Re: [Wien] problem when running berrypi

[halim said]

Dear Professor   Gavin,
Thank you for your suggestion, but for my case I am working with wien2k14, also 
you said that I need to use wien2wannier, should I compiled and use it with 
BerryPi?
I appreciate for your answer.

Regards,
Halim 

Le Vendredi 8 septembre 2017 11h45, Gavin Abo  a 
écrit :
 

  I cannot recall if BerryPI works with Python 2.6.  You can try it, but maybe 
it doesn't work as section "8.2 BerryPI (Modern theory of polarization)" in the 
WIEN2k 17.1 usersguide on page 149 has: "It consists of a set of Python scripts 
(requires Python 2.7 and the NumPi library) and uses wien2wannier for the 
calculation of overlap integrals."
  The current error, however, doesn't look like it is caused by Python 2.6.
 
 In your config.py, there is:
 
 #fix for location of python file locations when executing from the python 
commandline
 DEFAULT_BIN_PATH=/home/ha/SRC_BerryPI/BerryPI
 
 #Fix for python path to make sure it grabs the latest version
 DEFAULT_PYTHON_PATH=/usr/bin/python
 
 As Oleg mentioned, the current error will most likely be resolved if you edit 
it and add single quotes to those lines:
 
 #fix for location of python file locations when executing from the python 
commandline
 DEFAULT_BIN_PATH='/home/ha/SRC_BerryPI/BerryPI'
 
 #Fix for python path to make sure it grabs the latest version
 DEFAULT_PYTHON_PATH='/usr/bin/python'
 
 On 9/7/2017 8:40 PM, halim said wrote:
  
  Dear Prof Oleg, 
  
  Thank you for your suggestion, I don't work on personal computer and 
Python2.6 version is installed. Is it ok? please find config.py as attached 
file. 
  Your suggestion is very much appreciated. 
  Looking forward for your answer. 
  All my best, 
  Halim  
 
  Le Jeudi 7 septembre 2017 21h49, "Rubel, Oleg"  a 
écrit :
  
 
  Ok. Can you reply with config.py file attached?
 
 I remember python being picky about single quote signs for the text variable 
enclosures.
 
 ...
 #fix for location of python file locations when executing from the python 
commandline
 DEFAULT_BIN_PATH='/home/rubel/BerryPI'
 
 #Fix for python path to make sure it grabs the latest version
DEFAULT_PYTHON_PATH='/software/CentOS-6/tools/python-2.7.3/bin/python’
 …
 
 Also check
 [rubel@lg-1r14-n04 GaN-W]$ which berrypi
 
 Here is what I have:
 alias berrypi='/software/CentOS-6/tools/python-2.7.3/bin/python 
/home/rubel/BerryPI/berrypi'
     /software/CentOS-6/tools/python-2.7.3/bin/python
 
 Thanks
 Oleg
 
 > On Sep 7, 2017, at 14:28, halim said  wrote:
 > 
 > Dear Prof Oleg,
 > 
 > Thank you for your answer. I changed the path in config.py and set it  as in 
 > the mentioned folder, also the folder home/ha/SRC_BerryPI/BerryPI
 > exists.
 > 
 > The same error occurs after changing the path, please what to do to solve 
 > the problem?
 > 
 > I appreciate your help.
 > 
 > Halim
 > 
 > 
 > Le Jeudi 7 septembre 2017 19h23, "Rubel, Oleg"  a écrit :
 > 
 > 
 > Please check that the folder /home/ha/SRC_BerryPI/BerryPI
 > really exists. Your error message suggests that it can be 
 > /home/ha/WIEN2k/SRC_BerryPI/BerryPI
 > In this case you should edit DEFAULT_BIN_PATH in config.py
 > 
 > I hope it will fix your problem
 > Oleg
 > 
 > > On Sep 7, 2017, at 12:11, halim said  wrote:
 > > 
 > > Dear Wien2k  users community,
 > > 
 > > I am facing problem when running berrypi, i followed the example of GaN, 
 > > but i am getting this error. How to solve it.
 > > 
 > > gan> berrypi -k6:6:6
 > > Traceback (most recent call last):
 > >  File "/home/ha/WIEN2k/SRC_BerryPI/BerryPI/berrypi", line 25, in 
 > >    import submoduleProcess as b_PySubProcess
 > >  File "/home/ha/WIEN2k/SRC_BerryPI/BerryPI/submoduleProcess.py", line 11, 
 > >in 
 > >    from config import BERRY_DEFAULT_CONSOLE_PREFIX as DEFAULT_PREFIX
 > >  File "/home/ha/WIEN2k/SRC_BerryPI/BerryPI/config.py", line 14
 > >    DEFAULT_BIN_PATH=/home/ha/SRC_BerryPI/BerryPI
 > >                      ^
 > > SyntaxError: invalid syntax
 > > 
 > > 
 > > 
 > > I would be thankful for your suggestion and answer to solve the problem.
 > > 
 > > Looking forward your answer.
 > > 
 > > Halim Said
 > 
 > > 
 > > 
 > > 
 > > 
 > > 
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[Wien] (no subject)

[Abderrahmane Reggad]

Hi

Before doing the calculation again with the new energy and charge criterion
I let you this old article  http://journals.jps.jp/doi/abs/10.1143/JPSJ.14.196

Best regards
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Re: [Wien] Error in WIENNCM running in parallel mode

[Jianpeng Liu]

Dear Gavin,

Thank you for the helpful link! I think that's the bug!

Indeed I have fixed a bug of wienncm by modifying the lines related to
block size in zhcgst.f (SRC_lapw1), but here is one more...

