Re: [Wien] Installing WIEN2k, w2web not running

2021-04-13 Thread Pavel Ondračka 
On Wed, 2021-04-14 at 06:12 +, delamora wrote:
> Thank you Pavel
> 
> I do a search
> dnf search perl-Sys-Hostname
> and I get;
> perl-Sys-Hostname-Long.noarch : Try every conceivable way to get full
> hostname
> I will try it

I'm not sure about the perl-Sys-Hostname-Long.noarch package. On my
Fedora 33 I have perl-Sys-Hostname.x86_64 package.

I have no idea why you can't find it. BTW Another way how to determine
the correct package could be to really check for the missing file (from
your log this is: */Sys/Hostname.pm) with:
"dnf provides */Sys/Hostname.pm"

> By the way, is Pavel the same as Pablo but in your language? It seems
> that no.

I believe it is :-)

Best regards
Pavel

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Re: [Wien] Question about wave function and case.almblm file

2021-04-13 Thread Peter Blaha 
Of course also the local orbitals depend on "k" via the phase factor 
e^(ik.tau), where tau is the position of the atom. Otherwise the wave 
functions from the local orbital would be identical for all k-ponts (and 
then of course also their energy (eigenvalue) would be the same, ...


They do not depend on "K", although they also have ONE plane wave 
e^(iKr) attached to them (You find the K when you activate the WFPRI in 
case.in1) in order to obey the local point symmetry.


I suggest you dig into either lapw2 or lapw7 to see how the wave 
functions are constructed (and used).


Am 13.04.2021 um 18:14 schrieb gutow...@agh.edu.pl:

Dear Professor Blaha and users of Wien2k,

I am trying to get wave function from *.radwf and *.almblm files (in 
order to calculate Hopfield parameter).  However, I have a problem with 
local orbitals.


In User Guide there is an information that local orbitals are 
k-independent, so I thought, that in order to get local orbital I should 
multiply the corresponding basis functions from *radwf by A_lm, B_lm and 
C_lm of freely chosen k-point from *almblm file.


However, in *.almblm file the A_lm coefficients of local orbital (8th 
and 9th columns) seem to be k-dependent (they are different for 
different k-points), e.g.


  K-POINT:  0.020833  0.020833  0.020833    83  13 1
   1   1   5  jatom,nemin,nemax
   1   ATOM
   1  1.446759259259260E-004  NUM, weight
   0   0   1  0.11018906E-01  0.E+00   -0.34384483E-01 
0.E+00   -0.99978407E+00  0.E+00    0.E+00 
0.E+00    0.E+00  0.E+00
   1  -1   2  0.10910331E-02 -0.10910331E-02   -0.28815122E-02 
0.28815122E-02   -0.16313988E-02  0.16313988E-02    0.E+00 
0.E+00    0.E+00  0.E+00
   1   0   3  0.E+00 -0.15429538E-02    0.E+00 
0.40750736E-02    0.E+00  0.23071463E-02    0.E+00 
0.E+00    0.E+00  0.E+00
   1   1   4  0.10910331E-02  0.10910331E-02   -0.28815122E-02 
-0.28815122E-02   -0.16313988E-02 -0.16313988E-02    0.E+00 
0.E+00    0.E+00  0.E+00

...
  K-POINT:  0.041667  0.041667  0.020833    83  13 2
   1   1   5  jatom,nemin,nemax
   1   ATOM
   1  4.3402782E-004  NUM, weight
   0   0   1  0.10715529E-01  0.E+00   -0.33458040E-01 
0.E+00   -0.99972925E+00  0.E+00    0.E+00 
0.E+00    0.E+00  0.E+00
   1  -1   2  0.21642513E-02 -0.10795369E-02   -0.57119968E-02 
0.28476341E-02   -0.32356411E-02  0.16136986E-02    0.E+00 
0.E+00    0.E+00  0.E+00
   1   0   3  0.E+00 -0.30607136E-02    0.E+00 
0.80779833E-02    0.E+00  0.45758876E-02    0.E+00 
0.E+00    0.E+00  0.E+00
   1   1   4  0.21642513E-02  0.10795369E-02   -0.57119968E-02 
-0.28476341E-02   -0.32356411E-02 -0.16136986E-02    0.E+00 
0.E+00    0.E+00  0.E+00



How should I handle that?

