like to ask if someone recently 
installed Wien2k_21.1 on Ubuntu 22.04 LTS and can give me some directions?


Yes, I looked at Wien2k's FAQ, Wien2k mailing-list archive and Intel 
websites.


Also I'm not sure what I must have to do in order to have a fully 
efficient functioning computer, as we all know that even if you got 
the best machine money can buy, and for most of us this is not true, 
one needs to "prepare" it properly.


Best regards, Victor Zenou
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Re: [Wien] Problem in elastic properties

[Gavin Abo]

As seen in past posts [1-3], those "Mult not equal" and "ityp not equal" 
errors typically can be solved by answering y to do you want to use the 
new .struct_nn file.  For example:


-> DO YOU WANT TO USE THE NEW tetra.struct_nn file (y/n) y

However, after answering y to take .struct_nn as your new .struct file.  
Look at the new .struct in XCrySDen or VESTA [4] and in StructGen for 
checking yourself if the structure is as it should be.


If the structure isn't as it should be, it could be that special labels 
are needed like that described at [5].


With elastic constants you distort the original 'crystal' structure [6], 
such that have to be careful not to destroy the crystal by putting the 
atomic positions to close to each other or too far apart.


Also, you will want to make sure you are using the latest version of 
WIEN2k (21.1).  As on the updates page [7], you can see that the nn 
program has an improvement for bond angles where is has under 
"VERSION_21: 10.4.2021":


*SRC_nn*: calculates also bond angles

There is also a bug in the nn program of version 21.1 and older WIEN2k 
versions, the bug fix for the WIEN2k 21.1 version is at [8].  Instead of 
applying the fix by hand, if you prefer to use patch [9], there is a 
nn.patch that I made for that at [10].


[1] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg05509.html
[2] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg07769.html
[3] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg20320.html
[4] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg21157.html

[5] http://susi.theochem.tuwien.ac.at/reg_user/faq/supercells.html
[6] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19372.html

[7] http://susi.theochem.tuwien.ac.at/reg_user/updates/
[8] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg21257.html

[9] https://en.wikipedia.org/wiki/Patch_(Unix)
[10] https://github.com/gsabo/WIEN2k-Patches/tree/master/21.1

Kind Regards,
Gavin
WIEN2k user

On 7/23/2022 8:15 AM, upasana chauhan wrote:

Dear SIr/Ma'am
Greetings!
During running tetra calculations in elastic properties, i am getting 
following error:


Use old or new scheme (o/N)

n

specify nn-bondlength factor: (usually=2) [and optionally dlimit, 
dstmax (about


1.d-5, 20)]

DSTMAX: 23.555334420

iix,iiy,iiz 3 3 5 63.346335000

63.346335000 106.10511000


ATOM 1 Na ATOM 4 Br

RMT( 1)=2.5 AND RMT( 4)=2.31000

SUMS TO 4.81000 LT. NN-DIST= 7.46544


ATOM 2 Ag ATOM 4 Br

RMT( 2)=2.42000 AND RMT( 4)=2.31000

SUMS TO 4.73000 LT. NN-DIST= 5.27886


ATOM 3 Sb ATOM 4 Br

RMT( 3)=2.42000 AND RMT( 4)=2.31000

SUMS TO 4.73000 LT. NN-DIST= 5.27886


ATOM 4 Br ATOM 3 Sb

RMT( 4)=2.31000 AND RMT( 3)=2.42000

SUMS TO 4.73000 LT. NN-DIST= 5.27886

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

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

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

NN created a new tetra.struct_nn file

NN created a new CASE.STRUCT_NN FILE

0.0u 0.0s 0:00.00 0.0% 0+0k 0+80io 0pf+0w

atom Z RMT-max RMT

1 11.0 2.5 2.5

2 47.0 2.42 2.42

3 51.0 2.42 2.42

4 35.0 2.30 2.30

file tetra.struct_setrmt generated

Do you want to accept these radii; discard them; or rerun setRmt (a/d/r):

a

next is nn

> nn (19:38:04) specify nn-bondlength factor: (usually=2) [and 
optionally dlimit, dstmax (about


1.d-5, 20)]

3

DSTMAX: 23.555334420

iix,iiy,iiz 3 3 5 63.346335000

63.346335000 106.10511000


ATOM 1 Na ATOM 4 Br

RMT( 1)=2.5 AND RMT( 4)=2.3

SUMS TO 4.8 LT. NN-DIST= 7.46544


ATOM 2 Ag ATOM 4 Br

RMT( 2)=2.42000 AND RMT( 4)=2.3

SUMS TO 4.72000 LT. NN-DIST= 5.27886


ATOM 3 Sb ATOM 4 Br

RMT( 3)=2.42000 AND RMT( 4)=2.3

SUMS TO 4.72000 LT. NN-DIST= 5.27886


ATOM 4 Br ATOM 3 Sb

RMT( 4)=2.3 AND RMT( 3)=2.42000

SUMS TO 4.72000 LT. NN-DIST= 5.27886

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

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

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

NN created a new tetra.struct_nn file

NN created a new CASE.STRUCT_NN FILE

0.0u 0.0s 1:29.64 0.0% 0+0k 0+176io 0pf+0w

-> check in tetra.outputnn for overlapping spheres,

coordination and nearest neighbor distances

nn has created a new struct file with different multiplicities

-> DO YOU WANT TO USE THE NEW tetra.struct_nn file (y/n)


Kindly tell me the solution.
Thank You!
Best Regards!___
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Re: [Wien] how to change user name & password for w2web gui

[Gavin Abo]

See past mailing list posts.  For example:


https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg15629.html


On 7/14/2022 6:13 AM, Shahid Mahmood Chaudhry wrote:


Please share how this problem solved? because I want to change the 
Password.



Thanks


*From:* Wien  on behalf of 
shamik chakrabarti 

*Sent:* Thursday, July 14, 2022 11:43:47 AM
*To:* A Mailing list for WIEN2k users
*Subject:* Re: [Wien] how to change user name & password for w2web gui
The problem is solved. Thank you

On Thu, 14 Jul 2022 at 13:43, shamik chakrabarti 
 wrote:


Dear Wien2k users,

                          I want to change the user name &
password of w2web gui. Please suggest how to do it?

with regards,

-- 
Dr. Shamik Chakrabarti

Research Fellow
Department of Physics
Indian Institute of Technology Patna
Bihta-801103
Patna
Bihar, India



--
Dr. Shamik Chakrabarti
Research Fellow
Department of Physics
Indian Institute of Technology Patna
Bihta-801103
Patna
Bihar, India



Disclaimer:
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Re: [Wien] Incorrect space group symbol

[Gavin Abo]

Using the cif you sent, I get the following:

username@computername:~/wiendata/Li3Ni2SbO6$ ls
Li3Ni2SbO6.cif
username@computername:~/wiendata/Li3Ni2SbO6$ grep space_group *.cif
_space_group_name_H-M_alt  'A 2/m'
_space_group_IT_number 12
_space_group_symop_operation_xyz
username@computername:~/wiendata/Li3Ni2SbO6$ x cif2struct
 F �?UU�?
0.004u 0.004s 0:00.00 0.0%    0+0k 0+48io 0pf+0w
username@computername:~/wiendata/Li3Ni2SbO6$ x sgroup
error: gamma = 109.716000  and not equal 90. Exiting now.
error: gamma = 109.716000  and not equal 90. Exiting now.
diff: Li3Ni2SbO6.outputsgroup: No such file or directory
diff: Li3Ni2SbO6.outputsgroup1: No such file or directory
error: gamma = 109.716000  and not equal 90. Exiting now.
0.000u 0.002s 0:00.00 0.0%    0+0k 0+0io 0pf+0w
error: command   /home/username/WIEN2k/sgroup -wi Li3Ni2SbO6.struct -wo 
Li3Ni2SbO6.struct_sgroup  -set-TOL=0.1 failed


Now, if I open Li3Ni2SbO6.cif in VESTA [1], click Edit -> Edit data -> 
Unit Cell.  I see that the cif file is in the A 2/m (Unique axis c) 
setting, which is the wrong setting for WIEN2k.  I select the B 2/m 
(Unique axis c), click OK, click File -> Export Data, and Save the new 
cif file.


Then, when I rerun with the new cif file, I get the following:

username@computername:~/wiendata/Li3Ni2SbO6$ ls
Li3Ni2SbO6.cif
username@computername:~/wiendata/Li3Ni2SbO6$ grep space_group *.cif
_space_group_name_H-M_alt  'B 2/m'
_space_group_IT_number 12
_space_group_symop_operation_xyz

username@computername:~/wiendata/Li3Ni2SbO6$ x cif2struct
 F UU�?
0.003u 0.007s 0:00.01 0.0%    0+0k 0+48io 0pf+0w
username@computername:~/wiendata/Li3Ni2SbO6$ x sgroup
0.000u 0.004s 0:00.00 0.0%    0+0k 0+8io 0pf+0w
username@computername:~/wiendata/Li3Ni2SbO6$ grep "space group" 
*.outputsgroup

Number and name of space group: 12 (C 2/m) [unique axis c] cell choice 2

As seen, above WIEN2k then correctly detects the B 2/m (or B 112/m [2]) 
setting also known as "12 (C 2/m) [unique axis c] cell choice 2".