It seems to me WIENncm is really out-of-dated, and there are quite a few
bugs to be fixed. I am using it because I thought it allows one to couple
external magnetic field to orbital magnetic moments by adding orbital
potentials, so I want to make sure here: Is it true that WIENncm allows the
coupling between external magnetic field and the *orbital* magnetic moment?
And one more question, for body-centered tetragonal system, is it possible
to plot Fermi-surface? Since WIENncm is too old, I can not assume that it
has  the features of the latest WIEN2k. If it doesn't do these things, then
I will switch to some other codes.

Thanks again for the help.

Jianpeng


On Thu, Sep 7, 2017 at 11:00 PM, Jianpeng Liu  wrote:

> Dear Gavin,
>
> Thank you for your prompt replay. I have checked that energy_1 has been
> properly generated. The lapw2.error says:
>  'FERMI' - number of k-points inconsistent when reading kgen
>  'FERMI' - check IN1 and KGEN files!
>
> I have generated the k mesh using initncm, and set the total number of k
> points in BZ as 216 (the system is body-centered tetragonal, and there is
> no symmetry of the magnetic state, so there is also 216 k points in the
> irreducible BZ). I set up the .machines file to divide the 216 points to 12
> processors, 18 k points for each processor. Then there is the problem:
> there are 18 k points in case.klist_1 ... case.klist_11, but in
> case.klist_12, there are only 16 k points, i.e., 2 kpoints are just
> missing. This is probably why the system complains with the k point error?
>
> Later I tried to change the method of determining the Fermi level from the
> linear-tetrahedra method to Gaussian smearing, with eval=0.0005Ry, then
> everything works. Still, two k points are missing in case.klist_12, but now
> the calculation runs well with 12 processors. Can I ask why the linear
> tetrahedra method fails, and why the two k points are missing?
>
> Best,
> Jianpeng
>
>
>
> On Thu, Sep 7, 2017 at 9:17 PM, Gavin Abo  wrote:
>
>> You might try checking the lapw2.error file. Does it show a problem with
>> the case.energy_1 file like in the post at:
>>
>> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at
>> /msg07963.html
>>
>> If you have that same error, it might be that lapw1 failed in generating
>> the case.energy_1.  There are other files you may need to look for error
>> messages in as mentioned before in the mailing list archive [
>> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at
>> /msg15549.html ].
>>
>>
>> On 9/7/2017 5:32 PM, Jianpeng Liu wrote:
>>
>> Dear Wien2k/Wienncm users and developers,
>>
>> I am learning to use wienncm to run some noncollinear-magnetism
>> calculations. I have compiled the code without any error report, and the
>> code runs well in serial mode. But if I run the same calculation in
>> parallel mode,  the calculation is always aborted at the lapw2 step, and  I
>> got the following error:
>>
>> FERMI - Error
>> cp: cannot stat `.in.tmp': No such file or directory
>> rm: cannot remove `.in.tmp': No such file or directory
>> rm: cannot remove `.in.tmp1': No such file or directory
>>
>> The following is the .machine file:
>>
>> granularity:1
>> 1:node91
>> 1:node91
>> 1:node91
>> 1:node91
>> 1:node91
>> 1:node91
>> 1:node91
>> 1:node91
>> 1:node91
>> 1:node91
>> 1:node91
>> 1:node91
>>
>> I would appreciate your help.
>>
>> Best,
>> Jianpeng
>>
>>
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>> e...@zeus.theochem.tuwien.ac.at/index.html
>>
>>
>
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Re: [Wien] Regarding to generate CH3NH3PbI3 cubic struct file for space group Pm-3m (221)

[John McLeod]

To add to what Gavin said, I previously used WIEN2k to calculate 
(pseudo-)cubic CH3NH3PbI3. This structure had some geometry optimization 
(hence it is not a perfect cube anymore) and internal positions were 
optimized with the MSR1a method.



If you want to use that structure, the atomic coordinates of all atoms 
(including H) and RMT used can be found in the supporting information 
for Nano Letters 16 4720 (2016), see: 
http://pubs.acs.org/doi/abs/10.1021/acs.nanolett.6b02307.



Regards,

John


On 2017-09-08 08:05 PM, Gavin Abo wrote:


A brief view in XCrySDen of


Spacegroup: 221_Pm-3m

a = b = c = 6.3391

alpha = beta = gamma = 90

Pb (0, 0, 0)

I (0, 0.072, 0.5)

C (0.426, 0.426, 0.5) or (0.574, 0.574, 0.5)

N (0.627, 0.627, 0.5)


from the article titled "CH_3 NH_3 PbI_3 , A Potential Solar Cell 
Candidate: Structural and Spectroscopic Investigations" [ 
http://pubs.acs.org/doi/abs/10.1021/acs.jpca.6b09718 ] shows 
overlapping atoms indicating that this structure may have a partial 
occupancy.


WIEN2k does not accept case.struct files having a partial occupancy.  
Reference the links in the post at:


https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg13806.html

On 9/8/2017 3:44 AM, AJAY SINGH VERMA wrote:

Dear Sir,
thanks for your guidance about the cif files.
but i am trying to generate a struct file for CH3NH3PbI3 cubic with 
space group Pm-3m (221).

