Re: [Wien] Wien Digest, Vol 147, Issue 4

[Víctor Luaña Cabal]

On Sun, Feb 25, 2018 at 08:17:55AM +0100, William Lafargue-dit-Hauret wrote:
> Dear Victor,
> If you remove the space between « print » and the first parenthesis, you can 
> do it in python 3 ; this is the print function.

Before we enter in an interminable war of languages my

print (( 2.8*2)*2+(-0.31749*2)+( -0.98948))

can be used in "ANY" scripting language. In this case I had a window
in gnuplot close to my window for email. It could be bash, erl, python, ...

Best regards from coldy (today) northern Spain,
   Víctor Luaña
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Re: [Wien] Wien Digest, Vol 147, Issue 4

[William Lafargue-dit-Hauret]

Dear Victor,
If you remove the space between « print » and the first parenthesis, you can do 
it in python 3 ; this is the print function.

Best regards,
William

> Le 25 févr. 2018 à 08:04, Badis Bennecer  a écrit :
> 
> Dear Victor,
> I must confess,  that when I wrote the answer I did not even think about 
> using a correct fortran language, i mean using correct fortran statements. 
> 
> Thank you very much for correcting me.
> 
> All the best and have a nice day
> 
> Badis
> 
> 
> 
> 
> From: Wien  on behalf of Víctor 
> Luaña Cabal 
> Sent: Sunday, February 25, 2018 5:39 AM
> To: A Mailing list for WIEN2k users
> Cc: Victor Luaña
> Subject: Re: [Wien] Wien Digest, Vol 147, Issue 4
>  
> On Sun, Feb 25, 2018 at 06:06:39AM +, Badis Bennecer wrote:
> > Dear Victor,
> > 
> > 
> > It is minus signs
> 
> Badis,
> 
> Sorry, but my main question was the language (computer language).
> Otherwise
> 
> print (( 2.8*2)*2+(-0.31749*2)+( -0.98948))
> 
> the result is 6.82026
> 
> Maybe you were using some form of lisp? The odd number of parenthesis:
> open 5, close 4, were my main trouble. I had to add an extra ")".  Of
> course,  minus signs obtained from web pages may cause awful errors so
> it is important to prevent that.
> 
> Best regards,
>   Víctor Luaña
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Re: [Wien] Wien Digest, Vol 147, Issue 4

[Víctor Luaña Cabal]

On Sun, Feb 25, 2018 at 06:06:39AM +, Badis Bennecer wrote:
> Dear Victor,
> 
> 
> It is minus signs

Badis,

Sorry, but my main question was the language (computer language).
Otherwise

print (( 2.8*2)*2+(-0.31749*2)+( -0.98948))

the result is 6.82026

Maybe you were using some form of lisp? The odd number of parenthesis:
open 5, close 4, were my main trouble. I had to add an extra ")".  Of
course,  minus signs obtained from web pages may cause awful errors so
it is important to prevent that.

Best regards,
  Víctor Luaña
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Re: [Wien] Wien Digest, Vol 147, Issue 4

[Gavin Abo]

Maybe they are saying that by using the MULTI values given in case.struct:

:MMTOT = :MMI002*MULTI_Fe + :MMI001*MULTI_Y + :MMINT [ 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg16320.html ]


:MMTOT = 2.8*4 + (-0.31749*2)  + (-0.98948) = 6.82026 (same as MMTOT 
but to 4 places after the decimal point that is likely due to a bit of 
rounding error)



On 2/24/2018 4:27 PM, Víctor Luaña Cabal wrote:

On Sat, Feb 24, 2018 at 11:46:06PM +, Badis Bennecer wrote:

Hi

It looks like the total magnetic moment in the cell, with Z=2 (unit cell 
defined in your case.structure)

(( 2.8*2)*2+(-0.31749*2)+( -0.98948)= 8,4472-0,63498--0.98948=6,82274 
(unity)

Dear Badis,

Sorry, but I don't even recognize the computer languaje in which your
answer is written.

Can you clarify that point for me?
Is the "--" a misprint? Same thing for the odd number of parenthesis?

