Re: [SIESTA-L] FW: Concerning Denchar
Hi,
Den lør. 23. jan. 2021 kl. 22.00 skrev El-abed Haidar <
ehai2...@uni.sydney.edu.au>:
> Thank you for the reply.
>
>1. Because it was a different issue concerning Denchar but you are
>right!
>2. Will try to understand whats going on with such scripts
>3. I assume that is in python correct?
>
> Yes :)
>
>1. NA
>2. I understand.
>3. I was wondering for denchar version 3, where did you get the
>command from? Denchar -w 3 -k 4 ?? There is a manual for which you got that
>command from right?
>
> It is written in the denchar manual. Ok, it seems it was added after
4.1-b4 was released. So the next release will have it :)
> Thank you!
>
>
>
>
>
> El-abed Haidar | Doctor of Philosophy (Science)
> Condensed Matter Theory (CMT) Group| School of Physics
> THE UNIVERSITY OF SYDNEY | NSW | 2006
>
>
>
> *From: *Nick Papior
> *Sent: *Saturday, 23 January 2021 8:02 AM
> *To: *siesta-l
> *Subject: *Re: [SIESTA-L] FW: Concerning Denchar
>
>
>
> Hi,
>
>
>
> 1. You have created issue here https://github.com/zerothi/sisl/issues/290
> <https://protect-au.mimecast.com/s/FV8mCq71mwf52MOKsZs6UF?domain=github.com>,
> great!
>
> 2. You have to do some scripting, see tutorials here:
> http://zerothi.github.io/sisl/docs/latest/tutorials/tutorial_siesta_1.html
> <https://protect-au.mimecast.com/s/34h2Cr81nytvmBAPszZlDd?domain=zerothi.github.io>
> and
> http://zerothi.github.io/sisl/docs/latest/tutorials/tutorial_siesta_2.html
> <https://protect-au.mimecast.com/s/yHC7Cvl1rKi6lkWpFzNTyY?domain=zerothi.github.io>
>
> 3. You can read in the Hamiltonian from sisl, then do es = H.eigenstate()
> (produces Gamma-point eigenstates), then filter out the eigenvalues close
> to 0 (sisl automatically shifts electronic structure to Fermi-level)
>
> 4. See 2.
>
> 5. None, you have to write a small python script. :), but something like
>
> es_state4 =
> sisl.get_sile("RUN.fdf").read_hamiltonian().eigenstate(k=[0.25, 0.25,
> 0.25]).sub(3) # note C-indexing
>
> 6. I don't know what you mean here...
>
>
>
> Den lør. 16. jan. 2021 kl. 22.04 skrev El-abed Haidar <
> ehai2...@uni.sydney.edu.au>:
>
> Hello Nick, Thank you for the reply:
>
>
>
>1. Sisl can do what denchar can? That’s fantastic, I was wondering how
>because I will give you my feedback
>2. Can you let me know how though? As far I understand, sisl is made
>of 3 parts: sdata, sgeom, and sgrid. My guess to do a denchar calculation
>is to use sgrid. Then the real questions are:
>3. Which nc file should I use to get the homo and lumo as in denchar?
>4. Is there a specific sisl page tutorial for such?
>5. What are the main sisl commands that would be equivalent to*:
>denchar -k 3 -w 4 file.fdf ??*
>6. Since there is no GitHub for denchar and since I could not find the
>command in the denchar manual, where can I find the commands mentioned in
>4??
>
>
>
> Thank you and eager to reading your reply.
>
> EL-abed
>
>
>
> El-abed Haidar | Doctor of Philosophy (Science)
> Condensed Matter Theory (CMT) Group| School of Physics
> THE UNIVERSITY OF SYDNEY | NSW | 2006
>
>
>
> *From: *Nick Papior
> *Sent: *Saturday, 16 January 2021 8:02 AM
> *To: *siesta-l
> *Subject: *Re: [SIESTA-L] FW: Concerning Denchar
>
>
>
> Hmm.
