do you mean , it is apparently impossible to get this values using siesta code?
________________________________ 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 >>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>>> >>>> >>>> >>>> >>> >>> >>> >> >> >> > > > > >