I would appreciate any answer or hint.

Best regards,
Sylwia Gutowska
PhD student, AGH UST in Krakow, Poland
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--
--
Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
Email: bl...@theochem.tuwien.ac.atWIEN2k: http://www.wien2k.at
WWW:   http://www.imc.tuwien.ac.at
-
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Re: [Wien] Installing WIEN2k, w2web not running

2021-04-13 Thread delamora 
Thank you Pavel

I do a search
dnf search perl-Sys-Hostname
and I get;
perl-Sys-Hostname-Long.noarch : Try every conceivable way to get full hostname
I will try it

By the way, is Pavel the same as Pablo but in your language? It seems that no.

Pablo


Hi Pablo,

there is a difference between the package with hostname utility and the
missing perl package with Sys::Hostname module. The proper package
should be perl-Sys-Hostname.

Best regards
Pavel

On Tue, 2021-04-13 at 23:21 +, delamora wrote:
> I have a comment at the end
> Dear WIEN2k comunity,
> I am installing the WIEN2k package in a new computer, all seems to
> run well, except for
> w2web
>
> I run w2web
> it says;
> Can't locate Sys/Hostname.pm in @INC (you may need to install the
> Sys::Hostname module) (@INC contains: /usr/local/lib64/perl5/5.32
> /usr/local/share/perl5/5.32 /usr/lib64/perl5/vendor_perl
> /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5) at
> /home/Programas/WIEN2k-19.1/w2web line 3.BEGIN failed--compilation
> aborted at /home/Programas/WIEN2k-19.1/w2web line 3.
>
> I searched for "Sys::Hostname";
> dnf search Sys::Hostname
> => does not exist
>
> I searched for "Hostname"; dnf search Hostname
> and I found it, so I try to install it
> => dnf install hostname.x86_64
> and I get as an answer
> => "package already installed"perl-Sys-Hostname
>
> ==
> I just want to comment that /home/Programas/WIEN2k-
> 19.1/SRC_w2web/w2web
> gives;
> -
> #!/usr/bin/perl
>
> use Sys::Hostname;
> --
> So I do not know why w2web is not running with Fedora 33
>
>
> Pablo
>
> ___
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Re: [Wien] MPI error

2021-04-13 Thread Peter Blaha 
It cannot initialize an mpi job, because it is missing the interface 
software.


You need to ask the computing center / system administrators how one 
executes a mpi job on this computer.


It could be, that "mpirun" is not supported on this machine. You may try 
a wien2k installation with  system   "LS"  in siteconfig. This will 
configure the parallel environment/commands using "slurm" commands like 
srun -K -N_nodes_ -n_NP_  ..., replacing mpirun.
We used it once on our hpc machine, since it was recommended by the 
computing center people. However, it turned out that the standard mpirun 
installation was more stable because the "slurm controller" died too 
often leading to many random crashes. Anyway, if your system has what is 
called "tight integration of mpi", it might be necessary.


Am 13.04.2021 um 21:47 schrieb leila mollabashi:

Dear Prof. Peter Blaha and WIEN2k users,

Then by run x lapw1 –p:

starting parallel lapw1 at Tue Apr 13 21:04:15 CEST 2021

->  starting parallel LAPW1 jobs at Tue Apr 13 21:04:15 CEST 2021

running LAPW1 in parallel mode (using .machines)

2 number_of_parallel_jobs

[1] 14530

[e0467:14538] mca_base_component_repository_open: unable to open 
mca_btl_uct: libucp.so.0: cannot open shared object file: No such file 
or directory (ignored)


WARNING: There was an error initializing an OpenFabrics device.

