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 <http://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 >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>> >>> >> >
