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