Best regards,
  Víctor Luaña
--
 .  ."Never let your sense of morals prevent you from
/ `' \   doing what is right."
   /(o)(o)\  -- Salvor Hardin, "Foundation"
  /`. \/ .'\
/   '`'`   \ "Freedom!, freedom!, freedom! After that put whatever
|  \'`'`/  | term you like"
|  |'`'`|  |  --Largo Caballero (socialist, spanish president in the exile,
  \/`'`'`'\/   shortly before dying)
==(((==)))===+===
! Dr.Víctor Luaña, in silico chemist & prof. !
! Departamento de Química Física y Analítica !
! Universidad de Oviedo, 33006-Oviedo, Spain !
! e-mail:    !
! phone: +34-984080927fax: +34-985103125 !
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  Articles:  
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Re: [Wien] Wien Digest, Vol 147, Issue 4

[Víctor Luaña Cabal]

On Sat, Feb 24, 2018 at 11:46:06PM +, Badis Bennecer wrote:
> Hi
> 
> It looks like the total magnetic moment in the cell, with Z=2 (unit cell 
> defined in your case.structure)
> 
> (( 2.8*2)*2+(-0.31749*2)+( -0.98948)= 8,4472-0,63498--0.98948=6,82274 
> (unity)

Dear Badis,

Sorry, but I don't even recognize the computer languaje in which your
answer is written.

Can you clarify that point for me?
Is the "--" a misprint? Same thing for the odd number of parenthesis?

Best regards,
 Víctor Luaña
--
.  ."Never let your sense of morals prevent you from
   / `' \   doing what is right." 
  /(o)(o)\  -- Salvor Hardin, "Foundation"
 /`. \/ .'\  
/   '`'`   \ "Freedom!, freedom!, freedom! After that put whatever
|  \'`'`/  | term you like"
|  |'`'`|  |  --Largo Caballero (socialist, spanish president in the exile,
 \/`'`'`'\/   shortly before dying)
==(((==)))===+===
! Dr.Víctor Luaña, in silico chemist & prof. !
! Departamento de Química Física y Analítica !
! Universidad de Oviedo, 33006-Oviedo, Spain !
! e-mail:    !
! phone: +34-984080927fax: +34-985103125 !
++
 GroupPage: 
 Articles:  
 git-hub:   
 ORCID: -0003-4585-4627; RID: H-2045-2015
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Re: [Wien] Wien Digest, Vol 147, Issue 4

[Sherif Yehia]

Dear  Users  

  In calculating YFe2  I got this result for the moment as follows 

 SPIN MAGNETIC MOMENTS OF MIXED CHARGE DENSITY
:MMINT:  MAGNETIC MOMENT IN INTERSTITIAL  =   -0.98948
:MMI001: MAGNETIC MOMENT IN SPHERE   1    =   -0.31749
:MMI002: MAGNETIC MOMENT IN SPHERE   2    =    2.8
:MMTOT:  SPIN MAGNETIC MOMENT IN CELL =    6.82028
Can I ask is the  MMTOT  per formula unit 

Thank you

  
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Re: [Wien] Extra vertical lines in bandstructure in spaghetti

[Gavin Abo]

I quickly created a WIEN2k 17.1 test case (as shown below) and believe I 
have reproduced the issue.


The 7_SrPtAs.bands.agr that was generated shows 6 lines between the M 
and K labels with data toler /1.d-07/.  The 5_SrPtAs.bands.agr that was 
generated using data toler /1.d-05/ does not have those lines.  [ 
https://github.com/gsabo/WIEN2k-Patches/blob/master/17.1/SrPtAs_bandstructure_vlines.pdf 
]


However, the agr files are missing the SIGMA label specified in 
SRC_templates/hcp.klist and no vertical line appears at SIGMA.  The 
SIGMA label does seem to appear okay in the PostScript (ps) file created 
by "plot bandstructure" in w2web.


It may be that the vertical lines are because I just used an improper 
k-path for this structure, didn't include other special point labels, or 
perhaps, the algorithm used by the code to generate the vertical lines 
is limited or not yet designed to properly handle hexagonal lattice.  So 
I feel the issue might not be due to the data toler /1.d-07/, but 
something to do with eps1, eps2, and eps3 formulas used on lines 67-69 
in bz_lin.f.


