[Wien] error in x wplot -wf

2024-04-28 Thread 夏宇阳 
Dear all,

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

Local rotation matrix not orthogonal

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

Looking for your reply.

With regards!

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Re: [Wien] Query regarding wien2k_scratch directory

2024-04-28 Thread Gavin Abo 
The operating system /var log files I typically would not remove.  
Before attempting to remove any of them, I would ask the operating 
system experts if it would be safe to do so.  For Ubuntu for example, I 
think those experts would be over in the Ubuntu forums at [1].


The 15 GB is quite large such that I wouldn't expect the operating 
system with default logging to instantly cause that but get larger more 
gradually over time.


The du command [2] you might find helpful.  Below is an example.

First, I looked at the directories in the root folder for seeing which 
ones were using the most drive space:


username@computername:~$ sudo du --exclude=/proc --exclude=/run -csh /*
0    /bin
197M    /boot
4.0K    /cdrom
0    /dev
14M    /etc
2.6G    /home
0    /lib
0    /lib32
0    /lib64
0    /libx32
16K    /lost+found
44K    /media
4.0K    /mnt
4.0K    /opt
56K    /root
0    /sbin
3.7G    /snap
4.0K    /srv
2.1G    /swapfile
0    /sys
164K    /tmp
6.6G    /usr
3.2G    /var
19G    total

In my case, I'm storing my WIEN2k calculations under 
/home/username/wiendata and have my SCRATCH set to the case folders 
(with ./) that I put in that directory:


username@computername:~$ grep wiendata ~/.bashrc
alias cdw="cd /home/username/wiendata"
export W2WEB_CASE_BASEDIR=/home/username/wiendata
username@computername:~$ grep SCRATCH ~/.bashrc
export SCRATCH=./

I can check the space of just the /home directory with:

username@computername:~$ du -csh /home
2.6G    /home
2.6G    total

I see 2.6 GB of space is being used.

I check what I have under my home directory:

username@computername:~$ ls /home
username

There I see I only have one user account, which is named username.

I check how much space is being used by username:

username@computername:~$ du -csh /home/username
2.6G    /home/username
2.6G    total

Next, I check under /home/username to see what the 2.6 GB consists of:

username@computername:~$ cd /home/username/
username@computername:~$ du -csh * .[^.]*
4.0K    Desktop
4.0K    Documents
4.0K    Downloads
4.0K    Music
4.0K    Pictures
4.0K    Public
124M    snap
4.0K    Templates
4.0K    Videos
1.5G    WIEN2k
180M    wiendata
4.0K    .bash_history
4.0K    .bash_logout
4.0K    .bashrc
130M    .cache
176K    .config
12K    .gnupg
697M    .local
4.0K    .profile
4.0K    .ssh
0    .sudo_as_admin_successful
4.0K    .wget-hsts
2.6G    total

I see my WIEN2k installation is using 1.5 GB of the 2.6 GB used. My 
wiendata is currently only using 180 MB.


Looking in my wiendata folder, I currently only have one case 
calculation named Al:


username@computername:~$ ls /home/username/wiendata/
Al

I find it is taking the entire 180 MB:

username@computername:~$ du -csh /home/username/wiendata/*
180M    /home/username/wiendata/Al
180M    total

To display how much is used under the /home directory in MB, I use:

username@computername:~$ du -csh --block-size=M /home
2624M    /home
2624M    total

I want to move the Al directory from the computer to my USB connected 
external storage drive similar to what you described. First though, 
since my storage drive has a Windows NTFS partition, I have to rename 
the :log file to avoid a transfer error and I chose to name it log.txt:


username@computername:~$ mv /home/username/wiendata/Al/:log 
/home/username/wiendata/Al/log.txt


Creating an archive (.tar) or compressed file (.zip) of the Al directory 
would have been an alternate solution that would not have required 
renaming of the :log file.