I am facing the problem in the position OR coordinates of C & H
Kindly help me.
thanks





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Re: [Wien] Regarding to generate CH3NH3PbI3 cubic struct file for space group Pm-3m (221)

[Gavin Abo]

A brief view in XCrySDen of


Spacegroup: 221_Pm-3m

a = b = c = 6.3391

alpha = beta = gamma = 90

Pb (0, 0, 0)

I (0, 0.072, 0.5)

C (0.426, 0.426, 0.5) or (0.574, 0.574, 0.5)

N (0.627, 0.627, 0.5)


from the article titled "CH_3 NH_3 PbI_3 , A Potential Solar Cell 
Candidate: Structural and Spectroscopic Investigations" [ 
http://pubs.acs.org/doi/abs/10.1021/acs.jpca.6b09718 ] shows overlapping 
atoms indicating that this structure may have a partial occupancy.


WIEN2k does not accept case.struct files having a partial occupancy.  
Reference the links in the post at:


https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg13806.html

On 9/8/2017 3:44 AM, AJAY SINGH VERMA wrote:

Dear Sir,
thanks for your guidance about the cif files.
but i am trying to generate a struct file for CH3NH3PbI3 cubic with 
space group Pm-3m (221).

I am facing the problem in the position OR coordinates of C & H
Kindly help me.
thanks



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Re: [Wien] PBS run

[Gavin Abo]

You might have a look at the "WIEN2k-notes of the University of Texas" 
document (slide 7) at:


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

The line:

echo -n 'lapw0:' > .machines

It looks like that writes to the .machines file:

lapw0:

However, you need to have it write the "machine names" after it. So 
something like:


lapw0:gamma:2 delta:2 epsilon:4

However, you are having it write:

lapw0:granularity:1

Thus, the error about it not being able to find and connect to a 
hostname called "granularity".


On 9/8/2017 2:41 AM, Subrata Jana wrote:

Hi Gavin Abo,
It looks I am facing the same problem.

##

#!/bin/bash
#PBS -N wien2k
#PBS -o out.log
#PBS -j oe
#PBS -l nodes=1:ppn=1

# Load Intel environment
source 
/apps/intel_2016_u2/compilers_and_libraries_2016.2.181/linux/bin/compilervars.sh 
intel64

export OMP_NUM_THREADS=1
cd /home/sjana/WIEN2k/PBE/C_pbe
rm -f .machines

#source 
/apps/intel_2016_u2/compilers_and_libraries_2016.2.181/linux/bin/compilervars.sh 
intel64


cd /home/sjana/WIEN2k/PBE/C_pbe
rm -f .machines
echo '#' > .machines
echo -n 'lapw0:' > .machines
echo 'granularity:1' >>.machines
#awk '{print "1:"$1":1"}' $PBS_NODEFILE >>.machines
awk '{print "1:"$1":1"}' "$PBS_NODEFILE" >>.machines
echo 'extrafine:1' >>.machines
#/home/sjana/WIEN2k_14.2/run_lapw -p -i 40 -ec .0001 -I
run_lapw -p -i 40 -ec .0001 -I
#

My .machines file looks like


lapw0:granularity:1
1:r8n3:1
extrafine:1


out.log

ssh: Could not resolve hostname granularity: Name or service not known^M

>   stop error

Regards,
S. Jana
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Re: [Wien] problem when running berrypi

[Gavin Abo]

I cannot recall if BerryPI works with Python 2.6.  You can try it, but 
maybe it doesn't work as section "8.2 BerryPI (Modern theory of 
polarization)" in the WIEN2k 17.1 usersguide on page 149 has:


"It consists of a set of Python scripts (*requires* *Python 2.7* and the 
NumPi library) and uses wien2wannier for the calculation of overlap 
integrals."


The current error, however, doesn't look like it is caused by Python 2.6.

In your config.py, there is:

#fix for location of python file locations when executing from the 
python commandline

DEFAULT_BIN_PATH=/home/ha/SRC_BerryPI/BerryPI

#Fix for python path to make sure it grabs the latest version
DEFAULT_PYTHON_PATH=/usr/bin/python

As Oleg mentioned, the current error will most likely be resolved if you 
edit it and add single quotes to those lines:


#fix for location of python file locations when executing from the 
python commandline

DEFAULT_BIN_PATH='/home/ha/SRC_BerryPI/BerryPI'

#Fix for python path to make sure it grabs the latest version
DEFAULT_PYTHON_PATH='/usr/bin/python'

On 9/7/2017 8:40 PM, halim said wrote:

Dear Prof Oleg,


Thank you for your suggestion, I don't work on personal computer and 
Python2.6 version is installed.

Is it ok? please find config.py as attached file.

Your suggestion is very much appreciated.

Looking forward for your answer.

All my best,

Halim


Le Jeudi 7 septembre 2017 21h49, "Rubel, Oleg"  a 
écrit :



Ok. Can you reply with config.py file attached?

I remember python being picky about single quote signs for the text 
variable enclosures.


...
#fix for location of python file locations when executing from the 
python commandline

DEFAULT_BIN_PATH='/home/rubel/BerryPI'

#Fix for python path to make sure it grabs the latest version
DEFAULT_PYTHON_PATH='/software/CentOS-6/tools/python-2.7.3/bin/python’
…

Also check
[rubel@lg-1r14-n04  GaN-W]$ which berrypi

Here is what I have:
alias berrypi='/software/CentOS-6/tools/python-2.7.3/bin/python 
/home/rubel/BerryPI/berrypi'

    /software/CentOS-6/tools/python-2.7.3/bin/python

Thanks
Oleg

> On Sep 7, 2017, at 14:28, halim said > wrote:

>
> Dear Prof Oleg,
>
> Thank you for your answer. I changed the path in config.py and set 
it  as in the mentioned folder, also the folder 
home/ha/SRC_BerryPI/BerryPI

> exists.
>
> The same error occurs after changing the path, please what to do to 
solve the problem?