   Local host:   e0467

   Local device: mlx4_0

MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD

with errorcode 0.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.

You may or may not see output from other processes, depending on

exactly when Open MPI kills them.

--

[e0467:14567] 1 more process has sent help message 
help-mpi-btl-openib.txt / error in device init


[e0467:14567] 1 more process has sent help message 
help-mpi-btl-openib.txt / error in device init


[e0467:14567] Set MCA parameter "orte_base_help_aggregate" to 0 to see 
all help / error messages


[warn] Epoll MOD(1) on fd 27 failed.  Old events were 6; read change was 
0 (none); write change was 2 (del): Bad file descriptor



Somewhere there should be some documentation how one runs an mpi job on

your system.

Only I found this:

Before ordering a task, it should be encapsulated in an appropriate 
script understandable for the queue system, e.g .:


/home/users/user/submit_script.sl 

Sample SLURM script:

#! / bin / bash -l

#SBATCH -N 1

#SBATCH --mem 5000

#SBATCH --time = 20:00:00

/sciezka/do/pliku/binarnego/plik_binarny.in > 
/sciezka/do/pliku/wyjsciowego.out


To order a task to a specific queue, use the #SBATCH -p parameter, e.g.

#! / bin / bash -l

#SBATCH -N 1

#SBATCH --mem 5000

#SBATCH --time = 20:00:00

#SBATCH -p standard

/sciezka/do/pliku/binarnego/plik_binarny.in > 
/siezka/do/pliku/wyjsciowego.out


The task must then be ordered using the *sbatch* command

sbatch /home/users/user/submit_script.sl 

*Ordering interactive tasks***


Interactive tasks can be divided into two groups:

·interactive task (working in text mode)

·interactive task

*Interactive task (working in text mode)***


Ordering interactive tasks is very simple and in the simplest case it 
comes down to issuing the command below.


srun --pty / bin / bash

Sincerely yours,

Leila Mollabashi


On Wed, Apr 14, 2021 at 12:03 AM leila mollabashi 
mailto:le.mollaba...@gmail.com>> wrote:


Dear Prof. Peter Blaha and WIEN2k users,

Thank you for your assistances.

>  At least now the error: "lapw0 not found" is gone. Do you
understand why ??

Yes, I think that because now the path is clearly known.

>How many slots do you get by this srun command ?

Usually I went to node with 28 CPUs.

>Is this the node with the name  e0591 ???

Yes, it is.

>Of course the .machines file must be consistent (dynamically adapted)

with the actual nodename.

Yes, to do this I use my script.

>When I  use “srun --pty -n 8 /bin/bash” that goes to the node with 8 free
cores, and run x lapw0 –p then this happens:

starting parallel lapw0 at Tue Apr 13 20:50:49 CEST 2021

 .machine0 : 4 processors

[1] 12852

[e0467:12859] mca_base_component_repository_open: unable to open
mca_btl_uct: libucp.so.0: cannot open shared object file: No such
file or directory (ignored)

[e0467][[56319,1],1][btl_openib_component.c:1699:init_one_device]
error obtaining device attributes for mlx4_0 errno says Protocol not
supported

[e0467:12859] mca_base_component_repository_open: unable to open
mca_pml_ucx: libucp.so.0: cannot open shared object file: No such
file or directory (ignored)

LAPW0 END

[1]    Done  mpirun -np 4 -machinefile
.machine0 /home/users/mollabashi/v19.2/lapw0_mpi lapw0.def >> .time00

Sincerely

Re: [Wien] Installing WIEN2k, w2web not running

2021-04-13 Thread Pavel Ondračka 
Hi Pablo,

there is a difference between the package with hostname utility and the
missing perl package with Sys::Hostname module. The proper package
should be perl-Sys-Hostname.

