date:20200912

Re: [Wien] ssh command in Wien2k scripts

2020-09-12 Thread Laurence Marks

Peter's suggestion is essentially the same as the -F option in ssh, and
might work.

N.B., I strongly suggest not attempting to rewrite the Wien2k scripts.
Focus on getting ssh to pass WIENROOT or using a substitute such as rsh or
pbsh.

_
Professor Laurence Marks
"Research is to see what everybody else has seen, and to think what nobody
else has thought", Albert Szent-Gyorgi
www.numis.northwestern.edu

On Sat, Sep 12, 2020, 09:41 Peter Blaha 
wrote:

> Please read the ssh/sshd documentation.
>
> You can put into your local .ssh directory a file config and I believe
> you can specify there that you want to transfer the environment.
>
> As far as I know, this should overwrite the default ssh options in
> /etc/ssh/ssh_config and ssh_configd specifications.
>
>
> Am 12.09.2020 um 10:34 schrieb Ilias Miroslav, doc. RNDr., PhD.:
> > Hello,
> >
> > I have similar problem as decribed here
> >
> https://urldefense.com/v3/__https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19049.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!HvP7xTx0DxnNEWTGjuEaz2yor4mq6WKcY0hGUXNwLi5gDD450_vSQZVwufYUrxwS0tcBeA$
>  .
> >
> > ssh vsli2 'echo $WIENROOT'
> >
> >
> > The ssh connection does not preserve the WIENROOT envirovariable.
> >
> > IT admin does not want the variable ""PermitUserEnvironment"  in
> > .sshd_config to be set .
> >
> > Therefore, I have to change Wien2k scripts to incorporate enviromental
> > variable passing.
> >
> > Any hints, howtos ?
> >
> > Miro
> >
> >
> >
> > ___
> > Wien mailing list
> > Wien@zeus.theochem.tuwien.ac.at
> >
> https://urldefense.com/v3/__http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien__;!!Dq0X2DkFhyF93HkjWTBQKhk!HvP7xTx0DxnNEWTGjuEaz2yor4mq6WKcY0hGUXNwLi5gDD450_vSQZVwufYUrxyT3CPFHQ$
> > SEARCH the MAILING-LIST at:
> https://urldefense.com/v3/__http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!HvP7xTx0DxnNEWTGjuEaz2yor4mq6WKcY0hGUXNwLi5gDD450_vSQZVwufYUrxw4g_m9bw$
> >
>
> --
> --
> 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:
> https://urldefense.com/v3/__http://www.wien2k.at__;!!Dq0X2DkFhyF93HkjWTBQKhk!HvP7xTx0DxnNEWTGjuEaz2yor4mq6WKcY0hGUXNwLi5gDD450_vSQZVwufYUrxxPuIsMHA$
> WWW:
>
> https://urldefense.com/v3/__http://www.imc.tuwien.ac.at/tc_blaha-__;!!Dq0X2DkFhyF93HkjWTBQKhk!HvP7xTx0DxnNEWTGjuEaz2yor4mq6WKcY0hGUXNwLi5gDD450_vSQZVwufYUrxy75f0CMQ$
>
>
> ___
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>
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>
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Re: [Wien] ssh command in Wien2k scripts

2020-09-12 Thread Gavin Abo

A good IT admin should know the ins and outs their own particular 
computer system such that they should be able to better advise you on a 
solution for environmental variable passing for their specific system.



You may want to have that IT admin work for their paycheck.  At least 
according to [1], an IT admin on average is compensated $110k per year.



I don't see a lot of information provided about the computer system such 
as its configuration and policy for usage.  If you can provide in-depth 
knowledge about your computer system that your IT admin would already 
now about or could gather from the system, we might be able to provide 
more specific advice.  For example, it can be quite typical for cluster 
computer systems to disallow running commands directly on the main node 
and running such commands there can sometimes even lead to getting 
banned from using the computer system.  Instead, the commands are 
committed to compute nodes with a schedule (queue) system which may be 
tasked with propagating the environmental variables to the computation 
nodes.  Some queue systems can require a special flag in the job script 
to get the environmental variables to the compute node(s). For 
additional details on such a case, see the post:



https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17562.html


So it may be possible for a command to fail when executed on the main 
node that may run fine when submitted to queue system (such as PBS, 
slurm, etc. [3]) with a script such as your command:



ssh vsli2 'echo $WIENROOT'


[1] https://www.theladders.com/salary/it-systems-administrator-salary

[2] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17562.html


[3] https://slurm.schedmd.com/rosetta.pdf


On 9/12/2020 2:34 AM, Ilias Miroslav, doc. RNDr., PhD. wrote:

Hello,

I have similar problem as decribed here 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19049.html 
 .


ssh vsli2 'echo $WIENROOT'

The ssh connection does not preserve the WIENROOT envirovariable.