>
> I appreciate your help.
>
> Halim
>
>
> Le Jeudi 7 septembre 2017 19h23, "Rubel, Oleg" > a écrit :

>
>
> Please check that the folder /home/ha/SRC_BerryPI/BerryPI
> really exists. Your error message suggests that it can be 
/home/ha/WIEN2k/SRC_BerryPI/BerryPI

> In this case you should edit DEFAULT_BIN_PATH in config.py
>
> I hope it will fix your problem
> Oleg
>
> > On Sep 7, 2017, at 12:11, halim said > wrote:

> >
> > Dear Wien2k  users community,
> >
> > I am facing problem when running berrypi, i followed the example 
of GaN, but i am getting this error. How to solve it.

> >
> > gan> berrypi -k6:6:6
> > Traceback (most recent call last):
> >  File "/home/ha/WIEN2k/SRC_BerryPI/BerryPI/berrypi", line 25, in 


> >    import submoduleProcess as b_PySubProcess
> >  File "/home/ha/WIEN2k/SRC_BerryPI/BerryPI/submoduleProcess.py", 
line 11, in 

> >    from config import BERRY_DEFAULT_CONSOLE_PREFIX as DEFAULT_PREFIX
> >  File "/home/ha/WIEN2k/SRC_BerryPI/BerryPI/config.py", line 14
> > DEFAULT_BIN_PATH=/home/ha/SRC_BerryPI/BerryPI
> >                      ^
> > SyntaxError: invalid syntax
> >
> >
> >
> > I would be thankful for your suggestion and answer to solve the 
problem.

> >
> > Looking forward your answer.
> >
> > Halim Said
>
> >
> >
> >
> >
> >
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[Wien] PBS run

[Subrata Jana]

Hi Gavin Abo,
It looks I am facing the same problem.

##

#!/bin/bash
#PBS -N wien2k
#PBS -o out.log
#PBS -j oe
#PBS -l nodes=1:ppn=1

# Load Intel environment
source
/apps/intel_2016_u2/compilers_and_libraries_2016.2.181/linux/bin/compilervars.sh
intel64
export OMP_NUM_THREADS=1
cd /home/sjana/WIEN2k/PBE/C_pbe
rm -f .machines

#source
/apps/intel_2016_u2/compilers_and_libraries_2016.2.181/linux/bin/compilervars.sh
intel64

cd /home/sjana/WIEN2k/PBE/C_pbe
rm -f .machines
echo '#' > .machines
echo -n 'lapw0:' > .machines
echo 'granularity:1' >>.machines
#awk '{print "1:"$1":1"}' $PBS_NODEFILE >>.machines
awk '{print "1:"$1":1"}' "$PBS_NODEFILE" >>.machines
echo 'extrafine:1' >>.machines
#/home/sjana/WIEN2k_14.2/run_lapw -p -i 40 -ec .0001 -I
run_lapw -p -i 40 -ec .0001 -I
#

My .machines file looks like


lapw0:granularity:1
1:r8n3:1
extrafine:1


out.log

ssh: Could not resolve hostname granularity: Name or service not known^M

>   stop error

Regards,
S. Jana
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Re: [Wien] PBS run

[Gavin Abo]

It look like something is wrong with this line [ 
https://stackoverflow.com/questions/26816605/awk-fatal-cannot-open-file-for-reading-no-such-file-or-directory 
]:


awk '{print "1:"$1":1"}' $PBS_NODEFILE >>.machines

Maybe quotes are needed around the $PBS_NODEFILE:

awk '{print "1:"$1":1"}' "$PBS_NODEFILE" >>.machines

On 9/8/2017 2:20 AM, Subrata Jana wrote:

Hi Gavin Abo,
I change my job script as follows:

#
#!/bin/bash
#PBS -N wien2k
#PBS -o out.log
#PBS -j oe
#PBS -l nodes=1:ppn=1

# Load Intel environment
source 
/apps/intel_2016_u2/compilers_and_libraries_2016.2.181/linux/bin/compilervars.sh 
intel64


cd /home/sjana/WIEN2k/PBE/C_pbe
rm -f .machines
echo '#' > .machines
*echo -n 'lapw0:' > .machines*
echo 'granularity:1' >>.machines
awk '{print "1:"$1":1"}' $PBS_NODEFILE >>.machines
echo 'extrafine:1' >>.machines
/home/sjana/WIEN2k_14.2/run_lapw -p -i 40 -ec .0001 -I
###

Now the out.log

awk: cmd. line:1: fatal: cannot open file `-np' for reading (No such 
file or directory)

ssh: Could not resolve hostname granularity: Name or service not known^M

>   stop error

Regards,
S. Jana







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[Wien] PBS run

[Subrata Jana]

Hi Gavin Abo,
I change my job script as follows:

#
#!/bin/bash
#PBS -N wien2k
#PBS -o out.log
#PBS -j oe
#PBS -l nodes=1:ppn=1

# Load Intel environment
source 
/apps/intel_2016_u2/compilers_and_libraries_2016.2.181/linux/bin/compilervars.sh
intel64

cd /home/sjana/WIEN2k/PBE/C_pbe
rm -f .machines
echo '#' > .machines
*echo -n 'lapw0:' > .machines*
echo 'granularity:1' >>.machines
awk '{print "1:"$1":1"}' $PBS_NODEFILE >>.machines
echo 'extrafine:1' >>.machines
/home/sjana/WIEN2k_14.2/run_lapw -p -i 40 -ec .0001 -I
###

Now the out.log

awk: cmd. line:1: fatal: cannot open file `-np' for reading (No such file
or directory)
ssh: Could not resolve hostname granularity: Name or service not known^M

>   stop error

Regards,
S. Jana
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Re: [Wien] PBS run

[Gavin Abo]

Does lapw0 exist in your WIEN2k directory (/home/sjana/WIEN2k_14.2)?