[1] https://jp-minerals.org/vesta/en/download.html
[2] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg08153.html


Kind Regards,

Gavin
WIEN2k user

On 7/12/2022 4:05 AM, shamik chakrabarti wrote:

Dear Wien2k users,

 I want to start simulation on a structure whose cif 
file is attached herewith this mail. After structgen I am getting the 
error "incorrect space group symbol".


Kindly advice.

with regards,

--
Dr. Shamik Chakrabarti
Research Fellow
Department of Physics
Indian Institute of Technology Patna
Bihta-801103
Patna
Bihar, India___
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Re: [Wien] Ab inition and DFT

[Gavin Abo]

You may want to go by how Karlheinz Schwarz describes them.

ab initio translates to "first principles" meaning no experimental data 
is needed and just physical constants can be plugged in to solve the 
theoretical equation.


The exact statement Schwarz uses in [1] is:

/The advantage of//first-principle (ab initio) methods lies in the fact 
that//they can be carried out without knowing any experi//mental data of 
the system. /


Wikipedia says [2]:

/Ab initio means "from first principles" or "from the beginning", 
implying that the only inputs into an ab initio calculation are physical 
constants./


DFT (Density Functional Theory) means a quantum mechanical model were a 
many-body problem can be solved using a density functional.


The exact statements Schwarz uses in [3] are:

/In this way DFT is a universal approach to the quantum mechanical 
many-body problem, where the system of interacting electrons is mapped 
in a unique manner onto an effective non-interacting system that has the 
same total density./


/According to DFT all that is needed is the density ρ(r) which only 
depends on the position r, i.e. on three coordinates./


Wikipedia uses the words:

/Using this theory, the properties of a many-electron system can be 
determined by using functionals, i.e. functions of another function. In 
the case of DFT, these are functionals of the spatially dependent 
electron density./


Based on the above, WIEN2k calculations can be both DFT and ab initio.

For further details, see Schwarz's publications [1,3] or you may look at 
other explanations you might find in a textbook or on the Internet such 
as [5,6].



[1] https://doi.org/10.1016/S0022-4596(03)00213-5
[2] https://en.wikipedia.org/wiki/Ab_initio_quantum_chemistry_methods
[3] http://dx.doi.org/10.5772/59108
[4] https://en.wikipedia.org/wiki/Density_functional_theory
[5] https://dft.uci.edu/doc/g1.pdf
[6] 
http://ccl.net/chemistry/resources/messages/1995/05/17.001-dir/index.html


Kind Regards,

Gavin
WIEN2k user

On 7/6/2022 7:18 AM, ben amara imen wrote:

Dears users

Can someone please  explain the difference between ab initio 
calculation and DFT.


As I know , ab initio calculation is based on wave function without 
any empirical parameters . DFT is based on density of charge but it 
uses the empirical parameters (within Exchange-correlation potentiel 
PBE , GGA..).


Is it correct ?.

If it is correct , why some papers consider DFT as ab initio calculation.

Thanks


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Re: [Wien] Error in MoS2 doped with Ti

[Gavin Abo]

I believe I have experienced that in the past, where it seemed quite 
normal in some rare cases that sometimes sgroup would have to be ran 
more than once to shuffle the atomic positions and/or lattice parameters 
around until sgroup locked in on the equivalent arrangement that it likes.



However, you shouldn't ignore the Mult and ityp issues report by "x nn" 
that exist with the MoS2-Ti-2.struct that you attached. Usually, it is 
better to address those first before proceeding with "x sgroup".



Such advice you should find to not be new if you search the mailing list 
archive.  For example:



https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg09897.html

https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg21879.html

https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg05509.html

https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg10540.html

https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg07769.html

https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg20320.html


username@computername:~/wiendata/MoS2-Ti-2$ ls -l
total 8
-rw-r--r-- 1 username username 7754 Jul  5 10:17 MoS2-Ti-2.struct
username@computername:~/wiendata/MoS2-Ti-2$ x nn
 specify nn-bondlength factor: (usually=2) [and optionally dlimit, 
dstmax (about 1.d-5, 20)]

2
...
 WARNING: Mult not equal. PLEASE CHECK outputnn-file
 WARNING: ityp not equal. PLEASE CHECK outputnn-file
 WARNING: ityp not equal. PLEASE CHECK outputnn-file
 WARNING: ityp not equal. PLEASE CHECK outputnn-file
 WARNING: ityp not equal. PLEASE CHECK outputnn-file

  NN created a new MoS2-Ti-2.struct_nn file
STOP NN created a new CASE.STRUCT_NN FILE
0.274u 0.004s 0:00.95 28.4%    0+0k 0+600io 0pf+0w


Kind Regards,

Gavin

WIEN2k user


On 7/5/2022 4:14 PM, delamora wrote:

Thank you,
But there is something strange;

If

MoS2-Ti.struct

is the doped supercell but without having run "x struct", then if I do;

x sgroup
cp MoS2-Ti.struct_sgroup MoS2-Ti.struct
init -b

it does not work

But if I do;

x sgroup
cp MoS2-Ti.struct_sgroup MoS2-Ti.struct
x sgroup
cp MoS2-Ti.struct_sgroup MoS2-Ti.struct
init -b

it works

Pablo

The attached struct is the doped struct without having run "x struct"___
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Re: [Wien] Error while calculating elastic constant using IRelast

[Gavin Abo]

On page 138 of the WIEN2k 21.1 usersguide [1], you can see that the .in1 
file format of the second line should be:


7.500 10 4 ELPA pxq BL 64 (R-mt*K-max; MAX l, max l for hns )

However, your MgO.in1 has:

 8 8.0   4   ELPA pxq BL 64 (R-MT*K-MAX,MAX L IN WF,V-NMT,LIB)

The value for MAX L IN WF must be an integer (e.g., 10), but the error 
is happening because you put a float (e.g. 8.0).


[1] http://www.wien2k.at/reg_user/textbooks/usersguide.pdf

Kind Regards,

Gavin
WIEN2k user


On 7/5/2022 10:21 AM, 413119...@nitt.edu wrote:


i have attached the file with the mail.Please find the attachment

with regards

Narayanan

Quoting Gavin Abo :

There appears to a problem with the contents of your MgO.in1 file.  
You would need to share your MgO.in1 file, if you need further 
assistance with that.


Kind Regards,

Gavin
WIEN2k user

On 7/5/2022 9:01 AM, 413119...@nitt.edu wrote:

Thank you very much sir for your help.Now that error is resolved.
But again in SCF calculation i am getting error.I have attached the 
error below


STOP KGEN ENDS
 next is dstart

  dstart  -p    (20:17:43) running dstart in single mode

STOP DSTART ENDS
2.220u 0.313s 0:00.57 443.8%    0+0k 0+768io 0pf+0w
-> new MgO.in0 generated
  init_lapw finished ok
running dstart in single mode
STOP DSTART ENDS
2.230u 0.303s 0:00.57 443.8%    0+0k 0+696io 0pf+0w
0.047u 0.003s 0:00.05 80.0%    0+0k 0+680io 0pf+0w
clmextrapol_lapw has generated a new MgO.clmsum
STOP  LAPW0 END
At line 393 of file inilpw.f (unit = 5, file = 'MgO.in1')
Fortran runtime error: Bad integer for item 2 in list input

Error termination. Backtrace:
#0  0x14596cea132a
#1  0x14596cea1ed5
#2  0x14596cea269d
#3  0x14596d00eba4
#4  0x14596d011e9a
#5  0x14596d013379
#6  0x562e1cb22db5
#7  0x562e1cb26396
#8  0x562e1cafbd3e
#9  0x14596c2cac86
#10  0x562e1cafbd69
#11  0x
grep: lapw2*.error: No such file or directory


  stop error___
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Re: [Wien] Error while calculating elastic constant using IRelast

[Gavin Abo]

There appears to a problem with the contents of your MgO.in1 file.  You 
would need to share your MgO.in1 file, if you need further assistance 
with that.


