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