thank you so much for your best reply,I think I got it. but isolated molecule
doesn't have the band structure! I did all of mu programs for one gama point
befor.
Do I say correct? do you think this method is appropriate for this case?
thank you so much for your help
________________________________
From: Nicolas Leconte <[email protected]>
To: Mehrzad Sasanpoor <[email protected]>
Cc: siesta-l <[email protected]>
Sent: Monday, September 24, 2012 5:53 PM
Subject: Re: Fw: [SIESTA-L] read H matrix from .hsx file
Dear Mehrzad,
Don't get me wrong. The COOP analysis won't give you exact numerical values.
For that, you'd have to get the information out of the Hamiltonian, as
mentioned before by Nick as well. Methodology we're not familiar with.
However, a COOP analysis, as well as other (postprocessing) tools such as the
DOS, LDOS, charge density differences, etc can give you more information about
which orbitals participate in a specific bond. Once you have such
understanding, you can construct a minimal TB model to construct a electronic
bandstructure which you fit to the DFT electronic bandstructure.
As for your question on the use of the mprop utility, check the archive of the
mailing list. This has been discussed several times.
Good luck!
Nicolas
On Mon, Sep 24, 2012 at 4:13 PM, Mehrzad Sasanpoor <[email protected]> wrote:
dear Nicolas, I will be very thankful to explain me how to relate between a
band structure of molecule and the coop curve of molecule to get the
quatitative value of site and hopping energy of molecule. in the article you
referencedPRB 84, 235420 (2011), I really get confused how the TB curve achieve
and where the values extract?
>
>
>thanks a lot for your attention
>I really need
>
>
>
>
>
>
>
>
>________________________________
> From: Nicolas Leconte <[email protected]>
>
>To: Mehrzad Sasanpoor <[email protected]>
>Sent: Saturday, September 22, 2012 12:53 PM
>Subject: Re: Fw: [SIESTA-L] read H matrix from .hsx file
>
>
>
>Yes, you can. For theory and examples, check out http://www.cohp.de/ and
>references within.
>I haven't done it on molecules yet, but I guess interpretation of the curves
>will be much more straightforward than for crystals.
>
>
>
>Nicolas
>
>
>
>On Sat, Sep 22, 2012 at 6:49 AM, Mehrzad Sasanpoor <[email protected]> wrote:
>
>
>>
>>
>>
>>
>>
>>dear Nicolas thanks a lot for your useful reply,
my system is isolated molecule, in fact it is benzene molecule which is
functionalizd by methyl group, and I want to find the site and hopping energy
for every atom.
>>is it possible to do this task according to your suggestion or coop /cooh is
>>related to crystal system only?
>>
>>thanks in advance
>>
>>
>>________________________________
>> From: Nicolas Leconte <[email protected]>
>>To: [email protected]
>>Sent: Wednesday, September 19, 2012 12:22 PM
>>Subject: Re: [SIESTA-L] read H matrix from .hsx file
>>
>>
>>Dear Sf Kshp,
>>
>>
>>Indeed, all the information you need to get onsite energies and hopping
>>parameters is available in the Hamiltonian. But Siesta won't give them to you
>>just like that. You'll have to do some extra coding, and similar to Nick, I'm
>>not familiar enough with this to help you.
>>
>>
>>However, the way we did it recently, was exactly by combining different
>>output utilities in the siesta directory, including the COOP/COHP one. These
>>different tools can help you finding which orbitals are important in the
>>energy window you're interested in. In the end, a fit of the electronic
>>bandstructure was used to get the quantitative values. You can find more
>>information on this methodology in PRB 84, 235420 (2011).
>>
>>
>>Good luck,
>>Nicolas
>>
>>On Wed, Sep 19, 2012 at 10:26 AM, Nick Papior Andersen <[email protected]>
>>wrote:
>>
>>I would rather not take on this task, there is a substantial amount of
>>subtleties in obtaining these quantities (many of which I am not too familiar
>>with).
