[SIESTA-L] VACF and PHONON DOS in SIESTA

[Suman Chowdhury]

Dear SIESTA user : Is there any utility program is SIESTA which can
calculate the velocity autocorrelation function and the fourier transform
of it, because the fourier transform of velocity autocorrelation function
gives the phonon density of states which I want to calculate..

[SIESTA-L] PIEZOELECTRIC behavior

[Suman Chowdhury]

Dear all SIESTA users,

Does anyone have any idea about how to study the PIEZOELECTRIC behavior of
materials by using SIESTA??

Re: [SIESTA-L] Band Structure and PDOS results not matching

[Suman Chowdhury]

Again thank you so so much Prof. Nick Papior

On Sun, Feb 4, 2018 at 11:44 PM, Nick Papior <nickpap...@gmail.com> wrote:

> I used PDOS from siesta, just as you said you did in your original post.
>
> 2018-02-04 17:25 GMT+01:00 Suman Chowdhury <sumanchowdhur...@gmail.com>:
>
>> Just let me know how did you calculate the DOS..
>>
>> On Sat, Feb 3, 2018 at 3:04 AM, Nick Papior <nickpap...@gmail.com> wrote:
>>
>>> Dear Suman,
>>>
>>> I think you should solve this yourself.
>>>
>>> 2018-02-02 5:56 GMT+01:00 Suman Chowdhury <sumanchowdhur...@gmail.com>:
>>>
>>>> Dear Nick Papior,
>>>>
>>>> Thank you so so much for your help. Can you help me in this regard
>>>> about how I can get the correct coordinates for plotting the band
>>>> structure??
>>>>
>>>> On Thu, Feb 1, 2018 at 3:56 PM, Nick Papior <nickpap...@gmail.com>
>>>> wrote:
>>>>
>>>>> If I run your system without performing cell relaxations I find the
>>>>> attached eigenvalues (for the Monkhorst-Pack grid).
>>>>>
>>>>> In this case there is *only* a bandgab of ~0.5 eV. Provided that the
>>>>> cell-relaxation does not change the spectrum drastically then this is what
>>>>> you should suspect in the PDOS.
>>>>> Secondly, the PDOS is *exactly* reproducing the bandgab in this
>>>>> calculation.
>>>>>
>>>>> 1) I would highly suggest you to perform cell/coordinate relaxations
>>>>> in one directory, then afterwards perform analysis on the relaxed
>>>>> structure, PDOS, band-structure, optical, etc.
>>>>> 2) Possibly your band-structure coordinates are wrong because when I
>>>>> plot the bandstructure for this structure it does not capture the correct
>>>>> band gab (this *has* to be the problem).
>>>>>
>>>>> 2018-01-31 16:35 GMT+01:00 Suman Chowdhury <sumanchowdhur...@gmail.com
>>>>> >:
>>>>>
>>>>>> I have just tried to see the variation of TDOS by changing the
>>>>>> smearing parameter. But I could not observe any change in it.
>>>>>>
>>>>>> On Wed, Jan 31, 2018 at 6:44 PM, Suman Chowdhury <
>>>>>> sumanchowdhur...@gmail.com> wrote:
>>>>>>
>>>>>>> This is the fdf that I have used...
>>>>>>>
>>>>>>> On Thu, Jan 25, 2018 at 11:40 AM, Nick Papior <nickpap...@gmail.com>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> Dear Suman,
>>>>>>>>
>>>>>>>> Without data (plots) or fdf file it is very difficult to help you.
>>>>>>>> It could be that your smearing parameter is too large.
>>>>>>>>
>>>>>>>>
>>>>>>>> 2018-01-24 15:13 GMT+01:00 Suman Chowdhury <
>>>>>>>> sumanchowdhur...@gmail.com>:
>>>>>>>>
>>>>>>>>> Dear SIESTA User,
>>>>>>>>>
>>>>>>>>> Recently I am getting some confusing results by using SIESTA.
>>>>>>>>> While plotting a band structure I am getting a band gap which is quite
>>>>>>>>> large. However, when I am trying to plot its corresponding total 
>>>>>>>>> partial
>>>>>>>>> density of states (PDOS), I can clearly see that there is no 
>>>>>>>>> existence of
>>>>>>>>> any band gap. But interestingly the component PDOS are giving the 
>>>>>>>>> required
>>>>>>>>> band gap. The problem is with the total PDOS. Do any of you have any 
>>>>>>>>> idea
>>>>>>>>> about these kinds of results...
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> *Dr. Suman Chowdhury*
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> *Assistant Professor Dept. of Physics, Bangabasi College Kolkata-
>>>>>>>>> 79, West Bengal, India.*
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>> Kind regards Nick
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> *Dr. Suman Chowdhury*
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> *Assistant Professor Dept. of Physics, Bangabasi College Kolkata-
>>>>>>> 79, West Bengal, India.*
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> *Dr. Suman Chowdhury*
>>>>>>
>>>>>>
>>>>>>
>>>>>> *Assistant Professor Dept. of Physics, Bangabasi College Kolkata-
>>>>>> 79, West Bengal, India.*
>>>>>> * Ph no-+91-9830512232 <+91%2098305%2012232>*
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Kind regards Nick
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> *Dr. Suman Chowdhury*
>>>>
>>>>
>>>>
>>>> *Assistant Professor Dept. of Physics, Bangabasi College Kolkata-
>>>> 79, West Bengal, India.*
>>>> * Ph no-+91-9830512232 <+91%2098305%2012232>*
>>>>
>>>>
>>>
>>>
>>> --
>>> Kind regards Nick
>>>
>>
>>
>>
>> --
>> *Dr. Suman Chowdhury*
>>
>>
>>
>> *Assistant Professor Dept. of Physics, Bangabasi College Kolkata- 79,
>> West Bengal, India.*
>> * Ph no-+91-9830512232 <+91%2098305%2012232>*
>>
>>
>
>
> --
> Kind regards Nick
>