Maybe #PBS -V is needed [ 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg15985.html 
].


On 9/8/2017 1:42 AM, Subrata Jana wrote:

Dear All,
 I am trying to run WIEN2k parallel. My shell script is looking like 
this. However, in the out.log file it is showing

--
lapw0: Command not found.

>   stop error
---

please help.

### script ##

#!/bin/bash
#PBS -N wien2k
#PBS -o out.log
#PBS -j oe
#PBS -l nodes=1:ppn=1

# Load Intel environment
source 
/apps/intel_2016_u2/compilers_and_libraries_2016.2.181/linux/bin/compilervars.sh 
intel64


cd /home/sjana/WIEN2k/PBE/C_pbe
rm -f .machines
echo '#' > .machines
echo 'granularity:1' >>.machines
awk '{print "1:"$1":1"}' $PBS_NODEFILE >>.machines
echo 'extrafine:1' >>.machines
/home/sjana/WIEN2k_14.2/run_lapw -p -i 40 -ec .0001 -I

Regards,
S. Jana

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Re: [Wien] Error in WIENNCM running in parallel mode

[Gavin Abo]

Sorry, I currently don't know the answer to your question.  Maybe 
someone else does.


I don't know what version of WIEN2k that the WIENncm was branched and 
then modified from or what the last WIEN2k version it was kept up to 
date with.


The WIENncm page [ http://susi.theochem.tuwien.ac.at/reg_user/ncm/ ] 
shows the publication to cite being in 2004.  So it could be using code 
as old or older then the latest WIEN2k version that existed in 2004. 
Though, the WIENNCM/DOC/ncmdoc.pdf file is dated 2006.  So it may 
contain WIEN2k code as new as 2006.


Therefore, the WIENncm code might suffer from the same WIEN2k bugs found 
since 2006:


http://susi.theochem.tuwien.ac.at/reg_user/updates/

Perhaps the problem is caused by a possible bug in the lapw1cpara script 
similar to what was reported for the lapw1para script in the 2009 post at:


https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg01365.html

Maybe you could try the proposed fix to see if it resolves the problem 
or not, which I think was given in the post at:


https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg01385.html

You could also give the lapw1cpara script from WIEN2k 17.1 a try, but it 
might be that it has new changes making it not compatible with WIENncm.


On 9/8/2017 12:00 AM, Jianpeng Liu wrote:

Dear Gavin,

Thank you for your prompt replay. I have checked that energy_1 has 
been properly generated. The lapw2.error says:

 'FERMI' - number of k-points inconsistent when reading kgen
 'FERMI' - check IN1 and KGEN files!

I have generated the k mesh using initncm, and set the total number of 
k points in BZ as 216 (the system is body-centered tetragonal, and 
there is no symmetry of the magnetic state, so there is also 216 k 
points in the irreducible BZ). I set up the .machines file to divide 
the 216 points to 12 processors, 18 k points for each processor. Then 
there is the problem: there are 18 k points in case.klist_1 ... 
case.klist_11, but in case.klist_12, there are only 16 k points, i.e., 
2 kpoints are just missing. This is probably why the system complains 
with the k point error?


Later I tried to change the method of determining the Fermi level from 
the linear-tetrahedra method to Gaussian smearing, with eval=0.0005Ry, 
then everything works. Still, two k points are missing in 
case.klist_12, but now the calculation runs well with 12 processors. 
Can I ask why the linear tetrahedra method fails, and why the two k 
points are missing?


Best,
Jianpeng



On Thu, Sep 7, 2017 at 9:17 PM, Gavin Abo > wrote:


You might try checking the lapw2.error file. Does it show a
problem with the case.energy_1 file like in the post at:

https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg07963.html


If you have that same error, it might be that lapw1 failed in
generating the case.energy_1.  There are other files you may need
to look for error messages in as mentioned before in the mailing
list archive [
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg15549.html

].


On 9/7/2017 5:32 PM, Jianpeng Liu wrote:

Dear Wien2k/Wienncm users and developers,

I am learning to use wienncm to run some noncollinear-magnetism
calculations. I have compiled the code without any error report,
and the code runs well in serial mode. But if I run the same
calculation in parallel mode, the calculation is always aborted
at the lapw2 step, and  I got the following error:

FERMI - Error
cp: cannot stat `.in.tmp': No such file or directory
rm: cannot remove `.in.tmp': No such file or directory
rm: cannot remove `.in.tmp1': No such file or directory

The following is the .machine file:

granularity:1
1:node91
1:node91
1:node91
1:node91
1:node91
1:node91
1:node91
1:node91
1:node91
1:node91
1:node91
1:node91

I would appreciate your help.

Best,
Jianpeng


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Re: [Wien] About the magnetic moment of vanadium in vanadium sulphide

[Laurence Marks]

I would say that -cc 0.001 -ec 0.001 are certainly too large.

Also, a more subtle point. When you say you use "-eece" what hybrid
fraction? Is that the right fraction? How do you know if it is the right
value to use?