>
>
>
> Den tor. 14. jan. 2021 kl. 22.02 skrev ehai2584 <
> ehai2...@uni.sydney.edu.au>:
>
> Good evening,
>
>1. I was wondering if Denchar has problems with systems which are not
>orthorhombic as it was in 1.3 version? Because when I studied a molecule
>inside orthorhombic system, I could visualize cube files. When I study for
>example graphene in an hexagonal system, even though the file is not empty
>(13000 kb) I could not visualize it.
>
> I am pretty sure it works for other than orthorhombic cells. However, the
> output can only be in an orthorhomic cell.
>
>
>1.
>2. Does Denchar have its own GitHub like sisl? Alberto once gave a
>great advice of using denchar -k 3 -w 4 file.fdf which will plot only the
>wave-function with (original) index 4 of the third k-point in the (WFSX)
>file. An
>
> No, denchar is part of the siesta distribution.
>
> sisl can in principle do what denchar does, however it is not as tested as
> denchar (so any feedback on them would be really nice!)
>
>
>1.
>2. May I convert the output cube file to xsf files in siesta?
>
> You can do this with sisl
>
>
>
> sgrid input.cube output.xsf
>
> or
>
> sdata input.cube output.xsf
>
RE: [SIESTA-L] FW: Concerning Denchar
Thank you for the reply.
1. Because it was a different issue concerning Denchar but you are right!
2. Will try to understand whats going on with such scripts
3. I assume that is in python correct?
4. NA
5. I understand.
6. I was wondering for denchar version 3, where did you get the command
from? Denchar -w 3 -k 4 ?? There is a manual for which you got that command
from right?
Thank you!
El-abed Haidar | Doctor of Philosophy (Science)
Condensed Matter Theory (CMT) Group| School of Physics
THE UNIVERSITY OF SYDNEY | NSW | 2006
From: Nick Papior<mailto:nickpap...@gmail.com>
Sent: Saturday, 23 January 2021 8:02 AM
To: siesta-l<mailto:siesta-l@uam.es>
Subject: Re: [SIESTA-L] FW: Concerning Denchar
Hi,
1. You have created issue here
https://github.com/zerothi/sisl/issues/290<https://protect-au.mimecast.com/s/FV8mCq71mwf52MOKsZs6UF?domain=github.com>,
great!
2. You have to do some scripting, see tutorials here:
http://zerothi.github.io/sisl/docs/latest/tutorials/tutorial_siesta_1.html<https://protect-au.mimecast.com/s/34h2Cr81nytvmBAPszZlDd?domain=zerothi.github.io>
and
http://zerothi.github.io/sisl/docs/latest/tutorials/tutorial_siesta_2.html<https://protect-au.mimecast.com/s/yHC7Cvl1rKi6lkWpFzNTyY?domain=zerothi.github.io>
3. You can read in the Hamiltonian from sisl, then do es = H.eigenstate()
(produces Gamma-point eigenstates), then filter out the eigenvalues close to 0
(sisl automatically shifts electronic structure to Fermi-level)
4. See 2.
5. None, you have to write a small python script. :), but something like
es_state4 = sisl.get_sile("RUN.fdf").read_hamiltonian().eigenstate(k=[0.25,
0.25, 0.25]).sub(3) # note C-indexing
6. I don't know what you mean here...
Den lør. 16. jan. 2021 kl. 22.04 skrev El-abed Haidar
mailto:ehai2...@uni.sydney.edu.au>>:
Hello Nick, Thank you for the reply:
1. Sisl can do what denchar can? That’s fantastic, I was wondering how
because I will give you my feedback
2. Can you let me know how though? As far I understand, sisl is made of 3
parts: sdata, sgeom, and sgrid. My guess to do a denchar calculation is to use
sgrid. Then the real questions are:
3. Which nc file should I use to get the homo and lumo as in denchar?
4. Is there a specific sisl page tutorial for such?
5. What are the main sisl commands that would be equivalent to: denchar -k 3
-w 4 file.fdf ??
6. Since there is no GitHub for denchar and since I could not find the
command in the denchar manual, where can I find the commands mentioned in 4??
Thank you and eager to reading your reply.
