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 > > > > > > > > > > > > > > > > > > >