I transferred the entire directory to my USB connected flash drive 
(mounted at /media/username/1A50-FE2F/Al) using a mv command in the bash 
terminal:


username@computername:~$ mv /home/username/wiendata/Al 
/media/username/1A50-FE2F/Al


I rechecked wiendata directory after that and see the Al file is gone 
(i.e., was transferred successfully):


username@computername:~$ ls /home/username/wiendata/

I check the space of /home again:

username@computername:~$ du -csh --block-size=M /home
2445M    /home
2445M    total

I see that the used /home space dropped 179 MB (= 2624M - 2445M).  The 1 
MB could be due to rounding error or other active processes going on the 
system taking it, but I was essentially able to get an entire 180 MB of 
free space back for this case as expected.


[1] https://ubuntuforums.org/
[2] 
https://www.tecmint.com/check-linux-disk-usage-of-files-and-directories/


On 4/27/2024 11:23 AM, shamik chakrabarti wrote:
Sir, also it is showing 139 Mb however my device space get decreased 
by almost 15 GB


On Sat, 27 Apr 2024 at 22:51, shamik chakrabarti 
 wrote:


total 139M
4.0K drwxr-x--- 28 shamik shamik 4.0K Apr 26 23:48 .
...
4.0K drwxrwxr-x  2 shamik shamik 4.0K Jun 26  2023 WIEN2k

On Sat, 27 Apr 2024 at 22:48, Peter Blaha
 wrote:

ls -alsh


Am 27.04.2024 um 17:57 schrieb shamik chakrabarti:

Dear Prof. Gavin,

    Yes, wien2k is installed under the /home
directory. I have also

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

2024-04-28 Thread shamik chakrabarti 
Dear Prof. Gavin,

 Apart from that warning, rests are progressing well. Also, the
structure looks similar to earlier DFT calculation. I will go with this.

with regards,

On Sun, 28 Apr 2024 at 21:26, Gavin Abo  wrote:

> Sorry, missed a word, that should read "not an error message"
> On 4/28/2024 9:47 AM, Gavin Abo wrote:
>
> As far as I know, w2web is not able to automatically detect yet if you
> have entered the atomic positions correctly for space group 166.  So, the
> "positions must be specified in rhombohedral coordinates!" is NOT an
> error message but a reminder text that will always be there whether you
> enter position correctly or incorrectly.  Thus, you have to carefully check
> for yourself that you have entered the position correctly.
>
> As you might recall from the post at [1], WIEN2k is a bit unusual in that
> for the struct file it needs hexagonal lattice constants but rhombohedral
> for the atomic positions for an R lattice space group such as 166 R-3m.
> For LiNIO2, you should double check, but I believe the both lattice
> constants and atomic positions in the hexagonal setting are:
>
> Initial Setting: R-3m:h (No. 166)
>
> 166
> 5.404616 5.404616 26.569550 90 90 120 <= This is the hexagonal lattice
> parameters needed for the struct file of WIEN2k
> 3
> Li13a0.000.000.00 <= These are the
> hexagonal atomic positions, which would be incorrect to use for WIEN2k
> Ni13b0.000.000.50
> O16c0.000.000.240984
>
> Using SETSTRU [2], its equivalent in the rhombohedral setting should be:
>
>
> Final Setting: R-3m:r (No. 166)
>
> 166 #R-3m:r
> 9.3901 9.3901 9.3901 33.45 33.45 33.45 <= These are the rhombohedral
> lattice parameters, which would be incorrect to use for WIEN2k
> 3
> Li1-0.000.000.00 <= These are the
> rhomboderal atomic positions needed for the struct file of WIEN2k
> Ni1-0.500.500.50
> O1-0.2409840.2409840.240984
>
>
> In your LiNiO2_opt.struct, I see:
>
> a = 5.404616 bohr in hexagonal setting
>
> b = 5.404616 bohr in hexagonal setting
>
> c = 26.569550 bohr in hexagonal setting
>
> alpha = 90.00 deg in hexagonal setting
>
> beta = 90.00 deg in hexagonal setting
>
> beta = 120.00 deg in hexagonal setting
>
> Li x=0. y=0. z=0. in rhombohedral setting
>
> Ni z=0.5000 y=0.5000 z=0.5000 in rhombohedral setting
>
> O x=0.24098400 y=0.24098400 z=0.24098400 in rhombohedral setting
>
> [1]
> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg05554.html
>
> [2] https://www.cryst.ehu.es/cryst/setstru.html
>
>
> On 4/28/2024 8:00 AM, shamik chakrabarti wrote:
>
> Dear Wien2k users,
>
>I want to simulate properties of LiNiO2. However, adopting the
> structure (file attached) by bringing it into rhombohedral axis in Vesta,
> when I copy the cif file into the working directory & converting it into a
> struct file, after save structure, it complains about
>
> " positions must be specified in rhombohedral coordinates!"
>
> Please guide.
>
> with regards,
>
> --
> Dr. Shamik Chakrabarti
> Research Fellow
> Department of Physics
> Indian Institute of Technology Patna
> Bihta-801103
> Patna
> Bihar, India
>
> ___
> 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
>