EL-abed
El-abed Haidar | Doctor of Philosophy (Science)
Condensed Matter Theory (CMT) Group| School of Physics
THE UNIVERSITY OF SYDNEY | NSW | 2006
From: Nick Papior<mailto:nickpap...@gmail.com>
Sent: Saturday, 16 January 2021 8:02 AM
To: siesta-l<mailto:siesta-l@uam.es>
Subject: Re: [SIESTA-L] FW: Concerning Denchar
Hmm.
Den tor. 14. jan. 2021 kl. 22.02 skrev ehai2584
mailto:ehai2...@uni.sydney.edu.au>>:
Good evening,
1. I was wondering if Denchar has problems with systems which are not
orthorhombic as it was in 1.3 version? Because when I studied a molecule inside
orthorhombic system, I could visualize cube files. When I study for example
graphene in an hexagonal system, even though the file is not empty (13000 kb) I
could not visualize it.
I am pretty sure it works for other than orthorhombic cells. However, the
output can only be in an orthorhomic cell.
1.
2. Does Denchar have its own GitHub like sisl? Alberto once gave a great
advice of using denchar -k 3 -w 4 file.fdf which will plot only the
wave-function with (original) index 4 of the third k-point in the (WFSX) file.
An
No, denchar is part of the siesta distribution.
sisl can in principle do what denchar does, however it is not as tested as
denchar (so any feedback on them would be really nice!)
1.
2. May I convert the output cube file to xsf files in siesta?
You can do this with sisl
sgrid input.cube output.xsf
or
sdata input.cube output.xsf
Denchar does not write out xsf files.
1.
Thank you and looking forward to your reply.
EL-abed
El-abed Haidar | Doctor of Philosophy (Science)
Condensed Matter Theory (CMT) Group| School of Physics
THE UNIVERSITY OF SYDNEY | NSW | 2006
--
SIESTA is supported by the Spanish Research Agency (AEI) and by the European
H2020 MaX Centre of Excellence
(http://www.max-centre.eu/<https://protect-au.mimecast.com/s/zXxICwV1vMf1NwLJTKS214?domain=max-centre.eu/>)
--
Kind regards Nick
--
SIESTA is supported by the Spanish Research Agency (AEI) and by the European
H2020 MaX Centre of Excellence
(http://www.max-centre.eu/<https://protect-au.mimecast.com/s/zXxICwV1vMf1NwLJTKS214?domain=max-centre.eu/>)
--
Kind regards Nick
--
SIESTA is supported by the Spanish Research Agency (AEI) and by the European
H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
Re: [SIESTA-L] FW: Concerning Denchar
Hi,
1. You have created issue here https://github.com/zerothi/sisl/issues/290,
great!
2. You have to do some scripting, see tutorials here:
http://zerothi.github.io/sisl/docs/latest/tutorials/tutorial_siesta_1.html
and
http://zerothi.github.io/sisl/docs/latest/tutorials/tutorial_siesta_2.html
3. You can read in the Hamiltonian from sisl, then do es = H.eigenstate()
(produces Gamma-point eigenstates), then filter out the eigenvalues close
to 0 (sisl automatically shifts electronic structure to Fermi-level)
4. See 2.
5. None, you have to write a small python script. :), but something like
es_state4 = sisl.get_sile("RUN.fdf").read_hamiltonian().eigenstate(k=[0.25,
0.25, 0.25]).sub(3) # note C-indexing
6. I don't know what you mean here...
Den lør. 16. jan. 2021 kl. 22.04 skrev El-abed Haidar <
ehai2...@uni.sydney.edu.au>:
> Hello Nick, Thank you for the reply:
>
>
>
>1. Sisl can do what denchar can? That’s fantastic, I was wondering how
>because I will give you my feedback
>2. Can you let me know how though? As far I understand, sisl is made
>of 3 parts: sdata, sgeom, and sgrid. My guess to do a denchar calculation
>is to use sgrid. Then the real questions are:
>3. Which nc file should I use to get the homo and lumo as in denchar?
>4. Is there a specific sisl page tutorial for such?