On Sep 8, 2017 9:13 AM, "Fecher, Gerhard"  wrote:

> Now I am a little confused
> do you think that it was the convergence criteria that I found a magnetic
> moment of 2.5 mu_B instead of 0.05 mu_B at the V ?
> or did I make another mistake ;-)
>
> Indeed, you are right, the 0.05 mu_B might be a result of to bad
> convergence
> however, to check if such a moment is something reliable you will need
> brute force with respect to the number of k-points,
> that is, if you think you have enough k-points, then just double the
> number or use ten times more.
>
> 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 Inorganic and Analytical Chemistry
> Johannes Gutenberg - University
> 55099 Mainz
> and
> Max Planck Institute for Chemical Physics of Solids
> 01187 Dresden
> 
> Von: Wien [wien-boun...@zeus.theochem.tuwien.ac.at] im Auftrag von Gavin
> Abo [gs...@crimson.ua.edu]
> Gesendet: Freitag, 8. September 2017 03:14
> An: wien@zeus.theochem.tuwien.ac.at
> Betreff: Re: [Wien] About the magnetic moment of vanadium in vanadium
> sulphide
>
> Perhaps the -ec 0.001 and -cc 0.001 are too large of values.
>
> As I recall, to be well-converged, it is usually best to use about the
> default values seen in the post [1] or WIEN2k 17.1 usersguide [2] as:
>
> -cc 0.0001
> -ec 0.0001
>
> It sounded like about the default value for -ec was good unless something
> like -ec 0.1 was desired to reduce numerical noise, but anything
> smaller seemed useless [3,4].
>
> For -cc, 0.1 also may be the lowest limit [5] and quite ambitious to
> try to use [6].
>
> In section "4.5.4 Antiferromagnetic (AFM) calculations" on page 46 in the
> usersguide [2], there is the statement:
>
> "If nothing changes (E-tot and other properties), then you are ok,
> otherwise make sure the scf calculation is well converged (-cc 0.0001 or
> better)."
>
> If I read from the statement correctly, a well converged scf calculation
> typically uses -cc with a value of 0.0001 or smaller.  Though, there is a
> realistic limit as mentioned above on how small it could be set.
>
> In [7], it sounded important that the -cc value was low for the :MMIn
> values.
>
> So, maybe the calculation can still converge further such that possibly
> the "MMI for V1" and "MMI for V2" will both become zero when they reach
> better convergence.
>
> [1] https://urldefense.proofpoint.com/v2/url?u=https-3A__www.
> mail-2Darchive.com_wien-40zeus.theochem.tuwien.ac.at_
> msg12620.html=DwICAg=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws=U_
> T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0=IqtmMtrsPmzO8Q_
> 7OyBUFU8KovAS1oJ7eHocil7ijPM=f9OQB58xMpbV6Lxpk__
> HpxluI7of8Wtd-3YLf2lPt_8=
> [2] https://urldefense.proofpoint.com/v2/url?u=http-3A__susi.
> theochem.tuwien.ac.at_reg-5Fuser_textbooks_usersguide.pdf=DwICAg=
> yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws=U_
> T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0=IqtmMtrsPmzO8Q_
> 7OyBUFU8KovAS1oJ7eHocil7ijPM=TCMEVNSrK2nolGGe5-
> C05t8ketTafBun308-sPwbSr8=
> [3] https://urldefense.proofpoint.com/v2/url?u=https-3A__www.
> mail-2Darchive.com_wien-40zeus.theochem.tuwien.ac.at_
> msg10650.html=DwICAg=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws=U_
> T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0=IqtmMtrsPmzO8Q_
> 7OyBUFU8KovAS1oJ7eHocil7ijPM=VjvsRncxyQorRh7HOmO2fuwWOIHPpl
> dwZqlw7ILvngo=
> [4] https://urldefense.proofpoint.com/v2/url?u=https-3A__www.
> mail-2Darchive.com_wien-40zeus.theochem.tuwien.ac.at_
> msg16077.html=DwICAg=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws=U_
> T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0=IqtmMtrsPmzO8Q_
> 7OyBUFU8KovAS1oJ7eHocil7ijPM=lH1yPQOSaJ_GztqMkk026Tcc2fwAuxAXbhNQuhM_
> 2DI=
> [5] https://urldefense.proofpoint.com/v2/url?u=http-3A__zeus.
> theochem.tuwien.ac.at_pipermail_wien_2008-2DNovember_011797.html=
> DwICAg=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws=U_
> T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0=IqtmMtrsPmzO8Q_
> 7OyBUFU8KovAS1oJ7eHocil7ijPM=W5RtSfQEcEU0WsmZiU7e3_
> 5MWzhybsiJaRvTF6IyhTQ=
> [6] https://urldefense.proofpoint.com/v2/url?u=https-3A__www.
> mail-2Darchive.com_wien-40zeus.theochem.tuwien.ac.at_
> msg11558.html=DwICAg=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws=U_
> T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0=IqtmMtrsPmzO8Q_
> 7OyBUFU8KovAS1oJ7eHocil7ijPM=XeeQ2aYI6lqjBhzBFbXpOEQPUwE4SV
> EcnONj7dD1rQE=
> [7] https://urldefense.proofpoint.com/v2/url?u=https-3A__www.
> mail-2Darchive.com_wien-40zeus.theochem.tuwien.ac.at_
> msg09231.html=DwICAg=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws=U_
> 

Re: [Wien] About the magnetic moment of vanadium in vanadium sulphide

[Fecher, Gerhard]

First, as Gavin told, your convergence criteria are too bad to decide about 
your magnetic moments
just try to improve them in steps say up to ec 10^-6 cc 10^-3 and see what 
happens with the moments
(that was why I asked fror it)
however be sure you have enough k-points

I assume you used the same structure (with split V position) and you were 
setting the initial moments of V in case.inst to 
nm   0 MU_B both V
fm3 mu_B both V
afm +3 mu_B -3 mu_B

now with GGA you find that all magnetic moments vanish (I assume 0.05 mu_B is 
just numerics)
that is you found a simple metal without magnetic moment that is most probably 
a paramagnet
(try to do a calculation for the fm start values using a very high magnetic 
field to check that)

If you plot the density of states or band structures, you will find that they 
are rather the same in all three cases.