Kind Regards,

Gavin
WIEN2k user

On 7/5/2022 9:01 AM, 413119...@nitt.edu wrote:

Thank you very much sir for your help.Now that error is resolved.
But again in SCF calculation i am getting error.I have attached the 
error below


STOP KGEN ENDS
 next is dstart

  dstart  -p    (20:17:43) running dstart in single mode

STOP DSTART ENDS
2.220u 0.313s 0:00.57 443.8%    0+0k 0+768io 0pf+0w
-> new MgO.in0 generated
  init_lapw finished ok
running dstart in single mode
STOP DSTART ENDS
2.230u 0.303s 0:00.57 443.8%    0+0k 0+696io 0pf+0w
0.047u 0.003s 0:00.05 80.0%    0+0k 0+680io 0pf+0w
clmextrapol_lapw has generated a new MgO.clmsum
STOP  LAPW0 END
At line 393 of file inilpw.f (unit = 5, file = 'MgO.in1')
Fortran runtime error: Bad integer for item 2 in list input

Error termination. Backtrace:
#0  0x14596cea132a
#1  0x14596cea1ed5
#2  0x14596cea269d
#3  0x14596d00eba4
#4  0x14596d011e9a
#5  0x14596d013379
#6  0x562e1cb22db5
#7  0x562e1cb26396
#8  0x562e1cafbd3e
#9  0x14596c2cac86
#10  0x562e1cafbd69
#11  0x
grep: lapw2*.error: No such file or directory


  stop error

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Re: [Wien] [Junk released by User action] Re: Error while calculating elastic constant using IRelast

[Gavin Abo]

There is more than one way to apply it.  However, the easiest way I have 
found to apply it is as follows:


1. I go to: 
https://github.com/gsabo/WIEN2k-Patches/blob/master/21.1/calLa_Pre_elast.patch


2. I click on the Raw button

3. I get the raw url, which is:

https://raw.githubusercontent.com/gsabo/WIEN2k-Patches/master/21.1/calLa_Pre_elast.patch

I either use wget (or curl) latter to download the patch to my computer.

4. To apply the patch, I enter the commands shown below in a bash terminal:

username@computername:~/Desktop$ cd $WIENROOT/SRC_IRelast
username@computername:~/WIEN2k/SRC_IRelast$ wget 
https://raw.githubusercontent.com/gsabo/WIEN2k-Patches/master/21.1/calLa_Pre_elast.patch

...
username@computername:~/WIEN2k/SRC_IRelast$ patch -b calLa_Pre_elast.f 
calLa_Pre_elast.patch

patching file calLa_Pre_elast.f
username@computername:~/WIEN2k/SRC_IRelast$ cd ..
username@computername:~/WIEN2k$ ./siteconfig
...
  Selection: R
...
  Selection: S
...
   Which program to recompile? IRelast
...
Compile time errors (if any) were:


Check file   compile.msg   in the corresponding SRC_* directory for the
compilation log and more info on any compilation problem.

 Press RETURN to continue

  Selection: Q

Kind Regards,

Gavin
WIEN2k user

On 7/5/2022 4:32 AM, 413119...@nitt.edu wrote:

Sir

    how to apply this patch to the file.


Quoting Gavin Abo :

That may be due to a gfortran compiler incompatibility with the 
code.  There is an experimental patch named "calLa_Pre_elast.patch" 
that you could give a try.  It is at:


https://github.com/gsabo/WIEN2k-Patches/tree/master/21.1

Kind Regards,

Gavin
WIEN2k user

On 7/4/2022 7:46 AM, 413119...@nitt.edu wrote:


Respected sir,

  I am using WIEN@K.21.1 in my work station with 
ubuntu OS.I was trying to do the Elastic constant calculation using 
IRelast,but i was getting folllowing error.


I run 'set_elast_lapw'
then give no.of pressure
then value of pressure
After that i am getting as mentioned below


Read data from line 8 
At line 83 of file calLa_Pre_elast.f (unit = 10, file = 
'MgO.outputeos')

Fortran runtime error: Constant string in input format
(' V0,B(GPa),BP,E0',3f15.4,f18.6)
    ^

Error termination. Backtrace:
#0  0x154aa00e932a
#1  0x154aa00e9ed5
#2  0x154aa00ea69d
#3  0x154aa0253cb1
#4  0x154aa0262101
#5  0x154aa026372c
#6  0x154aa02642d2
#7  0x55d47934d7ef
#8  0x55d47934cd7e
#9  0x154a9f960c86
#10  0x55d47934cdb9
#11  0x
cp: cannot stat 'init.struct': No such file or directory


   (C)by Morteza Jamal
 (2014)
   *  * *  **
 *    *   *    *
 *    * *  **
 *    * *  *
   *  *   *    **


###
#  set_elast_lapw

###
# C_set_elast_lapw prepares   #
#    Directories  and job files.  #
# C(2017) by Morteza Jamal    #
#  it creates   c11+2c12, #
#   c11-c12, and c44 directories  #
#   and CUBIC.job file    #
# in them #
#  which must be executed #
#  and can be analyzed by #
# C_ana_elast_lapw    #
###
cp: -r not specified; omitting directory '../../MgO/.'
cp: -r not specified; omitting directory '../../MgO/..'

So i kindly request to help me to correct this error.

with regards
Narayanan Namboodiri P___
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Re: [Wien] problems with parallel version of run_bandplothf_lapw

[Gavin Abo]

I now have a run_lapw.patch and runsp_lapw.patch at [1] that I think 
utilizes the changes described below.  Is there any other run script 
that should also have the corresponding change (e.g., runsp_c_lapw, 
runafm_lapw, runfsm_lapw, ...)?


[1] https://github.com/gsabo/WIEN2k-Patches/tree/master/21.1

Thanks,

Gavin
WIEN2k user

On 6/8/2022 12:40 AM, Peter Blaha wrote:

Hi,

I'm NOT aware of a particular problem with run_bandplothf_lapw in 
parallel mode.
However, I know a severe problem of run_bandplothf due to 
non-selfconsistency and a wrong case.vsp_old file.


The problem is that   run_bandplothf  does NOT give the same 
eigenvalues as obtained in the last scf iteration (unless you are 
perfectly converged).


The problem comes actually from   run_lapw  (or  runsp_lapw), where the

cp case.vsp case.vsp_old

is placed at the end of the scf cycle. It should, however, be placed 
just before the lapw0 step.


The corresponding lines in run_lapw look like:

...
lapw0:
# insert the following 4 lines:
foreach i (vsp vns)
  if (-e $file.$i ) \
    cp $file.$i $file.${i}_old  #save last cycle
end

scf1:
#foreach i (clmsum vsp vns vrespsum tausum)
foreach i (clmsum vrespsum tausum)
  if (-e $file.$i ) \
    cp $file.$i $file.${i}_old  #save last cycle
end
...



Am 07.06.2022 um 17:11 schrieb Mikhail Nestoklon via Wien:

Dear wien2k community,
I have strange problem with results of YSPBE0 calculations with 
spinorbit (WIEN2k 21.1).
After lapw cycle (run_lapw -p -so -hf -redklist) I save the 
calculations and run ‘run_bandplothf_lapw -p -redklist -so’.
I expect the energies to be in case.energyhfso file, but this file is 
corrupted.
For my calculations, the klist_band has ~200 k points and it is split in 4 files with ~50 k points each. The resulting case.energyhfso_1, case.energyhfso_2, case.energyhfso_3, case.energyhfso_4 
files contain the same k points which may be found in klist_band_? 
files, but the case.energyhfso file contains only first 29 k points 
from each of them. In addition, they have the same enumeration as 
in klist_band_? files and not in case.klist_band (i.e., after 29th k 
it is 1st again and so on). With case.energyhf the numbering of k 
points is correct: it is consistent with the main case.klist_band file.

Is there something wrong with run_bandplothf_lapw or I am misusing it?
Thank you in advance.
Sincerely yours,
Mikhail Nestoklon



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Re: [Wien] Error in MoS2 doped with Ti

[Gavin Abo]

You might try the attached MoS2-Ti.struct which was generated by 
sgroup.  Though, you will probably want to double-check it for example 
in XCrySDen or VESTA to ensure that it still looks right.