>5. What are the main sisl commands that would be equivalent to*: d**enchar
>-k 3 -w 4 file.fdf ??*
>6. Since there is no GitHub for denchar and since I could not find the
>command in the denchar manual, where can I find the commands mentioned in
>4??
>
>
>
> Thank you and eager to reading your reply.
>
> EL-abed
>
>
>
> El-abed Haidar | Doctor of Philosophy (Science)
> Condensed Matter Theory (CMT) Group| School of Physics
> THE UNIVERSITY OF SYDNEY | NSW | 2006
>
>
>
> *From: *Nick Papior
> *Sent: *Saturday, 16 January 2021 8:02 AM
> *To: *siesta-l
> *Subject: *Re: [SIESTA-L] FW: Concerning Denchar
>
>
>
> Hmm.
>
>
>
> Den tor. 14. jan. 2021 kl. 22.02 skrev ehai2584 <
> ehai2...@uni.sydney.edu.au>:
>
> Good evening,
>
>1. I was wondering if Denchar has problems with systems which are not
>orthorhombic as it was in 1.3 version? Because when I studied a molecule
>inside orthorhombic system, I could visualize cube files. When I study for
>example graphene in an hexagonal system, even though the file is not empty
>(13000 kb) I could not visualize it.
>
> I am pretty sure it works for other than orthorhombic cells. However, the
> output can only be in an orthorhomic cell.
>
>
>1.
>2. Does Denchar have its own GitHub like sisl? Alberto once gave a
>great advice of using denchar -k 3 -w 4 file.fdf which will plot only the
>wave-function with (original) index 4 of the third k-point in the (WFSX)
>file. An
>
> No, denchar is part of the siesta distribution.
>
> sisl can in principle do what denchar does, however it is not as tested as
> denchar (so any feedback on them would be really nice!)
>
>
>1.
>2. May I convert the output cube file to xsf files in siesta?
>
> You can do this with sisl
>
>
>
> sgrid input.cube output.xsf
>
> or
>
> sdata input.cube output.xsf
>
>
>
> Denchar does not write out xsf files.
>
>
>1.
>
>
>
> Thank you and looking forward to your reply.
>
> EL-abed
>
>
>
> El-abed Haidar | Doctor of Philosophy (Science)
> Condensed Matter Theory (CMT) Group| School of Physics
> THE UNIVERSITY OF SYDNEY | NSW | 2006
>
>
>
>
>
>
> --
> SIESTA is supported by the Spanish Research Agency (AEI) and by the
> European H2020 MaX Centre of Excellence (http://www.max-centre.eu/
> <https://protect-au.mimecast.com/s/3lWHC3QNPBiE3LELIgu0O3?domain=max-centre.eu/>
> )
>
>
>
>
> --
>
> Kind regards Nick
>
>
>
> --
> SIESTA is supported by the Spanish Research Agency (AEI) and by the
> European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
>
--
Kind regards Nick
--
SIESTA is supported by the Spanish Research Agency (AEI) and by the European
H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
RE: [SIESTA-L] FW: Concerning Denchar
Hello Nick, Thank you for the reply: 1. Sisl can do what denchar can? That’s fantastic, I was wondering how because I will give you my feedback 2. Can you let me know how though? As far I understand, sisl is made of 3 parts: sdata, sgeom, and sgrid. My guess to do a denchar calculation is to use sgrid. Then the real questions are: 3. Which nc file should I use to get the homo and lumo as in denchar? 4. Is there a specific sisl page tutorial for such? 5. What are the main sisl commands that would be equivalent to: denchar -k 3 -w 4 file.fdf ?? 6. Since there is no GitHub for denchar and since I could not find the command in the denchar manual, where can I find the commands mentioned in 4?? Thank you and eager to reading your reply. EL-abed El-abed Haidar | Doctor of Philosophy (Science) Condensed Matter Theory (CMT) Group| School of Physics THE UNIVERSITY OF SYDNEY | NSW | 2006 From: Nick Papior<mailto:nickpap...@gmail.com> Sent: Saturday, 16 January 2021 8:02 AM To: siesta-l<mailto:siesta-l@uam.es> Subject: Re: [SIESTA-L] FW: Concerning Denchar Hmm. Den tor. 14. jan. 2021 kl. 22.02 skrev ehai2584 mailto:ehai2...