-- 
*Dr. Suman Chowdhury*



*Assistant Professor Dept. of Physics, Bangabasi College Kolkata- 79,
West Bengal, India.*
* Ph no-+91-9830512232*

Re: [SIESTA-L] Band Structure and PDOS results not matching

[Suman Chowdhury]

Just let me know how did you calculate the DOS..

On Sat, Feb 3, 2018 at 3:04 AM, Nick Papior <nickpap...@gmail.com> wrote:

> Dear Suman,
>
> I think you should solve this yourself.
>
> 2018-02-02 5:56 GMT+01:00 Suman Chowdhury <sumanchowdhur...@gmail.com>:
>
>> Dear Nick Papior,
>>
>> Thank you so so much for your help. Can you help me in this regard about
>> how I can get the correct coordinates for plotting the band structure??
>>
>> On Thu, Feb 1, 2018 at 3:56 PM, Nick Papior <nickpap...@gmail.com> wrote:
>>
>>> If I run your system without performing cell relaxations I find the
>>> attached eigenvalues (for the Monkhorst-Pack grid).
>>>
>>> In this case there is *only* a bandgab of ~0.5 eV. Provided that the
>>> cell-relaxation does not change the spectrum drastically then this is what
>>> you should suspect in the PDOS.
>>> Secondly, the PDOS is *exactly* reproducing the bandgab in this
>>> calculation.
>>>
>>> 1) I would highly suggest you to perform cell/coordinate relaxations in
>>> one directory, then afterwards perform analysis on the relaxed structure,
>>> PDOS, band-structure, optical, etc.
>>> 2) Possibly your band-structure coordinates are wrong because when I
>>> plot the bandstructure for this structure it does not capture the correct
>>> band gab (this *has* to be the problem).
>>>
>>> 2018-01-31 16:35 GMT+01:00 Suman Chowdhury <sumanchowdhur...@gmail.com>:
>>>
>>>> I have just tried to see the variation of TDOS by changing the smearing
>>>> parameter. But I could not observe any change in it.
>>>>
>>>> On Wed, Jan 31, 2018 at 6:44 PM, Suman Chowdhury <
>>>> sumanchowdhur...@gmail.com> wrote:
>>>>
>>>>> This is the fdf that I have used...
>>>>>
>>>>> On Thu, Jan 25, 2018 at 11:40 AM, Nick Papior <nickpap...@gmail.com>
>>>>> wrote:
>>>>>
>>>>>> Dear Suman,
>>>>>>
>>>>>> Without data (plots) or fdf file it is very difficult to help you.
>>>>>> It could be that your smearing parameter is too large.
>>>>>>
>>>>>>
>>>>>> 2018-01-24 15:13 GMT+01:00 Suman Chowdhury <
>>>>>> sumanchowdhur...@gmail.com>:
>>>>>>
>>>>>>> Dear SIESTA User,
>>>>>>>
>>>>>>> Recently I am getting some confusing results by using SIESTA. While
>>>>>>> plotting a band structure I am getting a band gap which is quite large.
>>>>>>> However, when I am trying to plot its corresponding total partial 
>>>>>>> density
>>>>>>> of states (PDOS), I can clearly see that there is no existence of any 
>>>>>>> band
>>>>>>> gap. But interestingly the component PDOS are giving the required band 
>>>>>>> gap.
>>>>>>> The problem is with the total PDOS. Do any of you have any idea about 
>>>>>>> these
>>>>>>> kinds of results...
>>>>>>>
>>>>>>> --
>>>>>>> *Dr. Suman Chowdhury*
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> *Assistant Professor Dept. of Physics, Bangabasi College Kolkata-
>>>>>>> 79, West Bengal, India.*
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Kind regards Nick
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> *Dr. Suman Chowdhury*
>>>>>
>>>>>
>>>>>
>>>>> *Assistant Professor Dept. of Physics, Bangabasi College Kolkata-
>>>>> 79, West Bengal, India.*
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> *Dr. Suman Chowdhury*
>>>>
>>>>
>>>>
>>>> *Assistant Professor Dept. of Physics, Bangabasi College Kolkata-
>>>> 79, West Bengal, India.*
>>>> * Ph no-+91-9830512232 <+91%2098305%2012232>*
>>>>
>>>>
>>>
>>>
>>> --
>>> Kind regards Nick
>>>
>>
>>
>>
>> --
>> *Dr. Suman Chowdhury*
>>
>>
>>
>> *Assistant Professor Dept. of Physics, Bangabasi College Kolkata- 79,
>> West Bengal, India.*
>> * Ph no-+91-9830512232 <+91%2098305%2012232>*
>>
>>
>
>
> --
> Kind regards Nick
>