Best regards
Pavel

On Tue, 2021-04-13 at 23:21 +, delamora wrote:
> I have a comment at the end
> Dear WIEN2k comunity,
> I am installing the WIEN2k package in a new computer, all seems to
> run well, except for
> w2web
> 
> I run w2web
> it says;
> Can't locate Sys/Hostname.pm in @INC (you may need to install the
> Sys::Hostname module) (@INC contains: /usr/local/lib64/perl5/5.32
> /usr/local/share/perl5/5.32 /usr/lib64/perl5/vendor_perl
> /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5) at
> /home/Programas/WIEN2k-19.1/w2web line 3.BEGIN failed--compilation
> aborted at /home/Programas/WIEN2k-19.1/w2web line 3.
> 
> I searched for "Sys::Hostname";
> dnf search Sys::Hostname
> => does not exist
> 
> I searched for "Hostname"; dnf search Hostname
> and I found it, so I try to install it
> => dnf install hostname.x86_64
> and I get as an answer
> => "package already installed"perl-Sys-Hostname
> 
> ==
> I just want to comment that /home/Programas/WIEN2k-
> 19.1/SRC_w2web/w2web
> gives;
> -
> #!/usr/bin/perl
> 
> use Sys::Hostname;
> --
> So I do not know why w2web is not running with Fedora 33
> 
> 
> Pablo
> 
> ___
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Re: [Wien] Installing WIEN2k, w2web not running

2021-04-13 Thread delamora 
I have a comment at the end

Dear WIEN2k comunity,
I am installing the WIEN2k package in a new computer, all seems to run well, 
except for
w2web

I run w2web
it says;
Can't locate Sys/Hostname.pm in @INC (you may need to install the Sys::Hostname 
module) (@INC contains: /usr/local/lib64/perl5/5.32 /usr/local/share/perl5/5.32 
/usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 
/usr/share/perl5) at /home/Programas/WIEN2k-19.1/w2web line 3.BEGIN 
failed--compilation aborted at /home/Programas/WIEN2k-19.1/w2web line 3.

I searched for "Sys::Hostname";
dnf search Sys::Hostname
=> does not exist

I searched for "Hostname"; dnf search Hostname
and I found it, so I try to install it
=> dnf install hostname.x86_64
and I get as an answer
=> "package already installed"

==
I just want to comment that
/home/Programas/WIEN2k-19.1/SRC_w2web/w2web
gives;
-
#!/usr/bin/perl

use Sys::Hostname;
--
So I do not know why w2web is not running with Fedora 33


Pablo

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[Wien] Installing WIEN2k, w2web not running

2021-04-13 Thread delamora 
Dear WIEN2k comunity,
I am installing the WIEN2k package in a new computer, all seems to run well, 
except for
w2web

I run w2web
it says;
Can't locate Sys/Hostname.pm in @INC (you may need to install the Sys::Hostname 
module) (@INC contains: /usr/local/lib64/perl5/5.32 /usr/local/share/perl5/5.32 
/usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 
/usr/share/perl5) at /home/Programas/WIEN2k-19.1/w2web line 3.BEGIN 
failed--compilation aborted at /home/Programas/WIEN2k-19.1/w2web line 3.

I searched for "Sys::Hostname";
dnf search Sys::Hostname
=> does not exist

I searched for "Hostname";
dnf search Hostname
and I found it, so I try to install it
=> dnf install hostname.x86_64
and I get as an answer
=> "package already installed"

Pablo

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Re: [Wien] MPI error

2021-04-13 Thread leila mollabashi 
Dear Prof. Peter Blaha and WIEN2k users,

Then by run x lapw1 –p:

starting parallel lapw1 at Tue Apr 13 21:04:15 CEST 2021

->  starting parallel LAPW1 jobs at Tue Apr 13 21:04:15 CEST 2021

running LAPW1 in parallel mode (using .machines)

2 number_of_parallel_jobs

[1] 14530

[e0467:14538] mca_base_component_repository_open: unable to open
mca_btl_uct: libucp.so.0: cannot open shared object file: No such file or
directory (ignored)

WARNING: There was an error initializing an OpenFabrics device.

  Local host:   e0467

  Local device: mlx4_0

MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD

with errorcode 0.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.