@uni.sydney.edu.au>>: Good evening, 1. I was wondering if Denchar has problems with systems which are not orthorhombic as it was in 1.3 version? Because when I studied a molecule inside orthorhombic system, I could visualize cube files. When I study for example graphene in an hexagonal system, even though the file is not empty (13000 kb) I could not visualize it. I am pretty sure it works for other than orthorhombic cells. However, the output can only be in an orthorhomic cell. 1. 2. Does Denchar have its own GitHub like sisl? Alberto once gave a great advice of using denchar -k 3 -w 4 file.fdf which will plot only the wave-function with (original) index 4 of the third k-point in the (WFSX) file. An No, denchar is part of the siesta distribution. sisl can in principle do what denchar does, however it is not as tested as denchar (so any feedback on them would be really nice!) 1. 2. May I convert the output cube file to xsf files in siesta? You can do this with sisl sgrid input.cube output.xsf or sdata input.cube output.xsf Denchar does not write out xsf files. 1. Thank you and looking forward to your reply. EL-abed El-abed Haidar | Doctor of Philosophy (Science) Condensed Matter Theory (CMT) Group| School of Physics THE UNIVERSITY OF SYDNEY | NSW | 2006 -- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/<https://protect-au.mimecast.com/s/3lWHC3QNPBiE3LELIgu0O3?domain=max-centre.eu/>) -- Kind regards Nick -- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
Re: [SIESTA-L] FW: Concerning Denchar
Hmm. Den tor. 14. jan. 2021 kl. 22.02 skrev ehai2584 : > Good evening, > >1. I was wondering if Denchar has problems with systems which are not >orthorhombic as it was in 1.3 version? Because when I studied a molecule >inside orthorhombic system, I could visualize cube files. When I study for >example graphene in an hexagonal system, even though the file is not empty >(13000 kb) I could not visualize it. > > I am pretty sure it works for other than orthorhombic cells. However, the output can only be in an orthorhomic cell. > >1. >2. Does Denchar have its own GitHub like sisl? Alberto once gave a >great advice of using denchar -k 3 -w 4 file.fdf which will plot only the >wave-function with (original) index 4 of the third k-point in the (WFSX) >file. An > > No, denchar is part of the siesta distribution. sisl can in principle do what denchar does, however it is not as tested as denchar (so any feedback on them would be really nice!) > >1. >2. May I convert the output cube file to xsf files in siesta? > > You can do this with sisl sgrid input.cube output.xsf or sdata input.cube output.xsf Denchar does not write out xsf files. > >1. > > > > Thank you and looking forward to your reply. > > EL-abed > > > > El-abed Haidar | Doctor of Philosophy (Science) > Condensed Matter Theory (CMT) Group| School of Physics > THE UNIVERSITY OF SYDNEY | NSW | 2006 > > > > > > -- > SIESTA is supported by the Spanish Research Agency (AEI) and by the > European H2020 MaX Centre of Excellence (http://www.max-centre.eu/) > -- Kind regards Nick -- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
[SIESTA-L] FW: Concerning Denchar
Good evening, 1. I was wondering if Denchar has problems with systems which are not orthorhombic as it was in 1.3 version? Because when I studied a molecule inside orthorhombic system, I could visualize cube files. When I study for example graphene in an hexagonal system, even though the file is not empty (13000 kb) I could not visualize it. 2. Does Denchar have its own GitHub like sisl? Alberto once gave a great advice of using denchar -k 3 -w 4 file.fdf which will plot only the wave-function with (original) index 4 of the third k-point in the (WFSX) file. An 3. May I convert the output cube file to xsf files in siesta? Thank you and looking forward to your reply. EL-abed El-abed Haidar | Doctor of Philosophy (Science) Condensed Matter Theory (CMT) Group| School of Physics THE UNIVERSITY OF SYDNEY | NSW | 2006 -- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