IT admin does not want the variable ""PermitUserEnvironment"  in 
.sshd_config to be set .


Therefore, I have to change Wien2k scripts to incorporate enviromental 
variable passing.


Any hints, howtos ?

Miro
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Re: [Wien] Segmentation fault in w2w

2020-09-12 Thread Laurence Marks

...please add -g ... (not -f, a typo).

On Sat, Sep 12, 2020 at 11:26 AM Laurence Marks 
wrote:

> Is this compiled with -g ? If not, please add -f, recompile and then
> repeat. (The reason is that optimizations can lead to segmentation faults
> appearing at an inappropriate location in the code.) If with -g it is still
> the same, please add before line 449 of  modules_rc.F a write command, i.e.
> so it has:
>
>   Nb = inwf%bmax-inwf%bmin+1
>   write(*,*) Nb, inwf%Nproj, num_kpts
>   projection = 0
>
> I suspect that num_kpts is wrong, so the dimensions of projection are
> incorrect. However, segmentation errors can be hard to locate.
>
> On Sat, Sep 12, 2020 at 10:20 AM Niraj Aryal 
> wrote:
>
>> Thank you all for your suggestions.
>> I tried your suggestions but so far, the problem remains.
>>
>> As per Prof. Rubel's request, I will share with you my struct file
>> privately along with the steps. Please watch out for my email (
>> aryalnir...@gmail.com).
>> To simplify, I was able to reproduce the problem for paramagnetic case
>> without spin orbit case.
>>
>> Prof. Marks, I have -traceback option in my compilation.
>> These are the line numbers where the seg fault occurs:
>>
>> w2w00432427  l2amn_m_mp_l2amn_ 449
>>  modules_rc.F
>> w2w0042D68E  MAIN__245  main.f
>>
>> This made me believe that the problem is in modules_rc.F file in the amn
>> routine.
>>
>> Thank you for the patch link Gavin.
>> I applied modules_rc.patch but the problem persists.
>>
>> I will continue trying to solve this problem. I will keep you updated if
>> something new comes up.
>> I look forward to your suggestions and feedback.
>>
>> Sincerely,
>> Niraj Aryal
>>
>> On Fri, Sep 11, 2020 at 8:08 PM Gavin Abo  wrote:
>>
>>> Not sure if it is related, but are you using the w2w fix that Jindrich
>>> previously posted for WIEN2k 19.2 [
>>> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19849.html
>>> 
>>> ] .  Or modules_rc.patch and modules_rc_wplot.patch related to w2web if you
>>> prefer to try them are at:
>>>
>>> https://github.com/gsabo/WIEN2k-Patches/tree/master/19.2
>>> 
>>> On 9/11/2020 12:02 PM, Niraj Aryal wrote:
>>>
>>> Dear w2w experts and developers,
>>>
>>> I am using Wien2k version 19.2 in scientific linux 7.5 using intel
>>> compilers (2018).
>>>
>>> I am trying to wannierize f-electron system with antiferromagnetic
>>> magnetic ordering using w2w version 2.0 in the presence of SOC.
>>>
>>> After self-consistent calculations, these are the steps I am following
>>> for the wannierisation:
>>>
>>> init_w2w (to write case.klist, case.inwf, case.win etc)
>>>
>>>  x lapw1 -up -p
>>>  x lapw1 -dn -p
>>>  x lapwso -up -orb -p
>>>
>>> x w2w -so -up -p  --> segmentation fault here
>>> x w2w -so -dn -p  --> segmentation fault here
>>> ..
>>>
>>> Everything works perfectly if I use small kmesh (about 100 kpoints) for
>>> the wannierisation.
>>> I have about 50 bands to wannierize.
>>> When I increase the number of kpoints, w2w crashes giving segmentation
>>> fault.
>>>
>>> I found that w2w can write case.mmn and case.eig with no problems but
>>> the seg fault occurred while writing case.amn.
>>> I confirmed the following hoping that it could help in the debugging
>>> process:
>>>
>>> 1) If I decrease the number of bands to wannierize, the number of
>>> kpoints in the wannierisation can be slightly increased without seg fault.
>>> 2)The problem persists without -so and -p (i.e. without parallel
>>> calculation) flag.
>>>
>>> In my opinion, there are some hard coded array size value(s) in the w2w
>>> program in amn/mmn subroutines which give segmentation fault when the
>>> number of projections*bands*kpoints exceeds that value.
>>> This was confirmed by doing calculations in a simpler system like
>>> silicon with a large number of kpoints and bands.
>>>
>>> I tried looking into the w2w source files and found few hard coded
>>> values.
>>> However, I am hesitant to make changes because I am worried this could
>>> ruin other things.
>>>
>>> This problem is similar to the one posted last year:
>>>
>>> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18896.html
>>> 
>>> which was not solved.
>>> I would greatly appreciate your suggestion/feedback regarding this
>>> problem.
>>> You could also guide me to the right subroutines if you