-- 
*Dr. Suman Chowdhury*



*Assistant Professor Dept. of Physics, Bangabasi College Kolkata- 79,
West Bengal, India.*
* Ph no-+91-9830512232*

Re: [SIESTA-L] Band Structure and PDOS results not matching

[Suman Chowdhury]

Dear Nick Papior,

Thank you so so much for your help. Can you help me in this regard about
how I can get the correct coordinates for plotting the band structure??

On Thu, Feb 1, 2018 at 3:56 PM, Nick Papior <nickpap...@gmail.com> wrote:

> If I run your system without performing cell relaxations I find the
> attached eigenvalues (for the Monkhorst-Pack grid).
>
> In this case there is *only* a bandgab of ~0.5 eV. Provided that the
> cell-relaxation does not change the spectrum drastically then this is what
> you should suspect in the PDOS.
> Secondly, the PDOS is *exactly* reproducing the bandgab in this
> calculation.
>
> 1) I would highly suggest you to perform cell/coordinate relaxations in
> one directory, then afterwards perform analysis on the relaxed structure,
> PDOS, band-structure, optical, etc.
> 2) Possibly your band-structure coordinates are wrong because when I plot
> the bandstructure for this structure it does not capture the correct band
> gab (this *has* to be the problem).
>
> 2018-01-31 16:35 GMT+01:00 Suman Chowdhury <sumanchowdhur...@gmail.com>:
>
>> I have just tried to see the variation of TDOS by changing the smearing
>> parameter. But I could not observe any change in it.
>>
>> On Wed, Jan 31, 2018 at 6:44 PM, Suman Chowdhury <
>> sumanchowdhur...@gmail.com> wrote:
>>
>>> This is the fdf that I have used...
>>>
>>> On Thu, Jan 25, 2018 at 11:40 AM, Nick Papior <nickpap...@gmail.com>
>>> wrote:
>>>
>>>> Dear Suman,
>>>>
>>>> Without data (plots) or fdf file it is very difficult to help you.
>>>> It could be that your smearing parameter is too large.
>>>>
>>>>
>>>> 2018-01-24 15:13 GMT+01:00 Suman Chowdhury <sumanchowdhur...@gmail.com>
>>>> :
>>>>
>>>>> Dear SIESTA User,
>>>>>
>>>>> Recently I am getting some confusing results by using SIESTA. While
>>>>> plotting a band structure I am getting a band gap which is quite large.
>>>>> However, when I am trying to plot its corresponding total partial density
>>>>> of states (PDOS), I can clearly see that there is no existence of any band
>>>>> gap. But interestingly the component PDOS are giving the required band 
>>>>> gap.
>>>>> The problem is with the total PDOS. Do any of you have any idea about 
>>>>> these
>>>>> kinds of results...
>>>>>
>>>>> --
>>>>> *Dr. Suman Chowdhury*
>>>>>
>>>>>
>>>>>
>>>>> *Assistant Professor Dept. of Physics, Bangabasi College Kolkata-
>>>>> 79, West Bengal, India.*
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> Kind regards Nick
>>>>
>>>
>>>
>>>
>>> --
>>> *Dr. Suman Chowdhury*
>>>
>>>
>>>
>>> *Assistant Professor Dept. of Physics, Bangabasi College Kolkata-
>>> 79, West Bengal, India.*
>>>
>>>
>>>
>>
>>
>> --
>> *Dr. Suman Chowdhury*
>>
>>
>>
>> *Assistant Professor Dept. of Physics, Bangabasi College Kolkata- 79,
>> West Bengal, India.*
>> * Ph no-+91-9830512232 <+91%2098305%2012232>*
>>
>>
>
>
> --
> Kind regards Nick
>