>>>As such I do not feel that I am the right person to help you with this task.
>>>
>>>
>>>I am not too experienced with the COOP code either. I cannot say whether it
>>>will or will not help you.
>>>
>>>
>>>Kind regards Nick
>>>
>>>
>>>2012/9/19 sf kshp <[email protected]>
>>>
>>> Dear Nick,
>>>>Now I get it.I 'm very thankful for you attention,
>>>>I want to open this file only to see how the Hamiltonian and S matrices are
>>>>wirtten but i can't, would you please instruct me what should I do?
>>>>and do you have any suggestion to find these parameters (hopping and onsit)
>>>>from siesta? do you think COOP can help me?
>>>>
>>>>thanks for your time.
>>>>Sf Kshp
>>>>
>>>>
>>>>
>>>>On Wed, Sep 19, 2012 at 10:45 AM, Nick Papior Andersen
>>>><[email protected]> wrote:
>>>>
>>>>I am not sure what you mean by "anything helpful".
>>>>>You have access to the Hamiltonian and overlap matrices that is used in
>>>>>siesta. Whatever, you want to gather from the Hamiltonian and the overlap
>>>>>matrix you in principle can.
>>>>>
>>>>>
>>>>>Kind regards Nick
>>>>>PS. It is no problem to open the file, it is more the interpretation of
>>>>>the records in the HS file which is the key.
>>>>>
>>>>>
>>>>>2012/9/19 sf kshp <[email protected]>
>>>>>
>>>>>Dear Nick,
>>>>>>thank you for your comprehensive help,
>>>>>> let me know if I understand your mean or not:
>>>>>>
>>>>>>suppose we can open hs file, we can see anything helpful. right?
>>>>>>
>>>>>>Best,
>>>>>>Sf Kshp
>>>>>>
>>>>>>
>>>>>>
>>>>>>On Wed, Sep 19, 2012 at 12:35 AM, Nick Papior Andersen
>>>>>><[email protected]> wrote:
>>>>>>
>>>>>>Yes, in the subfolder Utils, from where you gathered hsx2hs. :)
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>Whether it is impossible to get using siesta code, yes and no.
>>>>>>>To my knowledge you cannot ask siesta to pop out the value. However, you
>>>>>>>can program your way out of it.
>>>>>>>
>>>>>>>
>>>>>>>Kind regards Nick
>>>>>>>
>>>>>>>2012/9/18 Mehrzad Sasanpoor <[email protected]>
>>>>>>>
>>>>>>>do you mean the utilities in siesta?
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>________________________________
>>>>>>>> From: Nick Papior Andersen <[email protected]>
>>>>>>>>To: Mehrzad Sasanpoor <[email protected]>
>>>>>>>>Cc: siesta-l <[email protected]>
>>>>>>>>Sent: Wednesday, September 19, 2012 12:28 AM
>>>>>>>>
>>>>>>>>Subject: Re: [SIESTA-L] read H matrix from .hsx file
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>No, they are still in sparse format. Same problem as before.
>>>>>>>>
>>>>>>>>
>>>>>>>>Probably some of the utilities can be utilized for this. However, I do
>>>>>>>>not have experience with any utils of that sort.
>>>>>>>>
>>>>>>>>
>>>>>>>>Kind regards Nick
>>>>>>>>
>>>>>>>>2012/9/18 Mehrzad Sasanpoor <[email protected]>
>>>>>>>>
>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>dear Nick, how about the writeDMHS.History.NetCDF parameter of siesta
>>>>>>>>>that If true, a series of netCDF files with names of the
>>>>>>>>>form DMHS-NNNN.nc is created to hold the complete history of the input
>>>>>>>>>and output density
>>>>>>>>>matrix, and the Hamiltonian.Each file corresponds to a geometry step.
>>>>>>>>>The overlap matrix is stored only once per SCF cycl
>>>>>>>>>
>>>>>>>>>is it useful for this goal?
