dear Nicolas ,thanks a lot for your reply, I 'll check it
________________________________ 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 >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >> > > > > >