-- 
*Dr. Suman Chowdhury*



*Assistant Professor Dept. of Physics, Bangabasi College Kolkata- 79,
West Bengal, India.*
* Ph no-+91-9830512232*

Re: [SIESTA-L] Band Structure and PDOS results not matching

[Suman Chowdhury]

I have just tried to see the variation of TDOS by changing the smearing
parameter. But I could not observe any change in it.

On Wed, Jan 31, 2018 at 6:44 PM, Suman Chowdhury <sumanchowdhur...@gmail.com
> wrote:

> This is the fdf that I have used...
>
> On Thu, Jan 25, 2018 at 11:40 AM, Nick Papior <nickpap...@gmail.com>
> wrote:
>
>> Dear Suman,
>>
>> Without data (plots) or fdf file it is very difficult to help you.
>> It could be that your smearing parameter is too large.
>>
>>
>> 2018-01-24 15:13 GMT+01:00 Suman Chowdhury <sumanchowdhur...@gmail.com>:
>>
>>> Dear SIESTA User,
>>>
>>> Recently I am getting some confusing results by using SIESTA. While
>>> plotting a band structure I am getting a band gap which is quite large.
>>> However, when I am trying to plot its corresponding total partial density
>>> of states (PDOS), I can clearly see that there is no existence of any band
>>> gap. But interestingly the component PDOS are giving the required band gap.
>>> The problem is with the total PDOS. Do any of you have any idea about these
>>> kinds of results...
>>>
>>> --
>>> *Dr. Suman Chowdhury*
>>>
>>>
>>>
>>> *Assistant Professor Dept. of Physics, Bangabasi College Kolkata-
>>> 700009, West Bengal, India.*
>>>
>>>
>>
>>
>> --
>> Kind regards Nick
>>
>
>
>
> --
> *Dr. Suman Chowdhury*
>
>
>
> *Assistant Professor Dept. of Physics, Bangabasi College Kolkata- 79,
> West Bengal, India.*
>
>
>


-- 
*Dr. Suman Chowdhury*



*Assistant Professor Dept. of Physics, Bangabasi College Kolkata- 79,
West Bengal, India.*
* Ph no-+91-9830512232*

Re: [SIESTA-L] Band Structure and PDOS results not matching

[Suman Chowdhury]

This is the fdf that I have used...