Re: [Wien] Segmentation fault in w2w

2020-09-12 Thread Laurence Marks

Is this compiled with -g ? If not, please add -f, recompile and then
repeat. (The reason is that optimizations can lead to segmentation faults
appearing at an inappropriate location in the code.) If with -g it is still
the same, please add before line 449 of  modules_rc.F a write command, i.e.
so it has:

  Nb = inwf%bmax-inwf%bmin+1
  write(*,*) Nb, inwf%Nproj, num_kpts
  projection = 0

I suspect that num_kpts is wrong, so the dimensions of projection are
incorrect. However, segmentation errors can be hard to locate.

On Sat, Sep 12, 2020 at 10:20 AM Niraj Aryal 
wrote:

> Thank you all for your suggestions.
> I tried your suggestions but so far, the problem remains.
>
> As per Prof. Rubel's request, I will share with you my struct file
> privately along with the steps. Please watch out for my email (
> aryalnir...@gmail.com).
> To simplify, I was able to reproduce the problem for paramagnetic case
> without spin orbit case.
>
> Prof. Marks, I have -traceback option in my compilation.
> These are the line numbers where the seg fault occurs:
>
> w2w00432427  l2amn_m_mp_l2amn_ 449
>  modules_rc.F
> w2w0042D68E  MAIN__245  main.f
>
> This made me believe that the problem is in modules_rc.F file in the amn
> routine.
>
> Thank you for the patch link Gavin.
> I applied modules_rc.patch but the problem persists.
>
> I will continue trying to solve this problem. I will keep you updated if
> something new comes up.
> I look forward to your suggestions and feedback.
>
> Sincerely,
> Niraj Aryal
>
> On Fri, Sep 11, 2020 at 8:08 PM Gavin Abo  wrote:
>
>> Not sure if it is related, but are you using the w2w fix that Jindrich
>> previously posted for WIEN2k 19.2 [
>> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19849.html
>> 
>> ] .  Or modules_rc.patch and modules_rc_wplot.patch related to w2web if you
>> prefer to try them are at:
>>
>> https://github.com/gsabo/WIEN2k-Patches/tree/master/19.2
>> 
>> On 9/11/2020 12:02 PM, Niraj Aryal wrote:
>>
>> Dear w2w experts and developers,
>>
>> I am using Wien2k version 19.2 in scientific linux 7.5 using intel
>> compilers (2018).
>>
>> I am trying to wannierize f-electron system with antiferromagnetic
>> magnetic ordering using w2w version 2.0 in the presence of SOC.
>>
>> After self-consistent calculations, these are the steps I am following
>> for the wannierisation:
>>
>> init_w2w (to write case.klist, case.inwf, case.win etc)
>>
>>  x lapw1 -up -p
>>  x lapw1 -dn -p
>>  x lapwso -up -orb -p
>>
>> x w2w -so -up -p  --> segmentation fault here
>> x w2w -so -dn -p  --> segmentation fault here
>> ..
>>
>> Everything works perfectly if I use small kmesh (about 100 kpoints) for
>> the wannierisation.
>> I have about 50 bands to wannierize.
>> When I increase the number of kpoints, w2w crashes giving segmentation
>> fault.
>>
>> I found that w2w can write case.mmn and case.eig with no problems but the
>> seg fault occurred while writing case.amn.
>> I confirmed the following hoping that it could help in the debugging
>> process:
>>
>> 1) If I decrease the number of bands to wannierize, the number of kpoints
>> in the wannierisation can be slightly increased without seg fault.
>> 2)The problem persists without -so and -p (i.e. without parallel
>> calculation) flag.
>>
>> In my opinion, there are some hard coded array size value(s) in the w2w
>> program in amn/mmn subroutines which give segmentation fault when the
>> number of projections*bands*kpoints exceeds that value.
>> This was confirmed by doing calculations in a simpler system like silicon
>> with a large number of kpoints and bands.
>>
>> I tried looking into the w2w source files and found few hard coded values.
>> However, I am hesitant to make changes because I am worried this could
>> ruin other things.
>>
>> This problem is similar to the one posted last year:
>> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18896.html
>> 
>> which was not solved.
>> I would greatly appreciate your suggestion/feedback regarding this
>> problem.
>> You could also guide me to the right subroutines if you know the details
>> of the code.
>>
>> Thank you.
>>
>> Sincerely,
>> Niraj Aryal
>> Research Associate
>> Brookhaven National Lab.
>> Upton, NY
>>
>> ___
>> Wien mailing list
>>