What you missed  may be is a Mott insulator as for example NiO. In that case 
LDA+U is a good choice and you should find
fm = 2.5 mu_B   afm  =  +- 2.5 mu_B 
or at least something between 2 and 3 muB at the V atoms depending on your U 
value.
you should NOT start from the GGA or any LDA solution as they are non magnetic 
and the minimum of the magnetic solution
might be to far from the nonmagnetic one to be found, just start from scratch.
(that's why I asked for it)
You will also find that at least the afm solution has a gap.

in the same way you should find the magnetic solutions when using EECE or HYBR
with magnetic moments of at least about 2 mu_B.

So far, the magnetic moments might be from the spheres, a better way would be 
to use a Baader AIM analysis
to find the moments in the atomic basins here you can use the aim programs 
coming with Wien2k or the program CRITIC 2 from the software goodies.

Actually the existence of the "magnetic" solutions do NOT mean that this are 
the ground states and that those exist !

a) you should do an optimization of the lattice to find the structure for each 
magnetic state (for nm you may force a non-magnetic solution)
and then check which one has the lowest energy.

b) even this does not mean that the so determined state exists. Here you have 
to check whether the crystal is stable at all.
This can be done by calculating the elastic constants and veryfing the 
Born-Huang criteria and by calculating the phonons
to check that no soft modes appear that make the crystal unstable. 
Further you need to check that no soft magnon modes appear, otherwise the 
magnetic state is not stable.

About Hund's rules, please read and understand F Hund; Z. Phys. 33 (1925) 345
to find that those empirical rules are for free ATOMS.
There is a big difference between atoms and solids.
In atoms you have definit states that are occupied by integer numbers of 
electrons
In solids you have energy bands that my be occupied only partially
Immidiately you see that the results are not necessarily the same.
Magnetism in solids is a COLLECTIVE phenomenon (that is not possible in atoms) 
and the results may coincide or not depending whether or not you have purely 
localized, purely itinerant or mixed cases.
If one assumes that there are only covalent or ionic bonds then one just misses 
metals (and also rare gas solids).

There are many models to describe atoms, molecules and solids, however, one 
also needs to check which of those approximations is valid and applicable.


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 Inorganic and Analytical Chemistry
Johannes Gutenberg - University
55099 Mainz
and
Max Planck Institute for Chemical Physics of Solids
01187 Dresden

Von: Wien [wien-boun...@zeus.theochem.tuwien.ac.at] im Auftrag von Abderrahmane 
Reggad [jazai...@gmail.com]
Gesendet: Donnerstag, 7. September 2017 17:11
An: wien@zeus.theochem.tuwien.ac.at
Betreff: Re: [Wien] About the magnetic moment of vanadium in vanadium sulphide

Hi All

I have used the PBE+EECC calculation for 3 configurations: nm, fm and afm I and 
I found that the afm I is the most stable.

The energy criterion and charge are 0.001 Ry and 0.001 e respectively.

I don't worry about if the material is really antiferromagnetic or paramagnetic 
because of:

1- I found only one experimental study that they found the compound to be pauli 
magnetic and one theoritical study which they found the compound to be non 
magnetic and these two studies are not sufficient to judge the compound to be 
in a such state. The theoritical study used the GGA method which is not good 
for correlated systems.

2- In the anfiferromagnetic state afm I in the NiAs structure for vanadium 
sulphide I found the following results:

MMI for V1: 0.05 MB
MMI for V2 :- 0.05 MB
MMI for S:0 MB

My questions are now:

what's the definition of non magnetic compound ?

[Wien] PBS run

[Subrata Jana]

Dear All,
 I am trying to run WIEN2k parallel. My shell script is looking like this.
However, in the out.log file it is showing
--
lapw0: Command not found.

>   stop error
---

please help.

### script ##

#!/bin/bash
#PBS -N wien2k
#PBS -o out.log
#PBS -j oe
#PBS -l nodes=1:ppn=1

# Load Intel environment
source
/apps/intel_2016_u2/compilers_and_libraries_2016.2.181/linux/bin/compilervars.sh
intel64

cd /home/sjana/WIEN2k/PBE/C_pbe
rm -f .machines
echo '#' > .machines
echo 'granularity:1' >>.machines
awk '{print "1:"$1":1"}' $PBS_NODEFILE >>.machines
echo 'extrafine:1' >>.machines
/home/sjana/WIEN2k_14.2/run_lapw -p -i 40 -ec .0001 -I

Regards,
S. Jana
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Re: [Wien] About the magnetic moment of vanadium in vanadium sulphide

[Fecher, Gerhard]

Now I am a little confused
do you think that it was the convergence criteria that I found a magnetic 
moment of 2.5 mu_B instead of 0.05 mu_B at the V ?
or did I make another mistake ;-)

Indeed, you are right, the 0.05 mu_B might be a result of to bad convergence
however, to check if such a moment is something reliable you will need brute 
force with respect to the number of k-points,
that is, if you think you have enough k-points, then just double the number or 
use ten times more.