Currently, another way I can think of to remove the vertical lines as a 
workaround, would be to plot the bandstructure (using a less automated 
method; plotting more by hand) in another program, such as Origin [ 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg15255.html 
], using case.spaghetti_ene or use the Grace GUI (xmgrace) to edit by 
hand the agr file by selecting Plot->Axis properties followed by editing 
the "Tick location - Label" fields under the Special tab.


username@computername:~/wiendata/SrPtAs$ ls SrPtAs.struct
SrPtAs.struct
username@computername:~/wiendata/SrPtAs$ init_lapw -b
...
  init_lapw finished ok
username@computername:~/wiendata/SrPtAs$ run_lapw
...
in cycle 9    ETEST: .00017542   CTEST: .008216
hup: Command not found.
 LAPW0 END
 LAPW1 END
 LAPW2 END
 CORE  END
 MIXER END
ec cc and fc_conv 1 1 1

>   stop
username@computername:~/wiendata/SrPtAs$ cp 
$WIENROOT/SRC_templates/hcp.klist SrPtAs.klist_band

username@computername:~/wiendata/SrPtAs$ x lapw1 -band
 LAPW1 END
114.3u 2.9s 1:57.54 99.7% 0+0k 0+79704io 0pf+0w
username@computername:~/wiendata/SrPtAs$ x lapw2 -band -qtl
 LAPW2 END
16.5u 0.4s 0:17.00 99.7% 0+0k 8+51528io 1pf+0w
username@computername:~/wiendata/SrPtAs$ grepline_lapw :FER *.scf 1
in  1 files:
SrPtAs.scf::FER  : F E R M I - ENERGY(TETRAH.M.)=   0.5715462774
username@computername:~/wiendata/SrPtAs$ sed -n 9p SrPtAs.insp
1  0.  # Fermi switch,  Fermi-level (in Ry 
units)

username@computername:~/wiendata/SrPtAs$ gedit SrPtAs.insp
username@computername:~/wiendata/SrPtAs$ sed -n 9p SrPtAs.insp
1  0.5715462774  # Fermi switch, Fermi-level (in 
Ry units)

username@computername:~/wiendata/SrPtAs$ x spaghetti
 SPAGH: Read band energy from case.output1
 number of k-points read in case.vector=  61
SPAGH END
0.1u 0.0s 0:00.22 86.3% 0+0k 8+2000io 0pf+0w
username@computername:~/wiendata/SrPtAs$ cp SrPtAs.bands.agr 
7_SrPtAs.bands.agr

username@computername:~/wiendata/SrPtAs$ xmgrace 7_SrPtAs.bands.agr

*Change data toler  /1.d-07/ to /1.d-05/*

username@computername:~/WIEN2k/SRC_spaghetti$ wget 
https://raw.githubusercontent.com/gsabo/WIEN2k-Patches/master/17.1/bz_lin.patch

...
username@computername:~/WIEN2k/SRC_spaghetti$ patch -b bz_lin.f 
bz_lin.patch

patching file bz_lin.f
username@computername:~/WIEN2k/SRC_spaghetti$ make
username@computername:~/WIEN2k/SRC_spaghetti$ cp spaghetti ..
username@computername:~/WIEN2k/SRC_spaghetti$ cd ~/wiendata/SrPtAs/
username@computername:~/wiendata/SrPtAs$ x spaghetti
 SPAGH: Read band energy from case.output1
 number of k-points read in case.vector=  61
SPAGH END
0.1u 0.0s 0:00.19 100.0% 0+0k 0+2000io 0pf+0w
username@computername:~/wiendata/SrPtAs$ cp SrPtAs.bands.agr 
5_SrPtAs.bands.agr username@computername:~/wiendata/SrPtAs$ xmgrace 
5_SrPtAs.bands.agr