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>thank you so much for your reply
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>________________________________
>>>>>>>>> From: Nick Papior Andersen <[email protected]>
>>>>>>>>>To: Mehrzad Sasanpoor <[email protected]>
>>>>>>>>>Cc: "[email protected]" <[email protected]>
>>>>>>>>>Sent: Wednesday, September 19, 2012 12:12 AM
>>>>>>>>>Subject: Re: [SIESTA-L] read H matrix from .hsx file
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>Yes, it is not easier in HS or HSX. Nor is it in fact a "simple" path
>>>>>>>>>to get these values.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>For you to get to these values it is important that you look into the
>>>>>>>>>setup of the sparse matrix form of H and S. Try and search for this
>>>>>>>>>and see if you can find anything.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>Kind regards Nick
>>>>>>>>>
>>>>>>>>>2012/9/18 Mehrzad Sasanpoor <[email protected]>
>>>>>>>>>
>>>>>>>>>dear Nick, I want to find the value of site energy and hopping energy
>>>>>>>>>of atomic orbitals for typical molecules, according to manual and
>>>>>>>>>mailing list I thought by opening the HS file I can achieve these
>>>>>>>>>values,
>>>>>>>>>>do I made a mistake?
>>>>>>>>>>I get really confused
>>>>>>>>>>
>>>>>>>>>>thanks a lot for your attention
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>________________________________
>>>>>>>>>> From: Nick Papior Andersen <[email protected]>
>>>>>>>>>>To: Mehrzad Sasanpoor <[email protected]>
>>>>>>>>>>Cc: siesta-l <[email protected]>
>>>>>>>>>>Sent: Tuesday, September 18, 2012 7:13 PM
>>>>>>>>>>
>>>>>>>>>>Subject: Re: [SIESTA-L] read H matrix from .hsx file
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>Read through the mailing list there should be many examples of this.
>>>>>>>>>>If still in doubt read the code for hs2hsx about reading a HSX file.
>>>>>>>>>>Within this you can see what it contains and a little about the
>>>>>>>>>>formation of H and S.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>It seems as if you had no apparent reason for changing the format to
>>>>>>>>>>HS?
>>>>>>>>>>HSX and HS contain "the same" information, although HSX is more
>>>>>>>>>>compact.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>Kind regards Nick
>>>>>>>>>>
>>>>>>>>>>2012/9/18 Mehrzad Sasanpoor <[email protected]>
>>>>>>>>>>
>>>>>>>>>>dear Nick thanks a lot , I could achive mol.HS
>>>>>>>>>>>
>>>>>>>>>>>I really thank you very much
>>>>>>>>>>>but 1 thing , how can I open mol.HS file to read its information?
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>________________________________
>>>>>>>>>>> From: Nick Papior Andersen <[email protected]>
>>>>>>>>>>>To: Mehrzad Sasanpoor <[email protected]>
>>>>>>>>>>>Sent: Tuesday, September 18, 2012 5:46 PM
>>>>>>>>>>>
>>>>>>>>>>>Subject: Re: [SIESTA-L] read H matrix from .hsx file
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>It could mean that you have a corrupted HSX file. It is very hard to
>>>>>>>>>>>tell without having the file.
>>>>>>>>>>>
>>>>>>>>>>>It successfully read the first records without errors and then
>>>>>>>>>>>errors at a new read. This, to me suggests an erroneous file.
>>>>>>>>>>>However, just for a test you can try to copy the file instead of
>>>>>>>>>>>linking...
>>>>>>>>>>>So try this:
>>>>>>>>>>>rm -f HSX
>>>>>>>>>>>cp mol.hsx HSX
>>>>>>>>>>>hsx2hs
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>If this does not work try a simple system and do the same. If
>>>>>>>>>>>converting the hsx file from another run works, then you have a
>>>>>>>>>>>corrupt file.