The previous MoS2-Ti.struct that you sent stops with an error "STOP 2 
missing" in "x symmetry" for me. However, if I take struct file that was 
produced by sgroup, the initialization seems to finish fine.  The exact 
commands and output in a bash terminal are below (note: some of the 
output that didn't seem relevant I cut out so that it could be posted 
the mailing list):



username@computername:~/wiendata/MoS2-Ti$ ls -l
total 12
-rw-r--r-- 1 username username 8825 Jul  4 11:14 MoS2-Ti.struct
username@computername:~/wiendata/MoS2-Ti$ x nn
 specify nn-bondlength factor: (usually=2) [and optionally dlimit, 
dstmax (about 1.d-5, 20)]

2
...
    ATOM 22  Ti1    ATOM  9  S 2
 RMT( 22)=2.07000 AND RMT(  9)=1.78000
 SUMS TO 3.85000  LT.  NN-DIST= 3.87254
STOP NN ENDS
0.288u 0.016s 0:01.48 19.5%    0+0k 0+720io 0pf+0w
username@computername:~/wiendata/MoS2-Ti$ x sgroup
0.005u 0.000s 0:00.00 0.0%    0+0k 0+24io 0pf+0w
username@computername:~/wiendata/MoS2-Ti$ x symmetry
 SPACE GROUP DOES NOT CONTAIN INVERSION
STOP 2 missing
0.021u 0.010s 0:00.03 100.0%    0+0k 0+104io 0pf+0w'
username@computername:~/wiendata/MoS2-Ti$ cp MoS2-Ti.struct_sgroup 
MoS2-Ti.struct

username@computername:~/wiendata/MoS2-Ti$ x symmetry
 SPACE GROUP DOES NOT CONTAIN INVERSION
0.042u 0.007s 0:00.05 80.0%    0+0k 0+128io 0pf+0w
username@computername:~/wiendata/MoS2-Ti$ init_lapw -b
...
  init_lapw finished ok


Kind Regards,

Gavin

WIEN2k user


On 7/4/2022 4:41 PM, delamora wrote:

Dear Gavin,
Thank you for your reply, but I still get the same problem;
In the last struct file I did the supercell and added the Ti atom, but 
afterwards I did not calculated the Rmt.

Now in this struct I that I include here I did it and I get
Rmt Mo; 2.41, S; 1.78, Ti; 2.07

Then with "init" I get this message

next is kgen
>   kgen (17:33:38) forrtl: severe (24): end-of-file during read, unit 
20, file /home/pablo/WIEN2k/MoS2-Ti/MoS2-Ti.struct

Image              PC                Routine  Line        Source
kgen               0045C74B  Unknown Unknown  Unknown
kgen               00425E78  Unknown Unknown  Unknown
kgen               004047B5  MAIN__    195  main.f
kgen               004041B2  Unknown Unknown  Unknown
libc-2.24.so       1500989F3431  __libc_start_main Unknown  Unknown
kgen               004040AA  Unknown Unknown  Unknown
0.001u 0.000s 0:00.00 0.0% 0+0k 0+0io 0pf+0w
error: command   /home/Programas/WIEN2k-19.1/kgen kgen.def   failed
 \n stop error \n

or with the WIEN2k interface I still get a problem;

>   inputfiles for lapw1c/2c prepared, no inversion present	(17:35:21)  
  next is kgen

forrtl: severe (24): end-of-file during read, unit 20, file 
/home/pablo/WIEN2k/MoS2-Ti/MoS2-Ti.struct
Image              PC                Routine            Line        Source
kgen               0045C74B  Unknown               Unknown  Unknown
kgen               00425E78  Unknown               Unknown  Unknown
kgen               004047B5  MAIN__                    195  main.f
kgen               004041B2  Unknown               Unknown  Unknown
libc-2.24.so       14A887F27431  __libc_start_main     Unknown  Unknown
kgen               004040AA  Unknown               Unknown  Unknown
  \n stop error \n
--

I am using versions 19.1 and 21.1 with fedora

Cheers

PabloTitle  
H   LATTICE,NONEQUIV.ATOMS: 22 156 P3m1
MODE OF CALC=RELA unit=ang 
 17.959965 17.959965 23.285215 90.00 90.00120.00   
ATOM  -1: X=0. Y=0.7778 Z=0.5000
  MULT= 3  ISPLIT= 8
  -1: X=0. Y=0. Z=0.5000
  -1: X=0.2223 Y=0.4445 Z=0.5000
Mo1NPT=  781  R0=0.1000 RMT= 2.31Z: 42.0   
LOCAL ROT MATRIX:0.000 1.000 0.000
 0.000 0.000 1.000
 1.000 0.000 0.000
ATOM  -2: X=0. Y=0.6667 Z=0.
  MULT= 6  ISPLIT= 8
  -2: X=0. Y=0. Z=0.
  -2: X=0.6667 Y=0. Z=0.
  -2: X=0. Y=0. Z=0.
  -2: X=0.6667 Y=0.6667 Z=0.
  -2: X=0. Y=0. Z=0.
Mo2NPT=  781  R0=0.1000 RMT= 2.31Z: 42.0   
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. Y=0. 

Re: [Wien] Error in MoS2 doped with Ti

[Gavin Abo]

I suggest you address the errors from "x nn" first such as that for 
"RMT( 22)=2.0 AND RMT( 20)=2.1". Using setrmt and accepting the 
MoS2-Ti-3.struct_setrmt might fix that.  Then, you might want to accept 
the file from sgroup (e.g., cp MoS2-Ti-3.struct_sgroup 
MoS2-Ti-3.struct).  When I did that as shown below, it seemed to avoid 
that error you reported from kgen:



username@computername:~/wiendata/MoS2-Ti-3$ cat $WIENROOT/WIEN2k_VERSION
WIEN2k_21.1 (Release 14/4/2021)

Note: WIEN2k 21.1 in use has been patched with 
Makefile.orig-lapw2.patch, Makefile.orig.patch, 
analyse_phonon_lapw.patch, calLa_Pre_elast.patch, nn.patch, qdmft.patch, 
qtlpara_lapw.patch, and x_lapw.patch from 
https://github.com/gsabo/WIEN2k-Patches/tree/master/21.1


username@computername:~/wiendata/MoS2-Ti-3$ ls -l
total 12
-rw-r--r-- 1 username username 8825 Jul  4 08:05 MoS2-Ti-3.struct
username@computername:~/wiendata/MoS2-Ti-3$ x nn
 specify nn-bondlength factor: (usually=2) [and optionally dlimit, 
dstmax (about 1.d-5, 20)]

2
...
   ERROR !!!
 RMT( 22)=2.0 AND RMT( 20)=2.1
 SUMS TO 4.1 GT NNN-DIST= 4.07491
STOP NN ENDS
0.287u 0.019s 0:01.48 19.5%    0+0k 0+728io 0pf+0w
username@computername:~/wiendata/MoS2-Ti-3$ setrmt MoS2-Ti-3 -r 0
...
file    MoS2-Ti-3.struct_setrmt   generated
username@computername:~/wiendata/MoS2-Ti-3$ cp MoS2-Ti-3.struct_setrmt 
MoS2-Ti-3.struct

username@computername:~/wiendata/MoS2-Ti-3$ x sgroup
0.006u 0.000s 0:00.00 0.0%    0+0k 0+24io 0pf+0w
username@computername:~/wiendata/MoS2-Ti-3$ cp MoS2-Ti-3.struct_sgroup 
MoS2-Ti-3.struct

username@computername:~/wiendata/MoS2-Ti-3$ x symmetry
 SPACE GROUP DOES NOT CONTAIN INVERSION
0.032u 0.004s 0:00.03 100.0%    0+0k 0+128io 0pf+0w
username@computername:~/wiendata/MoS2-Ti-3$ init_lapw -b
 next is setrmt
 next is nn
 specify nn-bondlength factor: (usually=2) [and optionally dlimit, 
dstmax (about 1.d-5, 20)]

 ...
    ATOM 22  Ti1    ATOM  9  S 2
 RMT( 22)=2.07000 AND RMT(  9)=1.78000
 SUMS TO 3.85000  LT.  NN-DIST= 3.87254
STOP NN ENDS
0.252u 0.012s 0:00.26 100.0%    0+0k 0+720io 0pf+0w
 next is sgroup
>   sgroup    (14:38:11) 0.000u 0.006s 0:00.00 0.0%    0+0k 0+24io 0pf+0w
...
Number and name of space group: 156 (P 3 m 1)
 next is symmetry
>   symmetry    (14:38:12)  SPACE GROUP DOES NOT CONTAIN INVERSION
0.033u 0.007s 0:00.04 75.0%    0+0k 0+128io 0pf+0w
 next is lstart
 22 Atoms found:  with labels Mo1  Mo2  Mo3  Mo4  Mo5  Mo6  Mo7  S 1  S 
2  S 3  S 4  S 5  S 6  S 7  S 8  S 9  S 10 S 11 S 12 S 13 S 14 Ti1

generate atomic configuration for atom 1 : Mo1
...
generate atomic configuration for atom 22 : Ti1
  SELECT XCPOT:
  recommended: PBE    [(13) GGA of Perdew-Burke-Ernzerhof 96]
   LDA    [( 5)]
   WC [(11)  GGA of Wu-Cohen 2006]
   PBESOL [(19) GGA of Perdew etal. 2008]
  SELECT ENERGY to separate core and valence states:
  recommended: -6.0 Ry (check how much core charge leaks out of MT-sphere)
  ALTERNATIVELY: specify charge localization (between 0.97 and 1.0) to 
select core state