You may or may not see output from other processes, depending on

exactly when Open MPI kills them.

--

[e0467:14567] 1 more process has sent help message help-mpi-btl-openib.txt
/ error in device init

[e0467:14567] 1 more process has sent help message help-mpi-btl-openib.txt
/ error in device init

[e0467:14567] Set MCA parameter "orte_base_help_aggregate" to 0 to see all
help / error messages

[warn] Epoll MOD(1) on fd 27 failed.  Old events were 6; read change was 0
(none); write change was 2 (del): Bad file descriptor

>Somewhere there should be some documentation how one runs an mpi job on
your system.

Only I found this:

Before ordering a task, it should be encapsulated in an appropriate script
understandable for the queue system, e.g .:

/home/users/user/submit_script.sl

Sample SLURM script:

#! / bin / bash -l

#SBATCH -N 1

#SBATCH --mem 5000

#SBATCH --time = 20:00:00



/sciezka/do/pliku/binarnego/plik_binarny.in>
/sciezka/do/pliku/wyjsciowego.out

To order a task to a specific queue, use the #SBATCH -p parameter, e.g.

#! / bin / bash -l

#SBATCH -N 1

#SBATCH --mem 5000

#SBATCH --time = 20:00:00

#SBATCH -p standard



/sciezka/do/pliku/binarnego/plik_binarny.in>
/siezka/do/pliku/wyjsciowego.out

The task must then be ordered using the *sbatch* command

sbatch /home/users/user/submit_script.sl

*Ordering interactive tasks*


Interactive tasks can be divided into two groups:

· interactive task (working in text mode)

· interactive task

*Interactive task (working in text mode)*


Ordering interactive tasks is very simple and in the simplest case it comes
down to issuing the command below.

srun --pty / bin / bash



Sincerely yours,

Leila Mollabashi

On Wed, Apr 14, 2021 at 12:03 AM leila mollabashi 
wrote:

> Dear Prof. Peter Blaha and WIEN2k users,
>
> Thank you for your assistances.
>
> > At least now the error: "lapw0 not found" is gone. Do you understand
> why ??
>
> Yes, I think that because now the path is clearly known.
>
> >How many slots do you get by this srun command ?
>
> Usually I went to node with 28 CPUs.
>
> >Is this the node with the name  e0591  ???
>
> Yes, it is.
>
> >Of course the .machines file must be consistent (dynamically adapted)
>
> with the actual nodename.
>
> Yes, to do this I use my script.
>
> >When I use “srun --pty -n 8 /bin/bash” that goes to the node with 8 free
> cores, and run x lapw0 –p then this happens:
>
> starting parallel lapw0 at Tue Apr 13 20:50:49 CEST 2021
>
>  .machine0 : 4 processors
>
> [1] 12852
>
> [e0467:12859] mca_base_component_repository_open: unable to open
> mca_btl_uct: libucp.so.0: cannot open shared object file: No such file or
> directory (ignored)
>
> [e0467][[56319,1],1][btl_openib_component.c:1699:init_one_device] error
> obtaining device attributes for mlx4_0 errno says Protocol not supported
>
> [e0467:12859] mca_base_component_repository_open: unable to open
> mca_pml_ucx: libucp.so.0: cannot open shared object file: No such file or
> directory (ignored)
>
> LAPW0 END
>
> [1]Done  mpirun -np 4 -machinefile .machine0
> /home/users/mollabashi/v19.2/lapw0_mpi lapw0.def >> .time00
>
> Sincerely yours,
>
> Leila Mollabashi
>
>
>
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[Wien] MPI error

2021-04-13 Thread leila mollabashi 
Dear Prof. Peter Blaha and WIEN2k users,

Thank you for your assistances.

> At least now the error: "lapw0 not found" is gone. Do you understand why
??

Yes, I think that because now the path is clearly known.

>How many slots do you get by this srun command ?

Usually I went to node with 28 CPUs.