Re: [Wien] Segmentation fault in w2w

2020-09-12 Thread Niraj Aryal

Thank you all for your suggestions.
I tried your suggestions but so far, the problem remains.

As per Prof. Rubel's request, I will share with you my struct file
privately along with the steps. Please watch out for my email (
aryalnir...@gmail.com).
To simplify, I was able to reproduce the problem for paramagnetic case
without spin orbit case.

Prof. Marks, I have -traceback option in my compilation.
These are the line numbers where the seg fault occurs:

w2w00432427  l2amn_m_mp_l2amn_ 449
 modules_rc.F
w2w0042D68E  MAIN__245  main.f

This made me believe that the problem is in modules_rc.F file in the amn
routine.

Thank you for the patch link Gavin.
I applied modules_rc.patch but the problem persists.

I will continue trying to solve this problem. I will keep you updated if
something new comes up.
I look forward to your suggestions and feedback.

Sincerely,
Niraj Aryal

On Fri, Sep 11, 2020 at 8:08 PM Gavin Abo  wrote:

> Not sure if it is related, but are you using the w2w fix that Jindrich
> previously posted for WIEN2k 19.2 [
> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19849.html
> ] .  Or modules_rc.patch and modules_rc_wplot.patch related to w2web if you
> prefer to try them are at:
>
> https://github.com/gsabo/WIEN2k-Patches/tree/master/19.2
> On 9/11/2020 12:02 PM, Niraj Aryal wrote:
>
> Dear w2w experts and developers,
>
> I am using Wien2k version 19.2 in scientific linux 7.5 using intel
> compilers (2018).
>
> I am trying to wannierize f-electron system with antiferromagnetic
> magnetic ordering using w2w version 2.0 in the presence of SOC.
>
> After self-consistent calculations, these are the steps I am following for
> the wannierisation:
>
> init_w2w (to write case.klist, case.inwf, case.win etc)
>
>  x lapw1 -up -p
>  x lapw1 -dn -p
>  x lapwso -up -orb -p
>
> x w2w -so -up -p  --> segmentation fault here
> x w2w -so -dn -p  --> segmentation fault here
> ..
>
> Everything works perfectly if I use small kmesh (about 100 kpoints) for
> the wannierisation.
> I have about 50 bands to wannierize.
> When I increase the number of kpoints, w2w crashes giving segmentation
> fault.
>
> I found that w2w can write case.mmn and case.eig with no problems but the
> seg fault occurred while writing case.amn.
> I confirmed the following hoping that it could help in the debugging
> process:
>
> 1) If I decrease the number of bands to wannierize, the number of kpoints
> in the wannierisation can be slightly increased without seg fault.
> 2)The problem persists without -so and -p (i.e. without parallel
> calculation) flag.
>
> In my opinion, there are some hard coded array size value(s) in the w2w
> program in amn/mmn subroutines which give segmentation fault when the
> number of projections*bands*kpoints exceeds that value.
> This was confirmed by doing calculations in a simpler system like silicon
> with a large number of kpoints and bands.
>
> I tried looking into the w2w source files and found few hard coded values.
> However, I am hesitant to make changes because I am worried this could
> ruin other things.
>
> This problem is similar to the one posted last year:
> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18896.html
> which was not solved.
> I would greatly appreciate your suggestion/feedback regarding this
> problem.
> You could also guide me to the right subroutines if you know the details
> of the code.
>
> Thank you.
>
> Sincerely,
> Niraj Aryal
> Research Associate
> Brookhaven National Lab.
> Upton, NY
>
> ___
> 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
>
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Re: [Wien] ssh command in Wien2k scripts

2020-09-12 Thread Peter Blaha


Please read the ssh/sshd documentation.

You can put into your local .ssh directory a file config and I believe 
you can specify there that you want to transfer the environment.


As far as I know, this should overwrite the default ssh options in 
/etc/ssh/ssh_config and ssh_configd specifications.