STOP LSTART ENDS
 atom 1 has a large sphere , consider setting HDLOs and/or larger LVNS
 atom 2 has a large sphere , consider setting HDLOs and/or larger LVNS
 atom 3 has a large sphere , consider setting HDLOs and/or larger LVNS
 atom 4 has a large sphere , consider setting HDLOs and/or larger LVNS
 atom 5 has a large sphere , consider setting HDLOs and/or larger LVNS
 atom 6 has a large sphere , consider setting HDLOs and/or larger LVNS
 atom 7 has a large sphere , consider setting HDLOs and/or larger LVNS
>   inputfiles prepared    (14:38:20)
 inputfiles prepared
 inversion is NOT present
>   inputfiles for lapw1c/2c prepared, no inversion present (14:38:20)
 next is kgen
   6  symmetry operations without inversion
 inversion added (non-spinpolarized non-so calculation)
  NUMBER OF K-POINTS IN WHOLE CELL: (0 allows to specify 3 divisions of G)
 length of reciprocal lattice vectors:   0.404   0.404   0.270 11.440  
11.440   7.641

  94  k-points generated, ndiv=  11 11   7
STOP KGEN ENDS
 next is dstart
>   dstart -c -p > & .mist    (14:38:21) running dstart in single mode
STOP DSTART ENDS
46.329u 0.129s 0:46.46 99.9%    0+0k 0+23584io 0pf+0w

-> new MoS2-Ti-3.in0 generated
  init_lapw finished ok


Kind Regards,

Gavin

WIEN2k user


On 7/4/2022 1:21 PM, delamora wrote:

Dear Wien community,
I am trying to dope MoS2 which is
---
SG 194
a,b,c = 3.168, 3.168, 12.322
90, 90, 120
Mo: 1/3, 2/3, 1/4
S: 1/3, 2/3, 0.625
---
I make a 3x3x1 supercell and add a Ti atom at 8/9, 1/9, 0.95
With "sgroup" the SG=156 P3m1 (file attached)
and when I initiate the initiation stops with;
-
  atom 4 has a large sphere , consider setting HDLOs and/or larger LVNS
  atom 5 has a large sphere , consider setting HDLOs and/or larger LVNS
  atom 6 has a large sphere , consider setting HDLOs and/or larger LVNS
  atom 7 has a large 

Re: [Wien] Error while calculating elastic constant using IRelast

[Gavin Abo]

That may be due to a gfortran compiler incompatibility with the code.  
There is an experimental patch named "calLa_Pre_elast.patch" that you 
could give a try.  It is at:


https://github.com/gsabo/WIEN2k-Patches/tree/master/21.1

Kind Regards,

Gavin
WIEN2k user

On 7/4/2022 7:46 AM, 413119...@nitt.edu wrote:


Respected sir,

  I am using WIEN@K.21.1 in my work station with 
ubuntu OS.I was trying to do the Elastic constant calculation using 
IRelast,but i was getting folllowing error.


I run 'set_elast_lapw'
then give no.of pressure
then value of pressure
After that i am getting as mentioned below


Read data from line 8 
At line 83 of file calLa_Pre_elast.f (unit = 10, file = 'MgO.outputeos')
Fortran runtime error: Constant string in input format
(' V0,B(GPa),BP,E0',3f15.4,f18.6)
    ^

Error termination. Backtrace:
#0  0x154aa00e932a
#1  0x154aa00e9ed5
#2  0x154aa00ea69d
#3  0x154aa0253cb1
#4  0x154aa0262101
#5  0x154aa026372c
#6  0x154aa02642d2
#7  0x55d47934d7ef
#8  0x55d47934cd7e
#9  0x154a9f960c86
#10  0x55d47934cdb9
#11  0x
cp: cannot stat 'init.struct': No such file or directory


   (C)by Morteza Jamal
 (2014)
   *  * *  **
 *    *   *    *
 *    * *  **
 *    * *  *
   *  *   *    **


###
#  set_elast_lapw

###
# C_set_elast_lapw prepares   #
#    Directories  and job files.  #
# C(2017) by Morteza Jamal    #
#  it creates   c11+2c12, #
#   c11-c12, and c44 directories  #
#   and CUBIC.job file    #
# in them #
#  which must be executed #
#  and can be analyzed by #
# C_ana_elast_lapw    #
###
cp: -r not specified; omitting directory '../../MgO/.'
cp: -r not specified; omitting directory '../../MgO/..'

So i kindly request to help me to correct this error.

with regards
Narayanan Namboodiri P

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Re: [Wien] A basic question regarding atomic coordinates optimization

[Gavin Abo]

Not sure if it helpful or not, but should it be, there was a thread of 
posts related to force minimization back in March of 2021, in it you can 
see it references a "README_Constraints.pdf":


https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg20952.html

The README_Constraints.pdf appears to be identical to the "Constraint 
structure optimization (pdf)" link which is on the WIEN2k webpage among 
other structure optimization documentation (Structure 
optimization-notes, Notes on the mixer, ...):


http://www.wien2k.at/reg_user/textbooks/

Kind Regards,

Gavin
WIEN2k user

On 7/3/2022 1:26 PM, shamik chakrabarti wrote:

Dear Wien2k users,
                              I have a basic question. When the force 
at each atom is calculated & compared with the cut-off values ( ~ 2 
mRy/a.u.) & if the force at each atom is found to be larger than the 
cut-off values, the shifting of atomic coordinates occurs for 
searching equilibrium. Now, here the question arises:


*How did the algorithm know which way to proceed? *

For volume optimization, we fed the data of the lattice parameters & 
the code performs the calculation on the same. But during force 
minimization, we did not feed the values of atomic coordinates apart 
from the initial values, still the code search for new atomic 
coordinates spontaneously? Is it AI?


Looking forward to your reply

with regards,

--
Dr. Shamik Chakrabarti
Research Fellow
Department of Physics
Indian Institute of Technology Patna
Bihta-801103
Patna
Bihar, India___
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Re: [Wien] L2main - QTL-B Error

[Gavin Abo]

My notes on that error are below.  Feel free to correct or improve above 
them.


Kind Regards,

Gavin

WIEN2k user

QTL-B Error Notes

-

Not always but a lot (99% ??) of the time QTL-B errors are due to a bad 
struct file.  One possibility is wrong space group structure setting.  
WIEN2k tends to only accept the crystal setting that sgroup uses [1].  
Another possibility could be the repeating decimal (e.g., 1/3) issue 
[2]. Potentially another cause could be a RMT issue [3].


The WIEN2k FAQ has a page that has guidance on resolving the QTL-B error 
at [4].


The FAQ page at [5] gives some advice if the QTL-B is happening after a 
few iterations.


You might also find the QTL-B error being related to ghostbands errors.  
If that is the case, troubleshooting of ghostbands are described in 
section "12.1 Ghost bands" on page 254 of the WIEN2k 21.1 usersguide [6].


The meaning of QTL is given the mailing list post at [7].

Also, search the mailing list for other solutions that resolved QTL-B 
related errors.  For example, a proper case.inst seemed to resolve one 
recently in the mailing list [8].


[1] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg08148.html
[2] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18997.html
[3] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg16806.html

[4] http://susi.theochem.tuwien.ac.at/reg_user/faq/qtlb.html
[5] http://susi.theochem.tuwien.ac.at/reg_user/faq/scf.html
[6] http://www.wien2k.at/reg_user/textbooks/usersguide.pdf
[7] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg13577.html
[8] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg21748.html


On 6/28/2022 11:46 PM, Peeyush Kumar Kamlesh wrote:

Dear Users,
Greetings!
I am using WIEN2k_19.1. I am running perovskite material of space 
group 225(Fm-3m) with 1 k-point and cutoff energy -7.0 Ry. I used 
RMT reduction 5% but I am getting the following error during running 
scf calculations.

__

hup: Command not found.

LAPW0 END

LAPW1 END

LAPW1 END

LAPW1 END

LAPW1 END

LAPW2 - FERMI; weights written

LAPW2 END

LAPW2 END

LAPW2 END

LAPW2 END

SUMPARA END

CORE END

MIXER END

ec cc and fc_conv 0 0 1

in cycle 2    ETEST: 0 CTEST: 0

hup: Command not found.

LAPW0 END

LAPW1 END

LAPW1 END

LAPW1 END

LAPW1 END

LAPW2 - FERMI; weights written

LAPW2 END

LAPW2 END

LAPW2 END

LAPW2 END

SUMPARA END

CORE END

MIXER END

ec cc and fc_conv 0 0 1

in cycle 3    ETEST: 0 CTEST: 0

hup: Command not found.