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

2024-04-28 Thread Gavin Abo 

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

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


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


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


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


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

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

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

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

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


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

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

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

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


In your LiNiO2_opt.struct, I see:

a = 5.404616 bohr in hexagonal setting

b = 5.404616 bohr in hexagonal setting

c = 26.569550 bohr in hexagonal setting

alpha = 90.00 deg in hexagonal setting

beta = 90.00 deg in hexagonal setting

beta = 120.00 deg in hexagonal setting

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

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

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

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


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


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

Dear Wien2k users,

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


" positions must be specified in rhombohedral coordinates!"

Please guide.

with regards,

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

2024-04-28 Thread Gavin Abo 
As far as I know, w2web is not able to automatically detect yet if you 
have entered the atomic positions correctly for space group 166.  So, 
the "positions must be specified in rhombohedral coordinates!" is an 
error message but a reminder text that will always be there whether you 
enter position correctly or incorrectly.  Thus, you have to carefully 
check for yourself that you have entered the position correctly.


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


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


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

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

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

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

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


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

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

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

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


In your LiNiO2_opt.struct, I see:

a = 5.404616 bohr in hexagonal setting

b = 5.404616 bohr in hexagonal setting

c = 26.569550 bohr in hexagonal setting

alpha = 90.00 deg in hexagonal setting

beta = 90.00 deg in hexagonal setting

beta = 120.00 deg in hexagonal setting

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

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

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

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


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


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

Dear Wien2k users,

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


" positions must be specified in rhombohedral coordinates!"

Please guide.

with regards,

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

2024-04-28 Thread shamik chakrabarti 
Dear Prof. Delamora,

 After changing all the coordinates I am achieving
rather a complicated struct file as attached.

with regards,

On Sun, 28 Apr 2024 at 20:18, delamora  wrote:

> hx is hexagonal x
>
> --
> *De:* Wien  en nombre de shamik
> chakrabarti 
> *Enviado:* domingo, 28 de abril de 2024 08:40 a. m.
> *Para:* A Mailing list for WIEN2k users 
> *Asunto:* Re: [Wien] Rhombhohedral coordinates needed in simulation of
> LiNiO2
>
> It is asking for specifying hx,hy,hzwhat are these?
>
> On Sun, 28 Apr 2024 at 20:06, delamora  wrote:
>
> Use the command;
> hex2rhomb
> hexagonal to rhombohedral
> --
> *De:* Wien  en nombre de shamik
> chakrabarti 
> *Enviado:* domingo, 28 de abril de 2024 08:00 a. m.
> *Para:* A Mailing list for WIEN2k users 
> *Asunto:* [Wien] Rhombhohedral coordinates needed in simulation of LiNiO2
>
> Dear Wien2k users,
>
>I want to simulate properties of LiNiO2. However, adopting the
> structure (file attached) by bringing it into rhombohedral axis in Vesta,
> when I copy the cif file into the working directory & converting it into a
> struct file, after save structure, it complains about
>
> " positions must be specified in rhombohedral coordinates!"
>
> Please guide.
>
> with regards,
>
> --
> Dr. Shamik Chakrabarti
> Research Fellow
> Department of Physics
> Indian Institute of Technology Patna
> Bihta-801103
> Patna
> Bihar, India
> ___
> 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
>
>
>
> --
> Dr. Shamik Chakrabarti
> Research Fellow
> Department of Physics
> Indian Institute of Technology Patna
> Bihta-801103
> Patna
> Bihar, India
> ___
> Wien mailing list
> Wien@zeus.theochem.tuwien.ac.at
> 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
>