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>Kind regards Nick
>>>>>>>>>>>
>>>>>>>>>>>2012/9/18 Mehrzad Sasanpoor <[email protected]>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>dear Sir
>>>>>>>>>>>>
>>>>>>>>>>>>thank you very much
>>>>>>>>>>>>after doing ln -s mol.hsx HSX
>>>>>>>>>>>>when I type hsx2hs
>>>>>>>>>>>>again, I have this error
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>Using unit: 10
>>>>>>>>>>>>At line 80 of file hsx_m.f90 (unit = 10, file = 'HSX')
>>>>>>>>>>>>
>>>>>>>>>>>>please help me
>>>>>>>>>>>>
>>>>>>>>>>>>thanks a lot
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>________________________________
>>>>>>>>>>>> From: Nick Papior Andersen <[email protected]>
>>>>>>>>>>>>To: Mehrzad Sasanpoor <[email protected]>
>>>>>>>>>>>>Cc: "[email protected]" <[email protected]>
>>>>>>>>>>>>Sent: Tuesday, September 18, 2012 5:12 PM
>>>>>>>>>>>>
>>>>>>>>>>>>Subject: Re: [SIESTA-L] read H matrix from .hsx file
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>Dear Mehrzad
>>>>>>>>>>>>
>>>>>>>>>>>>That function is not intented to read in from stdin.
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>It reads the HSX file from a file called "HSX".
>>>>>>>>>>>>Thus you should do this:
>>>>>>>>>>>>ln -s mol.hsx HSX
>>>>>>>>>>>>hsx2hs
>>>>>>>>>>>>mv HS mol.HS
>>>>>>>>>>>>rm HSX
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>And that should be it...
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>Kind regards Nick
>>>>>>>>>>>>
>>>>>>>>>>>>2012/9/18 Mehrzad Sasanpoor <[email protected]>
>>>>>>>>>>>>
>>>>>>>>>>>>dear Sir
>>>>>>>>>>>>>thank a lot for your response, I understood that mprop.f90 read
>>>>>>>>>>>>>only hs file;
>>>>>>>>>>>>>however when I convert the mol.HSX to HS file,
>>>>>>>>>>>>>hsx2hs <mol.hsx
>>>>>>>>>>>>> I face with this error
>>>>>>>>>>>>>
>>>>>>>>>>>>> Using unit: 10
>>>>>>>>>>>>>At line 67 of file hsx_m.f90 (unit = 10, file = '')
>>>>>>>>>>>>>Fortran runtime error: File 'HSX' does not exist
>>>>>>>>>>>>>
>>>>>>>>>>>>>what should I do?
>>>>>>>>>>>>>thanks a lot
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>________________________________
>>>>>>>>>>>>> From: Huang Bing <[email protected]>
>>>>>>>>>>>>>To: Mehrzad Sasanpoor <[email protected]>
>>>>>>>>>>>>>Cc: siesta-l <[email protected]>
>>>>>>>>>>>>>Sent: Tuesday, September 18, 2012 3:53 PM
>>>>>>>>>>>>>Subject: Re: [SIESTA-L] read H matrix from .hsx file
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>Hi,
>>>>>>>>>>>>>Having a look at the mprop.f90 (siesta-3.1/Util/COOP/mprop.f90)
>>>>>>>>>>>>>could perhaps gives you some hint.
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>Best Regards,
>>>>>>>>>>>>>Bing
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>2012/9/18 Mehrzad Sasanpoor <[email protected]>
>>>>>>>>>>>>>
>>>>>>>>>>>>>hi siesta users,
>>>>>>>>>>>>>>I want to open and read the *.HSX file which have the site and
>>>>>>>>>>>>>>hopping energy of my typical molecule,
>>>>>>>>>>>>>>but I couldn't,
>>>>>>>>>>>>>>can anybody tell me how I open and read my informations from it,
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>I really need these informations soon
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>thanks a lot
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>>
>>
>>
>>
>
>
>