LAPW0 END

LAPW1 END

LAPW1 END

LAPW1 END

LAPW1 END

LAPW2 - FERMI; weights written

L2main - QTL-B Error

L2main - QTL-B Error

L2main - QTL-B Error

L2main - QTL-B Error

cp: cannot stat '.in.tmp': No such file or directory

>   stop error

 __

Kindly help!
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Re: [Wien] Missing packages

[Gavin Abo]

The perl-Math-Complex.noarch seems to be for an old Fedora 
distribution.  For the Ubuntu 20.04 distribution, you need to install 
the Perl package [1] (e.g., sudo apt install perl).



The Fedora libXScrnSaver might be libxss-dev in Ubuntu [2].


The compat-libstdc++-33 might be libstdc++6 in Ubuntu [3].


[1] https://packages.ubuntu.com/focal/perl

[2] https://launchpad.net/ubuntu/focal/+package/libxss-dev

[3] https://packages.ubuntu.com/focal/libstdc++6


On 5/16/2022 4:10 PM, delamora wrote:

Dear WIEN2k Comunity,
I am installing the WIEN2k 19.1 version in Ubuntu 20.04 and I try to 
install;


perl-Math-Complex.noarch
libXScrnSaver
compat-libstdc++-33

I get as an answer
package cannot be found
Any suggestion is welcome

Saludos

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Re: [Wien] WIEN2k Questions: Volume Optimization and Fermi Surfaces

[Gavin Abo]

Regarding 1, you may want to look at past posts with good advice related 
to that:


https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17074.html
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg02246.html
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg14814.html
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19181.html

Regarding 2, you might find helpful past posts related to that too. For 
example:


https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg02052.html
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18107.html
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17847.html


On 5/10/2022 3:02 PM, Tenzin, K. wrote:

Hello
I am a new user of WIEN2k, and I am using WIEN2k_21.1 on the slurm 
cluster (intel) system.  I have two questions with regard to proper 
usage of wien2k for DFT calculations:


*1*. I performed volume optimization for different exchange 
functionals (GGA and LSDA) and I got different optimized values, which 
is not a surprise for me. My question is: Do I need to perform volume 
optimization again after I add spin-orbit coupling as a second 
variational method to proceed with further calculations?


*2*.  I calculate fermi surface, for spin orbit coupling, using the 
following command in my slurm job script to run parallel with:

*x lapw1 -p
*
*x lapwso -p
x lapw2 -so -p -fermi*
But when I visualize the fermi surface/s on XCrysden (version 1.6), it 
seems like I am getting fermi surfaces for non-spin-orbit calculations 
only, that is XCrysden is reading data from case.output1. Please 
advise me on how to properly visualize fermi surfaces that are 
generated using the above three commands.


My system is non-magnetic (so performing non-spin-polarized 
calculations) and the system contains heavy atoms, so I need to 
incorporate spin-orbit coupling in the calculations.


Thank you so much for your advice and time.

Karma, PhD student
Theory of Condensed Matter Physics
University of Groningen, Netherlands
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Re: [Wien] Bandstructure with SO

[Gavin Abo]

The WIEN2k updates page [1] has:


*VERSION_21: 10.4.2021 *

...


**• *SRC_spaghetti:* bz_lin.f: consistent use of toler (fixing 
additional black lines)



Have you tried WIEN2k 21.1 having the above band structure black lines fix?


You might also have to be careful with the band structure commands with 
there being differences for the SOC case [2,3].



[1] http://www.wien2k.at/reg_user/updates/

[2] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg13143.html


[3] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg12338.html



On 5/9/2022 4:41 PM, delamora wrote:

Dear Wien community,
I am doing a calculation with SOC, and when I try to plot the band 
structure without SOC

spaghetti -p -up
 it looks fine

but when I put it with SOC
spaghetti -p -up -so
I get a bandstructure with many vertical lines

Is there a way to fix it?
(WIEN2k-19.1)

Thanks

Pablo
===
I sent a message with a bandstructure, and it was too big
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Re: [Wien] Install Wien2k using oneAPI

[Gavin Abo]

The block of informational messages that starts with "initializing 
oneAPI environment" and ends with "oneAPI environment initialized" is 
normal.  However, the WARNING message after that is not normal.  
Although, it is just a warning such that oneAPI will likely still work 
fine.  However, just as the warning says it is detecting that you are 
running setvars.sh more than one time in your .bashrc (or .cshrc).  
Thus, if you edit .bashrc to have only the one source line with the 
setvars.sh then the warning should disappear.



Kind Regards,

Gavin

WIEN2k user


On 3/8/2022 5:25 PM, delamora wrote:

Thank you Gavin,
Sorry for replying so late.

I have Fedora,
I put; source /opt/intel/oneapi/setvars.sh intel64
I still get many messages:
--
:: initializing oneAPI environment ...
   -bash: BASH_VERSION = 5.1.8(1)-release
   args: Using "$@" for setvars.sh arguments: intel64
:: advisor -- latest
:: ccl -- latest
:: clck -- latest
:: compiler -- latest
:: dal -- latest
:: debugger -- latest
:: dev-utilities -- latest
:: dnnl -- latest
:: dpcpp-ct -- latest
:: dpl -- latest
:: inspector -- latest
:: intelpython -- latest
:: ipp -- latest
:: ippcp -- latest
:: ipp -- latest
:: itac -- latest
:: mkl -- latest
:: mpi -- latest
:: tbb -- latest
:: vpl -- latest
:: vtune -- latest
:: oneAPI environment initialized ::
:: WARNING: setvars.sh has already been run. Skipping re-execution.
   To force a re-execution of setvars.sh, use the '--force' option.
   Using '--force' can result in excessive use of your environment 
variables.

usage: source setvars.sh [--force] [--config=file] [--help] [...]
  --force        Force setvars.sh to re-run, doing so may overload 
environment.

  --config=file  Customize env vars using a setvars.sh configuration file.
  --help         Display this help message and exit.
  ...            Additional args are passed to individual env/vars.sh 
scripts

                 and should follow this script's arguments.
  Some POSIX shells do not accept command-line options. In that case, 
you can pass
  command-line options via the SETVARS_ARGS environment variable. For 
example:

  $ SETVARS_ARGS="ia32 --config=config.txt" ; export SETVARS_ARGS
  $ . path/to/setvars.sh
  The SETVARS_ARGS environment variable is cleared on exiting setvars.sh.
--

Is this ok?

--------
*De:* Wien  en nombre de 
Gavin Abo 

*Enviado:* miércoles, 23 de febrero de 2022 01:03 a. m.
*Para:* wien@zeus.theochem.tuwien.ac.at 
*Asunto:* Re: [Wien] Install Wien2k using oneAPI

I believe it might have been the webpage at [1] that I followed to 
install oneAPI within Ubuntu, which had me run a single terminal 
command to install it:



sudo apt install intel-hpckit


I think I came across that webpage on the website at [2] having links 
to installation of oneAPI also for other Package Managers used by 
other Linux distributions such as Fedora, CentOS, etc.



For the source line in .bashrc, I think it was webpages [3,4] that I 
followed to put oneAPI (such as the ifort compiler) in the operating 
system environment which had me use:



source /opt/intel/oneapi/setvars.sh intel64


[1] 
https://www.intel.com/content/www/us/en/develop/documentation/installation-guide-for-intel-oneapi-toolkits-linux/top/installation/install-using-package-managers/apt.html#apt 
<https://www.intel.com/content/www/us/en/develop/documentation/installation-guide-for-intel-oneapi-toolkits-linux/top/installation/install-using-package-managers/apt.html#apt>


[2] 
https://www.intel.com/content/www/us/en/develop/documentation/installation-guide-for-intel-oneapi-toolkits-linux/top/installation/install-using-package-managers.html#install-using-package-managers 
<https://www.intel.com/content/www/us/en/develop/documentation/installation-guide-for-intel-oneapi-toolkits-linux/top/installation/install-using-package-managers.html#install-using-package-managers>


[3] 
https://www.intel.com/content/www/us/en/develop/documentation/fortran-compiler-oneapi-dev-guide-and-reference/top/compiler-setup/using-the-command-line/specifying-the-location-of-compiler-components.html 
<https://www.intel.com/content/www/us/en/develop/documentation/fortran-compiler-oneapi-dev-guide-and-reference/top/compiler-setup/using-the-command-line/specifying-the-location-of-compiler-components.html>


[4] https://estuarine.jp/2021/03/install-oneapi/?lang=en 
<https://estuarine.jp/2021/03/install-oneapi/?lang=en>



Kind Regards,

Gavin

WIEN2k user


On 2/22/2022 12:29 PM, delamora wrote:


I installed the intel oneAPI
I have in /etc/bashrc;
source 
/opt/intel/compilers_and_libraries_2019.0.117/linux/bin/compilervars.sh 
-arch intel64 -platform linux

Now I need the oneAPI source

Saludos

Pablo


*De:* Wien  
<mailto:wien-boun...@

Re: [Wien] Install Wien2k using oneAPI

[Gavin Abo]

I believe it might have been the webpage at [1] that I followed to 
install oneAPI within Ubuntu, which had me run a single terminal command 
to install it:



sudo apt install intel-hpckit


I think I came across that webpage on the website at [2] having links to 
installation of oneAPI also for other Package Managers used by other 
Linux distributions such as Fedora, CentOS, etc.