-- 
Dr. Shamik Chakrabarti
Research Fellow
Department of Physics
Indian Institute of Technology Patna
Bihta-801103
Patna
Bihar, India


LiNiO2_opt.struct
Description: Binary data
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Re: [Wien] Rhombhohedral coordinates needed in simulation of LiNiO2

2024-04-28 Thread delamora 
hx is hexagonal x


De: Wien  en nombre de shamik 
chakrabarti 
Enviado: domingo, 28 de abril de 2024 08:40 a. m.
Para: A Mailing list for WIEN2k users 
Asunto: Re: [Wien] Rhombhohedral coordinates needed in simulation of LiNiO2

It is asking for specifying hx,hy,hzwhat are these?

On Sun, 28 Apr 2024 at 20:06, delamora 
mailto:delam...@unam.mx>> wrote:
Use the command;
hex2rhomb
hexagonal to rhombohedral

De: Wien 
mailto:wien-boun...@zeus.theochem.tuwien.ac.at>>
 en nombre de shamik chakrabarti 
mailto:shamik15041...@gmail.com>>
Enviado: domingo, 28 de abril de 2024 08:00 a. m.
Para: A Mailing list for WIEN2k users 
mailto:wien@zeus.theochem.tuwien.ac.at>>
Asunto: [Wien] Rhombhohedral coordinates needed in simulation of LiNiO2

Dear Wien2k users,

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

" positions must be specified in rhombohedral coordinates!"

Please guide.

with regards,

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

2024-04-28 Thread shamik chakrabarti 
It is asking for specifying hx,hy,hzwhat are these?

On Sun, 28 Apr 2024 at 20:06, delamora  wrote:

> Use the command;
> hex2rhomb
> hexagonal to rhombohedral
> --
> *De:* Wien  en nombre de shamik
> chakrabarti 
> *Enviado:* domingo, 28 de abril de 2024 08:00 a. m.
> *Para:* A Mailing list for WIEN2k users 
> *Asunto:* [Wien] Rhombhohedral coordinates needed in simulation of LiNiO2
>
> Dear Wien2k users,
>
>I want to simulate properties of LiNiO2. However, adopting the
> structure (file attached) by bringing it into rhombohedral axis in Vesta,
> when I copy the cif file into the working directory & converting it into a
> struct file, after save structure, it complains about
>
> " positions must be specified in rhombohedral coordinates!"
>
> Please guide.
>
> with regards,
>
> --
> Dr. Shamik Chakrabarti
> Research Fellow
> Department of Physics
> Indian Institute of Technology Patna
> Bihta-801103
> Patna
> Bihar, India
> ___
> 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
>


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

2024-04-28 Thread delamora 
Use the command;
hex2rhomb
hexagonal to rhombohedral

De: Wien  en nombre de shamik 
chakrabarti 
Enviado: domingo, 28 de abril de 2024 08:00 a. m.
Para: A Mailing list for WIEN2k users 
Asunto: [Wien] Rhombhohedral coordinates needed in simulation of LiNiO2

Dear Wien2k users,

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

" positions must be specified in rhombohedral coordinates!"

Please guide.

with regards,

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

2024-04-28 Thread shamik chakrabarti 
Dear Wien2k users,

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

" positions must be specified in rhombohedral coordinates!"

Please guide.

with regards,

-- 
Dr. Shamik Chakrabarti
Research Fellow
Department of Physics
Indian Institute of Technology Patna
Bihta-801103
Patna
Bihar, India


LiNiO2_opt.struct
Description: Binary data
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