>Is this the node with the name  e0591  ???

Yes, it is.

>Of course the .machines file must be consistent (dynamically adapted)

with the actual nodename.

Yes, to do this I use my script.

>When I use “srun --pty -n 8 /bin/bash” that goes to the node with 8 free
cores, and run x lapw0 –p then this happens:

starting parallel lapw0 at Tue Apr 13 20:50:49 CEST 2021

 .machine0 : 4 processors

[1] 12852

[e0467:12859] mca_base_component_repository_open: unable to open
mca_btl_uct: libucp.so.0: cannot open shared object file: No such file or
directory (ignored)

[e0467][[56319,1],1][btl_openib_component.c:1699:init_one_device] error
obtaining device attributes for mlx4_0 errno says Protocol not supported

[e0467:12859] mca_base_component_repository_open: unable to open
mca_pml_ucx: libucp.so.0: cannot open shared object file: No such file or
directory (ignored)

LAPW0 END

[1]Done  mpirun -np 4 -machinefile .machine0
/home/users/mollabashi/v19.2/lapw0_mpi lapw0.def >> .time00

Sincerely yours,

Leila Mollabashi
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[Wien] Question about wave function and case.almblm file

2021-04-13 Thread gutowska 

Dear Professor Blaha and users of Wien2k,

I am trying to get wave function from *.radwf and *.almblm files (in 
order to calculate Hopfield parameter).  However, I have a problem with 
local orbitals.


In User Guide there is an information that local orbitals are 
k-independent, so I thought, that in order to get local orbital I should 
multiply the corresponding basis functions from *radwf by A_lm, B_lm and 
C_lm of freely chosen k-point from *almblm file.


However, in *.almblm file the A_lm coefficients of local orbital (8th 
and 9th columns) seem to be k-dependent (they are different for 
different k-points), e.g.


  K-POINT:  0.020833  0.020833  0.02083383  13   
1

   1   1   5  jatom,nemin,nemax
   1   ATOM
   1  1.446759259259260E-004  NUM, weight
   0   0   1  0.11018906E-01  0.E+00   -0.34384483E-01  
0.E+00   -0.99978407E+00  0.E+000.E+00  
0.E+000.E+00  0.E+00
   1  -1   2  0.10910331E-02 -0.10910331E-02   -0.28815122E-02  
0.28815122E-02   -0.16313988E-02  0.16313988E-020.E+00  
0.E+000.E+00  0.E+00
   1   0   3  0.E+00 -0.15429538E-020.E+00  
0.40750736E-020.E+00  0.23071463E-020.E+00  
0.E+000.E+00  0.E+00
   1   1   4  0.10910331E-02  0.10910331E-02   -0.28815122E-02 
-0.28815122E-02   -0.16313988E-02 -0.16313988E-020.E+00  
0.E+000.E+00  0.E+00

...
  K-POINT:  0.041667  0.041667  0.02083383  13   
2

   1   1   5  jatom,nemin,nemax
   1   ATOM
   1  4.3402782E-004  NUM, weight
   0   0   1  0.10715529E-01  0.E+00   -0.33458040E-01  
0.E+00   -0.99972925E+00  0.E+000.E+00  
0.E+000.E+00  0.E+00
   1  -1   2  0.21642513E-02 -0.10795369E-02   -0.57119968E-02  
0.28476341E-02   -0.32356411E-02  0.16136986E-020.E+00  
0.E+000.E+00  0.E+00
   1   0   3  0.E+00 -0.30607136E-020.E+00  
0.80779833E-020.E+00  0.45758876E-020.E+00  
0.E+000.E+00  0.E+00
   1   1   4  0.21642513E-02  0.10795369E-02   -0.57119968E-02 
-0.28476341E-02   -0.32356411E-02 -0.16136986E-020.E+00  
0.E+000.E+00  0.E+00



How should I handle that?

I would appreciate any answer or hint.

Best regards,
Sylwia Gutowska
PhD student, AGH UST in Krakow, Poland
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