Am 12.09.2020 um 10:34 schrieb Ilias Miroslav, doc. RNDr., PhD.:

Hello,

I have similar problem as decribed here 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19049.html .


ssh vsli2 'echo $WIENROOT'


The ssh connection does not preserve the WIENROOT envirovariable.

IT admin does not want the variable ""PermitUserEnvironment"  in 
.sshd_config to be set .


Therefore, I have to change Wien2k scripts to incorporate enviromental 
variable passing.


Any hints, howtos ?

Miro



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


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Re: [Wien] ssh command in Wien2k scripts

2020-09-12 Thread Laurence Marks

Unfortunately IT admins sometimes decide to violate standards, and this can
break Wien2k (as well as many other codes). What you are going to have to
do is duplicate setting up the environment. This is perhaps what they don't
want done, so you might run into trouble with the admins. Suggestions:

a) Try the -F option in ssh; you never know.
b) Use something else, e.g. rsh instead of ssh. You would change this for
the parallel scripts using siteconfig. With Intel impi you can change the
launcher using --bootstrap-exec
c) For mpi you might want to use openmpi, as this has flags which may allow
you to set WIENROOT.
d) The unsupported SRC_mpirun contains pbsh, which is just:
 mpirun -x LD_LIBRARY_PATH -x PATH -np 1 --host $1 /bin/csh -c " $2 "
 If you use openmpi, this can replace ssh at least for non-mpi launching.
(Yes, it is nuts to use mpirun to replace ssh, but then your IT people are
a bit ...)

Of course the right solution is for your IT people to not violate
standards, but they will probably not listen to you.

_
Professor Laurence Marks
"Research is to see what everybody else has seen, and to think what nobody
else has thought", Albert Szent-Gyorgi
www.numis.northwestern.edu

On Sat, Sep 12, 2020, 03:35 Ilias Miroslav, doc. RNDr., PhD. <
miroslav.il...@umb.sk> wrote:

> Hello,
>
> I have similar problem as decribed here
> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19049.html
> 
>  .
>
> ssh vsli2 'echo $WIENROOT'
>
>
> The ssh connection does not preserve the WIENROOT envirovariable.
>
> IT admin does not want the variable ""PermitUserEnvironment"  in
> .sshd_config to be set .
>
> Therefore, I have to change Wien2k scripts to incorporate enviromental
> variable passing.
>
> Any hints, howtos ?
>
> Miro
>
>
> ___
> Wien mailing list
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>
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[Wien] ssh command in Wien2k scripts

2020-09-12 Thread Ilias Miroslav, doc. RNDr., PhD.

Hello,

I have similar problem as decribed here 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19049.html .


ssh vsli2 'echo $WIENROOT'

The ssh connection does not preserve the WIENROOT envirovariable.

IT admin does not want the variable ""PermitUserEnvironment"  in .sshd_config 
to be set .

Therefore, I have to change Wien2k scripts to incorporate enviromental variable 
passing.

Any hints, howtos ?

Miro


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Re: [Wien] hyperfine field anisotropic of Li in battery materials

2020-09-12 Thread 林敏

Dear Prof. Peter Blaha, I quite sure that the orbital isotropic and anisotropic are not important in my cases, which locate in very narrow range for Li,  several or dozen ppm. The hyperfine isotropic and anisotropic leads to paramagnetic shift that locate in very broad range, even reach thousands of ppm. We are probably not talking the same topic, the gap of “paramagnetic shift” between metal and transition metal oxide. Best, Min———Min Lin2018 Ph. D studentPhysical Chemistry Chemistry Department Chemistry & College of Chemistry and Chemical EngineeringXiamen UniversityChinae-mail: lin...@stu.xmu.edu.cn
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Re: [Wien] hyperfine field anisotropic of Li in battery materials

2020-09-12 Thread 林敏

Dear Prof. Peter Blaha, 

I quite sure that the orbital isotropic and anisotropic are not important in my 
cases, which locate in very narrow range for Li,  several or dozen ppm. 

The hyperfine isotropic and anisotropic leads to paramagnetic shift that locate 
in very broad range, even reach thousands of ppm. 

We are probably not talking the same topic, the gap of “paramagnetic shift” 
between metal and transition metal oxide. 

Best, 

Min

———
Min Lin
2018 Ph. D student
Physical Chemistry 
Chemistry Department Chemistry & College of Chemistry and Chemical Engineering
Xiamen University
China
e-mail: lin...@stu.xmu.edu.cn___
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[Wien] ssh command in Wien2k scripts

Re: [Wien] hyperfine field anisotropic of Li in battery materials

Re: [Wien] hyperfine field anisotropic of Li in battery materials

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