*Restore data toler back to /1.d-07/*

username@computername:~/WIEN2k/SRC_spaghetti$ mv bz_lin.f.orig bz_lin.f
username@computername:~/WIEN2k/SRC_spaghetti$ make clean
...
username@computername:~/WIEN2k/SRC_spaghetti$ make
...
username@computername:~/WIEN2k/SRC_spaghetti$ cp spaghetti ..
SrPtAs 
H   LATTICE,NONEQUIV.ATOMS:  3 194_P63/mmc 
MODE OF CALC=RELA unit=ang 
  8.121290  8.121290 17.174594 90.00 90.00120.00   
ATOM  -1: X=0. Y=0. Z=0.
  MULT= 2  ISPLIT= 4
  -1: X=0. Y=0. Z=0.5000
Sr NPT=  781  R0=0.1000 RMT=2.   Z: 38.000 
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=0.6667 Z=0.2500
   

Re: [Wien] dstart error when run 'init_lapw' from terminal

[Gavin Abo]

Good to hear that your problem seems to be solved.

If you use serial mode "x dstart -p" again and encounter a problem, 
below is possibly an error message improvement for dstartpara_lapw that 
one could try.  It's the dstartpara_lapw.patch at: 
https://github.com/gsabo/WIEN2k-Patches/tree/master/17.1


*Before Patch*

username@computername:~/wiendata/test$ rm test.rsp
username@computername:~/wiendata/test$ init_lapw -s dstart
 next is dstart
 next is dstart
>   dstart -c -p    (07:05:28) running dstart in single mode
DSTART - Error
**  dstart crashed!
cat: No match.
0.0u 0.0s 0:00.02 0.0% 0+0k 0+56io 0pf+0w
error: command   /home/username/WIEN2k/dstartpara -c dstart.def failed
 n stop error n
username@computername:~/wiendata/test$ cat dstart.error
**  Error in Parallel dstart
**  dstart STOPPED at Sat Feb 24 07:05:28 MST 2018
**  check ERROR FILES!

*After Patch*

username@computername:~/wiendata/test$ cd $WIENROOT
username@computername:~/WIEN2k$ wget 
https://raw.githubusercontent.com/gsabo/WIEN2k-Patches/master/17.1/dstartpara_lapw.patch

...
username@computername:~/WIEN2k$ patch -b dstartpara_lapw 
dstartpara_lapw.patch

patching file dstartpara_lapw
username@computername:~/WIEN2k$ cd ~/wiendata/test
username@computername:~/wiendata/test$ init_lapw -s dstart
...
username@computername:~/wiendata/test$ cat dstart.error
**  Error in Parallel dstart
**  dstart STOPPED at Sat Feb 24 07:09:48 MST 2018
**  check ERROR FILES!
 'DSTART' - can't open unit: 81
 'DSTART' -    filename: test.rsp
 'DSTART' -  status: old  form: formatted

On 2/24/2018 4:06 AM, Hemza KHERIBOT wrote:

Thank you all.
I use 'init_lapw' and follow all steps. I verify that all necessary 
files for dstart are generated.


I follow Govin suggestion and fgenerate .machines file and execute 'x 
dstart -p' and I think it solved my problem
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Re: [Wien] dstart error when run 'init_lapw' from terminal

[Hemza KHERIBOT]

Thank you all.
I use 'init_lapw' and follow all steps. I verify that all necessary files
for dstart are generated.

I follow Govin suggestion and fgenerate .machines file and execute 'x
dstart -p' and I think it solved my problem

On 22 February 2018 at 03:15, Gavin Abo  wrote:

> The reason init_lapw uses "-p" for dstart is likely so that the program
> can autodetect whether or not dstart should run in serial or parallel mode.
>
> As shown below, you should see it runs dstart in serial mode just fine
> without or with "-p":
> username@computername:~/wien/test$ ls -l
> total 60
> -rwxr-xr-x 1 username group   185 Feb 21 11:17 test.in0
> -rwxr-xr-x 1 username group   634 Feb 21 11:17 test.in1c
> -rwxr-xr-x 1 username group   297 Feb 21 11:17 test.in2c
> -rwxr-xr-x 1 username group   282 Feb 21 11:17 test.inst
> -rwxr-xr-x 1 username group 37146 Feb 21 11:20 test.rsp
> -rwxr-xr-x 1 username group  2510 Feb 21 11:20 test.struct
> username@computername:~/wien/test$ x dstart
> DSTART ENDS
> 1.9u 0.0s 0:02.66 72.1% 0+0k 20040+504io 74pf+0w
> username@computername:~/wien/test$ x dstart -p
> running dstart in single mode <- This means it's actually running as just
> "x dstart", because it autodetected that there was no .machines with
> "dstart:".
> DSTART ENDS
> 1.9u 0.0s 0:01.91 100.0% 0+0k 40+512io 0pf+0w
>
> The error you have might be because one of the input files test.in0,
> test.in1(c), test.in2(c), test.rsp, or test.struct needed by dstart is
> missing.
>
> For example, purposely removing the test.rsp file seems to give the same
> error message:
>
> username@computername:~/wien/test$ rm test.rsp
> username@computername:~/wien/test$ x dstart -p
> running dstart in single mode
> DSTART - Error
> **  dstart crashed!
> cat: No match.
> 0.0u 0.0s 0:00.03 100.0% 0+0k 0+48io 0pf+0w
> error: command   /home/username/WIEN2k/dstartpara -c dstart.def   failed
>
> The test.rsp is recreated with lstart (as shown on page 35 in "Table 4.1:
> Input and output files of init programs" of the WIEN2k 17.1 UG [
> http://susi.theochem.tuwien.ac.at/reg_user/textbooks/usersguide.pdf ]):
>
> username@computername:~/wien/test$ x lstart
> username@computername:~/wien/test$ ls -l test.rsp
> -rw-r--r-- 1 username group 37146 Feb 21 19:14 test.rsp
>
> To run dstart in parallel mode, one needs a .machines file with a
> "dstart:" line:
>
> username@computername:~/wien/test$ echo "dstart: localhost localhost" >
> .machines
> username@computername:~/wien/test$ x dstart -p
> starting parallel dstart at Wed Feb 21 19:15:15 MST 2018 <- This means
> it's trying to run as "x dstart -p"
>  .machine0 : 2 processors
> [1] 2476
> [proxy:0:0@computername] HYDU_create_process
> (./utils/launch/launch.c:75): execvp error on file
> /home/username/WIEN2k/dstart_mpi (No such file or directory) <- Yes, it
> shows that parallel dstart did not run correctly on my system.  That is
> just because I purposely selected in siteconfig to not compile WIEN2k to
> use mpi.
> [proxy:0:0@computername] HYDU_create_process
> (./utils/launch/launch.c:75): execvp error on file
> /home/username/WIEN2k/dstart_mpi (No such file or directory)
> [1]Exit -1mpirun -np 2 /home/username/WIEN2k/dstart_mpi
> dstart.def >> .time00
> 0.0u 0.0s 0:01.28 10.1% 0+0k 2248+64io 6pf+0w
>
>
> On 2/21/2018 8:14 AM, Lyudmila Dobysheva wrote:
>
> 21.02.2018 17:55, Hemza KHERIBOT wrote:
>
> I'm testing with Wien2k tying to use terminal for initialization I always
> get this error:
>   next is dstart
>  >   dstart  -p  (14:44:25) running dstart in single mode
> STOP DSTART - Error
> **  dstart crashed!
> cat: No match.
> 0.032u 0.002s 0:00.05 60.0% 0+0k 0+40io 0pf+0w
> error: command   /home/user/WIEN2k/dstartpara -c dstart.def   failed
>   \n stop error \n
>
>
> 1. There should be file dstart.error
> What it contains?
>
> 2. There should be files created by dstart, are there any?
>
> 3. What about previous programs of the initialization (nn, setrmt...)? Do
> they work normally?
>
> I usually resume this step using w2web (no error). lookign at :log I find
> that w2web invokes dstart without '-p', why command line init_lap invoke
> dstart with '-p' (dstartpara).
>
>
> I think this is not important.
>
> Best wishes
> Lyudmila Dobysheva
> --
> Physics-Techn.Institute,
> Udmurt Federal Research Center, Ural Br. of Rus.Ac.Sci.
> 426000 Izhevsk Kirov str. 132
> Russia
> ---
> Tel. +7 (34I2)43-24-59 (office), +7 (9I2)OI9-795O (home)
> Skype: lyuka18 (office), lyuka17 (home)
> E-mail: lyuk...@mail.ru (office), lyuk...@gmail.com (home)
>
>
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