For the source line in .bashrc, I think it was webpages [3,4] that I 
followed to put oneAPI (such as the ifort compiler) in the operating 
system environment which had me use:



source /opt/intel/oneapi/setvars.sh intel64


[1] 
https://www.intel.com/content/www/us/en/develop/documentation/installation-guide-for-intel-oneapi-toolkits-linux/top/installation/install-using-package-managers/apt.html#apt


[2] 
https://www.intel.com/content/www/us/en/develop/documentation/installation-guide-for-intel-oneapi-toolkits-linux/top/installation/install-using-package-managers.html#install-using-package-managers


[3] 
https://www.intel.com/content/www/us/en/develop/documentation/fortran-compiler-oneapi-dev-guide-and-reference/top/compiler-setup/using-the-command-line/specifying-the-location-of-compiler-components.html


[4] https://estuarine.jp/2021/03/install-oneapi/?lang=en


Kind Regards,

Gavin

WIEN2k user


On 2/22/2022 12:29 PM, delamora wrote:


I installed the intel oneAPI
I have in /etc/bashrc;
source 
/opt/intel/compilers_and_libraries_2019.0.117/linux/bin/compilervars.sh 
-arch intel64 -platform linux

Now I need the oneAPI source

Saludos

Pablo


*De:* Wien  en nombre de 
Peter Blaha 

*Enviado:* jueves, 11 de marzo de 2021 09:59 a. m.
*Para:* wien@zeus.theochem.tuwien.ac.at 
*Asunto:* Re: [Wien] Install Wien2k using oneAPI

I just installed oneAPI today  (it is free !!!). You need the Base and 
the HPC (high performance computing) toolkit.


It was trivial to install, but the setting of the environment is 
slightly different.



Once installed, WIEN2k compiles with the standard option (ifort+mkl) 
without any changes.



Am 11.03.2021 um 16:52 schrieb Laurence Marks:
Since nobody has responded, I will. I have oneAPI running without any 
issue for some months. Of course sometimes the installation is 
tricky. I suggest going ahead, then coming back to the list if there 
are any problems.


On Wed, Mar 10, 2021 at 12:38 AM Riyajul Islam  
wrote:


Dear Wien2k users,
I have used Intel parallel studio for intel fortran compiler to
install Wien2k 19.2 but the license has expired. As they have
recently transitioned from Intel Parallel Studio XE to Intel
oneAPI, so is there any way that I can install Wien2k using Intel
oneAPI?

Kind regards
-- 
Riyajul Islam

National Institute of Technology Nagaland

--
Professor Laurence Marks
Department of Materials Science and Engineering
Northwestern University
www.numis.northwestern.edu 
"Research is to see what everybody else has seen, and to think what 
nobody else has thought" Albert Szent-Györgyi



--
---
Peter Blaha,  Inst. f. Materials Chemistry, TU Vienna, A-1060 Vienna
Phone: +43-158801165300
Email:peter.bl...@tuwien.ac.at     
WWW:http://www.imc.tuwien.ac.at     WIEN2k:http://www.wien2k.at  

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Re: [Wien] FINDLOC issue with latest version of Wien2k with fortran v.15

[Gavin Abo]

Intel oneAPI has its own support forums such as "Intel oneAPI 
Registration" and "Toolkits & SDKs" at [1].  The group in the forums 
over there is likely to be more experienced with oneAPI installations.


In your previous post, it looked like you were installing the oneAPI HPC 
Toolkit (i.e., l_HPCKit_p_2022.1.2.117_offline.sh). OneAPI has multiple 
toolkits [2].  One possibility is that the missing Sqlite SQL might be 
part of the oneAPI Base Toolkit such that you might have to install it 
first before installing the oneAPI HPC Toolkit.


[1] 
https://community.intel.com/t5/Developer-Software-Forums/ct-p/developer-software-forums
[2] 
https://www.intel.com/content/www/us/en/developer/tools/oneapi/toolkits.html


On 2/16/2022 4:34 AM, Dr. K. C. Bhamu wrote:

Dear Gavin,
Thanks for your detailed reply.
I have followed your suggestion but the problem still persists.
I have three directories: installercache  oneapi  packagemanager

kcbhamu@kcbhamu:~$ls oneapi/installer/lib
libQt6Core5Compat.so        libQt6QmlModels.so libQt6QuickLayouts.so   
        libQt6XcbQpa.so  libxcb-render.so             libxcb-sync.so 
 libxcb-xkb.so
libQt6Core5Compat.so.6      libQt6QmlModels.so.6 
libQt6QuickLayouts.so.6         libQt6XcbQpa.so.6  libxcb-render.so.0 
          libxcb-sync.so.1  libxcb-xkb.so.1
libQt6Core5Compat.so.6.1.3  libQt6QmlModels.so.6.1.3 
libQt6QuickLayouts.so.6.1.3     libQt6XcbQpa.so.6.1.3 
 libxcb-render.so.0.0.0       libxcb-sync.so.1.0.0  libxcb-xkb.so.1.0.0
libQt6Core.so               libQt6Qml.so libQt6QuickShapes.so         
   libxcb-icccm.so  libxcb-render-util.so        libxcb-util.so 
 libxkbcommon.so
libQt6Core.so.6             libQt6Qml.so.6 libQt6QuickShapes.so.6     
     libxcb-icccm.so.4  libxcb-render-util.so.0      libxcb-util.so.1 
 libxkbcommon.so.0
libQt6Core.so.6.1.3         libQt6Qml.so.6.1.3 
libQt6QuickShapes.so.6.1.3      libxcb-icccm.so.4.0.0 
 libxcb-render-util.so.0.0.0  libxcb-util.so.1.0.0  libxkbcommon.so.0.0.0
libQt6DBus.so               libQt6QmlWorkerScript.so libQt6Quick.so   
               libxcb-image.so  libxcb-shape.so             
 libxcb-xfixes.so  libxkbcommon-x11.so
libQt6DBus.so.6             libQt6QmlWorkerScript.so.6 
libQt6Quick.so.6                libxcb-image.so.0  libxcb-shape.so.0   
         libxcb-xfixes.so.0  libxkbcommon-x11.so.0
libQt6DBus.so.6.1.3         libQt6QmlWorkerScript.so.6.1.3 
libQt6Quick.so.6.1.3            libxcb-image.so.0.0.0 
 libxcb-shape.so.0.0.0        libxcb-xfixes.so.0.0.0 
 libxkbcommon-x11.so.0.0.0
libQt6Gui.so                libQt6QuickControls2Impl.so 
 libQt6QuickTemplates2.so        libxcb-keysyms.so  libxcb-shm.so     
           libxcb-xinerama.so
libQt6Gui.so.6              libQt6QuickControls2Impl.so.6 
 libQt6QuickTemplates2.so.6      libxcb-keysyms.so.1  libxcb-shm.so.0 
             libxcb-xinerama.so.0
libQt6Gui.so.6.1.3          libQt6QuickControls2Impl.so.6.1.3 
 libQt6QuickTemplates2.so.6.1.3  libxcb-keysyms.so.1.0.0 
 libxcb-shm.so.0.0.0          libxcb-xinerama.so.0.0.0
libQt6Network.so            libQt6QuickControls2.so  libQt6Widgets.so 
               libxcb-randr.so  libxcb.so                   
 libxcb-xinput.so
libQt6Network.so.6          libQt6QuickControls2.so.6 
 libQt6Widgets.so.6              libxcb-randr.so.0  libxcb.so.1       
           libxcb-xinput.so.0
libQt6Network.so.6.1.3      libQt6QuickControls2.so.6.1.3 
 libQt6Widgets.so.6.1.3          libxcb-randr.so.0.1.0 
 libxcb.so.1.1.0              libxcb-xinput.so.0.1.0



Thank you very much
Bhamu


On Wed, Feb 16, 2022 at 4:30 PM Gavin Abo  wrote:

With your offline install [1] command below, it will likely try to
install it in Intel's default location (/opt/intel) which is
typically for root permissions.

