Dear Kind Nick, Thank you for sharing your time and useful information.
Best, Sf Kshp On Wed, Sep 19, 2012 at 11:56 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 <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 >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>> >>>> >>> >> >