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 Inorganic and Analytical Chemistry
Johannes Gutenberg - University
55099 Mainz
and
Max Planck Institute for Chemical Physics of Solids
01187 Dresden

Von: Wien [wien-boun...@zeus.theochem.tuwien.ac.at] im Auftrag von Gavin Abo 
[gs...@crimson.ua.edu]
Gesendet: Freitag, 8. September 2017 03:14
An: wien@zeus.theochem.tuwien.ac.at
Betreff: Re: [Wien] About the magnetic moment of vanadium in vanadium sulphide

Perhaps the -ec 0.001 and -cc 0.001 are too large of values.

As I recall, to be well-converged, it is usually best to use about the default 
values seen in the post [1] or WIEN2k 17.1 usersguide [2] as:

-cc 0.0001
-ec 0.0001

It sounded like about the default value for -ec was good unless something like 
-ec 0.1 was desired to reduce numerical noise, but anything smaller seemed 
useless [3,4].

For -cc, 0.1 also may be the lowest limit [5] and quite ambitious to try to 
use [6].

In section "4.5.4 Antiferromagnetic (AFM) calculations" on page 46 in the 
usersguide [2], there is the statement:

"If nothing changes (E-tot and other properties), then you are ok, otherwise 
make sure the scf calculation is well converged (-cc 0.0001 or better)."

If I read from the statement correctly, a well converged scf calculation 
typically uses -cc with a value of 0.0001 or smaller.  Though, there is a 
realistic limit as mentioned above on how small it could be set.

In [7], it sounded important that the -cc value was low for the :MMIn values.

So, maybe the calculation can still converge further such that possibly the 
"MMI for V1" and "MMI for V2" will both become zero when they reach better 
convergence.

[1] https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg12620.html
[2] http://susi.theochem.tuwien.ac.at/reg_user/textbooks/usersguide.pdf
[3] https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg10650.html
[4] https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg16077.html
[5] http://zeus.theochem.tuwien.ac.at/pipermail/wien/2008-November/011797.html
[6] https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg11558.html
[7] https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg09231.html

On 9/7/2017 9:11 AM, Abderrahmane Reggad wrote:
Hi All

I have used the PBE+EECC calculation for 3 configurations: nm, fm and afm I and 
I found that the afm I is the most stable.

The energy criterion and charge are 0.001 Ry and 0.001 e respectively.

I don't worry about if the material is really antiferromagnetic or paramagnetic 
because of:

1- I found only one experimental study that they found the compound to be pauli 
magnetic and one theoritical study which they found the compound to be non 
magnetic and these two studies are not sufficient to judge the compound to be 
in a such state. The theoritical study used the GGA method which is not good 
for correlated systems.

2- In the anfiferromagnetic state afm I in the NiAs structure for vanadium 
sulphide I found the following results:

MMI for V1: 0.05 MB
MMI for V2 :- 0.05 MB
MMI for S:0 MB

My questions are now:

what's the definition of non magnetic compound ?

I think we can talk about non magnetic calculation and not about non magnetic 
compounds.

As Blaha said we can't silulate the paramagnetic state or at at least it's 
difficult to do it because we can't orientate the spins randomly ang maintain 
the total magnetic moment equals to zero.

Because of the Hind's prediction and because the impaired number of the V2+ ion 
to equal 3 I believe the atomic magnetic moment to be different from zero.

Best regards
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Re: [Wien] Error in WIENNCM running in parallel mode

[Jianpeng Liu]

Dear Gavin,

Thank you for your prompt replay. I have checked that energy_1 has been
properly generated. The lapw2.error says:
 'FERMI' - number of k-points inconsistent when reading kgen
 'FERMI' - check IN1 and KGEN files!

I have generated the k mesh using initncm, and set the total number of k
points in BZ as 216 (the system is body-centered tetragonal, and there is
no symmetry of the magnetic state, so there is also 216 k points in the
irreducible BZ). I set up the .machines file to divide the 216 points to 12
processors, 18 k points for each processor. Then there is the problem:
there are 18 k points in case.klist_1 ... case.klist_11, but in
case.klist_12, there are only 16 k points, i.e., 2 kpoints are just
missing. This is probably why the system complains with the k point error?

Later I tried to change the method of determining the Fermi level from the
linear-tetrahedra method to Gaussian smearing, with eval=0.0005Ry, then
everything works. Still, two k points are missing in case.klist_12, but now
the calculation runs well with 12 processors. Can I ask why the linear
tetrahedra method fails, and why the two k points are missing?

Best,
Jianpeng



On Thu, Sep 7, 2017 at 9:17 PM, Gavin Abo  wrote:

> You might try checking the lapw2.error file. Does it show a problem with
> the case.energy_1 file like in the post at:
>
> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg07963.html
>
> If you have that same error, it might be that lapw1 failed in generating
> the case.energy_1.  There are other files you may need to look for error
> messages in as mentioned before in the mailing list archive [
> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg15549.html
> ].
>
>
> On 9/7/2017 5:32 PM, Jianpeng Liu wrote:
>
> Dear Wien2k/Wienncm users and developers,
>
> I am learning to use wienncm to run some noncollinear-magnetism
> calculations. I have compiled the code without any error report, and the
> code runs well in serial mode. But if I run the same calculation in
> parallel mode,  the calculation is always aborted at the lapw2 step, and  I
> got the following error:
>
> FERMI - Error
> cp: cannot stat `.in.tmp': No such file or directory
> rm: cannot remove `.in.tmp': No such file or directory
> rm: cannot remove `.in.tmp1': No such file or directory
>
> The following is the .machine file:
>
> granularity:1
> 1:node91
> 1:node91
> 1:node91
> 1:node91
> 1:node91
> 1:node91
> 1:node91
> 1:node91
> 1:node91
> 1:node91
> 1:node91
> 1:node91
>
> I would appreciate your help.
>
> Best,
> Jianpeng
>
>
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