You would need to install it in a user directory that you have
user permission to.  That might be for example
/home/username/intel.  As seen at [2], the --install-dir option
may need to be added to your command:

bash ./l_HPCKit_p_2022.1.2.117_offline.sh
<http://l_HPCKit_p_2022.1.2.117_offline.sh> -s -a --silent --eula
accept --install-dir /home/username/intel

According to [3], before executing the above command, you might
also need to set $HOME as well, for example in the terminal with:

export HOME=/home/username/intel

You may also need to ask your administrative staff what user
directories are available and what free disk space is available
for each of them.  For an all component install, the Intel webpage
at [4] shows upwards of about 30 GB (=24 GB  for components + 6 GB
temporary space) is needed. Though at [2], there is a --components
option that you might be able to use to install a minimized set of
components [5] such as Intel Fortran Compiler Classic
(intel.oneapi.lin.ifort-compiler) in the oneAPI HPC Toolkit and
Intel MKL (intel.oneapi.lin.mkl.devel) in the oneAPI Base Toolkit.

[1] https://www.youtube.

Re: [Wien] FINDLOC issue with latest version of Wien2k with fortran v.15

[Gavin Abo]

With your offline install [1] command below, it will likely try to 
install it in Intel's default location (/opt/intel) which is typically 
for root permissions.


You would need to install it in a user directory that you have user 
permission to.  That might be for example /home/username/intel.  As seen 
at [2], the --install-dir option may need to be added to your command:


bash ./l_HPCKit_p_2022.1.2.117_offline.sh  -s -a --silent --eula accept 
--install-dir /home/username/intel


According to [3], before executing the above command, you might also 
need to set $HOME as well, for example in the terminal with:


export HOME=/home/username/intel

You may also need to ask your administrative staff what user directories 
are available and what free disk space is available for each of them.  
For an all component install, the Intel webpage at [4] shows upwards of 
about 30 GB (=24 GB  for components + 6 GB temporary space) is needed.  
Though at [2], there is a --components option that you might be able to 
use to install a minimized set of components [5] such as Intel Fortran 
Compiler Classic (intel.oneapi.lin.ifort-compiler) in the oneAPI HPC 
Toolkit and Intel MKL (intel.oneapi.lin.mkl.devel) in the oneAPI Base 
Toolkit.


[1] https://www.youtube.com/watch?v=VC_ucczGR_Y
[2] 
https://www.intel.com/content/www/us/en/develop/documentation/installation-guide-for-intel-oneapi-toolkits-linux/top/installation/install-with-command-line.html
[3] 
https://community.intel.com/t5/Intel-oneAPI-Registration/oneAPI-installation-fails/td-p/1299826
[4] 
https://www.intel.com/content/www/us/en/developer/articles/system-requirements/intel-oneapi-base-toolkit-system-requirements.html

[5] https://oneapi-src.github.io/oneapi-ci/#linux-web-installer

On 2/15/2022 9:00 PM, Dr. K. C. Bhamu wrote:

Dear Prof. Peter,
I have tried to install oneapi but getting another error of SQL:
bash ./l_HPCKit_p_2022.1.2.117_offline.sh 
  -s -a --silent --eula accept

Checking system requirements...
Done.
Wait while the installer is preparing...
Done.
Launching the installer...
Installer failed with the error Sqlite SQL execution failed.
#

and I do not see any compilers in oneapi directory.

#---
From SQL installation procedure, I see it needs a root access: 
https://phoenixnap.com/kb/sql-server-linux



Any help will be appreciated.

Regards
Bhamu

On Mon, Feb 7, 2022 at 4:13 PM Peter Blaha 
 wrote:


You probably can install it. root is not required. Try it.

Am 07.02.2022 um 11:31 schrieb Dr. K. C. Bhamu:

Thanks Prof. Peter.

But unfortunately I can not install this version in cluster.
Admistrative staff also denied as they are moved on GPU so not
helping for CPU calculations.


Regards
Bhamu

On Mon, Feb 7, 2022, 7:27 PM Peter Blaha
 wrote:

It does not work with an old compiler.

The intel compiler is now free.

Am 07.02.2022 um 11:02 schrieb Dr. K. C. Bhamu:

A gentle reminder for the help.

Regards
Bhamu

On Fri, Feb 4, 2022 at 8:10 AM Dr. K. C. Bhamu
 wrote:

Dear Experts,
I am facing an issue [1] with a recent version of Wien2k
installation with Fortran v.15 "composer_xe_2015.2.164".
Earlier reported issue was resolved by upgrading the
Fortran version.
But for me, I have no choice of updating the
intel compilers.

Could someone please help me to resolve this issue?

[1].

https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg21006.html

Please let me know what else information you need.

Regards
Bhamu
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Re: [Wien] orb -up / orb -dn status is not coming during SCF

[Gavin Abo]

What cycle is that for?  As described at [1], case.dmatup/dn must be 
present for orb to run.  If it is happening in the first scf cycle, it 
might be fine since I believe case.dmatup/dn are created during cycle 1 
such that you won't see orb until cycle 2.


[1] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19351.html


Kind Regards,
Gavin
WIEN2k user

On 2/12/2022 6:35 AM, shamik chakrabarti wrote:

Dear Wien2k users,

                            I have started a simulation with GGA+U 
approach. However, during SCF, I have noticed, orb -up/orb - dn is not 
coming...the case.dayfile is given below as;


:CHARGE convergence:  0 0.0001 .1006582
:ENERGY convergence:  0 0.0001 .048892945000
>   mixer  -orb (19:00:27) 0.2u 0.1s 0:00.15 226.6% 0+0k 0+2048io 0pf+0w
>   lcore -dn (19:00:26) 0.0u 0.0s 0:00.01 100.0% 0+0k 0+240io 0pf+0w
>   lcore -up (19:00:26) 0.0u 0.0s 0:00.02 0.0% 0+0k 24+240io 1pf+0w
>   lapw2 -dn       -orb (19:00:22) 6.2u 4.9s 0:04.63 241.9% 0+0k 
0+1720io 0pf+0w
>   lapw2 -up       -orb (19:00:17) 7.0u 5.7s 0:04.96 257.8% 0+0k 
408+1752io 2pf+0w
>   lapw1  -dn   -orb   (18:59:49) 49.8u 20.2s 0:27.96 250.8% 0+0k 
0+27168io 0pf+0w
>   lapw1  -up   -orb   (18:59:20) 48.8u 22.1s 0:28.78 246.7% 0+0k 
416+27704io 2pf+0w

>   lapw0   (18:59:17) 3.7u 0.0s 0:02.34 163.6% 0+0k 960+864io 3pf+0w

Am I doing something wrong??

with regards,

--
Dr. Shamik Chakrabarti
Research Fellow
Department of Physics
Indian Institute of Technology Patna
Bihta-801103
Patna
Bihar, India___
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Re: [Wien] problems installing 21.1

[Gavin Abo]

Apparently, that FFTPACK error in your message below is an intended 
feature for WIEN2k 21.1.  It seems to be because FFTPACK support was 
removed.  Since on the WIEN2k updates page [1], there is the following:


*all codes SRC_*/** have changed cmplx(a,b) to dcmplx(a,b), conjg to 
dconjg and in general gfortran (version 10) compatibility has been 
enforced. In addition, *we have dropped **FFTPACK* and FFTW2 *support 
and require now FFTW3 also for the sequential code.*


Thus, the solution should be to install and link with a FFTW3 library.

One option might be to link against the operating system FFTW3 library  
For example in Ubuntu the library is provided by the operating system 
development packages [2]:


libfftw3-dev (for serial)
libfftw3-mpi-dev (for mpi parallel)

However, these GNU compiled (e.g., gcc, gfrotran) library files might 
not always play nicely with the Intel compilers (e.g., icc, ifort).


Another option, better for the Intel compiler, would be to get the FFTW3 
package (fftw-3.3.10.tar.gz) [3] and install it [4,5].


[1] http://susi.theochem.tuwien.ac.at/reg_user/updates/
[2] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg21493.html

[3] http://www.fftw.org/download.html
[4] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg07220.html
[5] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18664.html


On 2/7/2022 1:19 PM, Igor I Mazin wrote:

my installations bombs with messages such as

--
make: Circular modules.o <- modules.o dependency dropped.
make: Circular fft_modules.o <- modules.o dependency dropped.
make: Circular fft_modules.o <- fft_modules.o dependency dropped.

ifort -c -O -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -traceback
-assume buffered_io
-I/data/opt/intel/compilers_and_libraries_2020.0.166/linux/mkl/include
-qopenmp 3ddens.F
3ddens.F(20): error #7002: Error in opening the compiled module file.
Check INCLUDE paths.   [*FFTPACK*]
   use fftpack
--

or

--
fft_modules.F(165): error #5102: Cannot open include file 'fftw3.f03'
  include 'fftw3.f03'
fft_modules.F(188): error #6404: This name does not have a type, and
must have an explicit type.   [FFTW_FORWARD]
  FFTW_FORWARD, FFTW_ESTIMATE)
--

etc

Any idea how can I fix it?

P.S.: ./check_minimal_software_requirements.sh has found all necessary
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