On Thu, Jan 25, 2018 at 11:40 AM, Nick Papior <nickpap...@gmail.com> wrote:

> Dear Suman,
>
> Without data (plots) or fdf file it is very difficult to help you.
> It could be that your smearing parameter is too large.
>
>
> 2018-01-24 15:13 GMT+01:00 Suman Chowdhury <sumanchowdhur...@gmail.com>:
>
>> Dear SIESTA User,
>>
>> Recently I am getting some confusing results by using SIESTA. While
>> plotting a band structure I am getting a band gap which is quite large.
>> However, when I am trying to plot its corresponding total partial density
>> of states (PDOS), I can clearly see that there is no existence of any band
>> gap. But interestingly the component PDOS are giving the required band gap.
>> The problem is with the total PDOS. Do any of you have any idea about these
>> kinds of results...
>>
>> --
>> *Dr. Suman Chowdhury*
>>
>>
>>
>> *Assistant Professor Dept. of Physics, Bangabasi College Kolkata- 79,
>> West Bengal, India.*
>>
>>
>
>
> --
> Kind regards Nick
>



-- 
*Dr. Suman Chowdhury*



*Assistant Professor Dept. of Physics, Bangabasi College Kolkata- 79,
West Bengal, India.*


SiC.fdf
Description: Binary data

[SIESTA-L] Band Structure and PDOS results not matching

[Suman Chowdhury]

Dear SIESTA User,

Recently I am getting some confusing results by using SIESTA. While
plotting a band structure I am getting a band gap which is quite large.
However, when I am trying to plot its corresponding total partial density
of states (PDOS), I can clearly see that there is no existence of any band
gap. But interestingly the component PDOS are giving the required band gap.
The problem is with the total PDOS. Do any of you have any idea about these
kinds of results...

-- 
*Dr. Suman Chowdhury*



*Assistant Professor Dept. of Physics, Bangabasi College Kolkata- 79,
West Bengal, India.*
* Ph no-+91-9830512232*

[SIESTA-L] Application of strain in SIESTA

[Suman Chowdhury]

Dear All,

Does any one know how to introduce strain in siesta. What I know is,
suppose I want to introduce strain in the x-direction. Then I have to
change the x-component of the each of the lattice vector as well as the
unit cell coordinate, then let it relax. Am I right or wrong?? Please
explain.Should I keep the volume of the supercell constant or variable cell
relaxation. Please help me.

-- 
*Dr. Suman Chowdhury*



*Assistant Professor Dept. of Physics, Bangabasi College Kolkata- 79,
West Bengal, India.*
* Ph no-+91-9830512232*

[SIESTA-L] Determination of Spin-Orbit strength

[Suman Chowdhury]

Dear SIESTA User,

I am doing some simulation with spin-orbit coupling. Is there any way in
SIESTA to determine the actual strength of the spin-orbit coupling. I have
taken a material for which the spin-orbit coupling is not known, which I
want to know by performing a self-consistent calculation. I can able to
vary the strength of spin-orbit coupling in SIESTA. But I want to determine
it. How to do that in SIESTA...

From

Dr. Suman Chowdhury

-- 
*Dr. Suman Chowdhury*



*Assistant Professor Dept. of Physics, Bangabasi College Kolkata- 79,
West Bengal, India.*
* Ph no-+91-9830512232*

Re: [SIESTA-L] Problem in siesta parallel job

[Suman Chowdhury]

Dear Barnali,

May be this is slightly an off topic but I need some help from you. As you
are using the k2 cluster of IUAC, which I am also using. But Iam facing
some problems while using SIESTA. While running siesta in the serial mode,
the program runs but the output file is not generated. While trying to run
the parallel version, the program is not even started even after waiting
for 2-3 days. Have you even faced similar kind of problems??

On Thu, Mar 30, 2017 at 1:05 PM, Barnali Bhattacharya <
barnalidgbh...@gmail.com> wrote:

> Dear SIESTA user
>
>
> I have installed parallel version of siesta 3.2 in k2 cluster and I am
> trying to run transiesta job in all.q queue. I have found that, siesta
> and  transiesta successfully run on the serial.q, but In case of all.q
> queue the job started successfully and goes to  first MD  step ‘New_DM.
> Step: 1’, then stop automatically and a new file namely
> ‘transiesta.80s-28515,compute-11-14.local’is generated which contain the
> following error massage-
>
> ….
>
>
>
> transiesta:28515 terminated with signal 11 at PC=668de0 SP=7fff67d08118.
> Backtrace:
>
> /mnt/oss/sarkar_au/install/siesta-3.2-pl3/Obj/transiesta(
> zdotc_+0x70)[0x668de0]
>
> /opt/intel/composer_xe_2013_sp1.2.144/mkl/lib/intel64/
> libmkl_scalapack_lp64.so(zvvdotc_+0x16)[0x2b758d717a26]
>
> /opt/intel/composer_xe_2013_sp1.2.144/mkl/lib/intel64/
> libmkl_scalapack_lp64.so(pzdotc_+0xbe4)[0x2b758d7b3584]
>
> /opt/intel/composer_xe_2013_sp1.2.144/mkl/lib/intel64/
> libmkl_scalapack_lp64.so(pzlatrd_+0xdce)[0x2b758d5845ce]
>
> /opt/intel/composer_xe_2013_sp1.2.144/mkl/lib/intel64/
> libmkl_scalapack_lp64.so(pzhetrd_+0x721)[0x2b758d534801]
>
> /opt/intel/composer_xe_2013_sp1.2.144/mkl/lib/intel64/
> libmkl_scalapack_lp64.so(pzheevd_+0x7e9)[0x2b758d524d79]
>
> /mnt/oss/sarkar_au/install/siesta-3.2-pl3/Obj/transiesta[0x4d0eb9]
>
> /mnt/oss/sarkar_au/install/siesta-3.2-pl3/Obj/transiesta[0x43b51e]
>
> /mnt/oss/sarkar_au/install/siesta-3.2-pl3/Obj/transiesta[0x42a2af]
>
> /mnt/oss/sarkar_au/install/siesta-3.2-pl3/Obj/transiesta[0x4ec9f3]
>
> /mnt/oss/sarkar_au/install/siesta-3.2-pl3/Obj/transiesta[0x5085d5]
>
> /mnt/oss/sarkar_au/install/siesta-3.2-pl3/Obj/transiesta[0x508768]
>
> /mnt/oss/sarkar_au/install/siesta-3.2-pl3/Obj/transiesta[0x6fb60a]
>
> /lib64/libc.so.6(__libc_start_main+0xfd)[0x365ba1ecdd]
>
> /mnt/oss/sarkar_au/install/siesta-3.2-pl3/Obj/transiesta[0x404d79]
>
>
>
> ……
>
> *Question  1:*
>
> Could anyone please help me to solve this problem? Any help will be
> greatfully acknowledged.
>
> Here I am attaching the input, output and error file  for siesta
> installation for detailed information.
>
>
> Thanking you.
>
>
> Sincerely
>
>
> Barnali Bhattachrya
>
> Ph. D. student, Department of Physics
>
> Assam University, Silchar
>
>
>
>


-- 



*Senior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

[SIESTA-L] Stoner Parameter

[Suman Chowdhury]

Dear SIESTA user, does anyone know how to calculate the Stoner-Exchange
parameter from SIESTA??

-- 



*Senior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

[SIESTA-L] mobility, effective mass etc..

[Suman Chowdhury]

Dear SIESTA use,
Does anyone know how to calculate effective mass, mobility, thermal and
electrical conductivity, Seebeck coefficient through siesta simulation???

-- 



*Senior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

Re: [SIESTA-L] problem with gnubands

[Suman Chowdhury]

you can get them from published paper..

On Sep 10, 2016 4:25 PM, "Uttam Paliwal" <uttam...@gmail.com> wrote:

> is there any resource or website from where  can get the above data
>
> On Sat, Sep 10, 2016 at 12:30 PM, Suman Chowdhury <
> sumanchowdhur...@gmail.com> wrote:
>
>> For that you need to provide two quantities. The lattice vectors and the
>> unit cell coordinate. That is all to specify the crystal structure.
>>
>> On Sat, Sep 10, 2016 at 12:10 PM, Uttam Paliwal <uttam...@gmail.com>
>> wrote:
>>
>>> then how to specify the crystal structures
>>>
>>> On Sat, Sep 10, 2016 at 12:00 PM, Suman Chowdhury <
>>> sumanchowdhur...@gmail.com> wrote:
>>>
>>>> Dear Uttam,
>>>>
>>>> In SIESTA there is no option to provide space group number as far as I
>>>> know.
>>>>
>>>> On Sat, Sep 10, 2016 at 11:57 AM, Uttam Paliwal <uttam...@gmail.com>
>>>> wrote:
>>>>
>>>>> thanks prof Alberto
>>>>>
>>>>> Kindly clear my another small doubt. In siesta where we provide the
>>>>> space group number eg for Si the space group is #216 zinc blende type
>>>>> crystal structure.
>>>>>
>>>>> thanks and regards
>>>>>
>>>>> On Fri, Sep 9, 2016 at 6:16 PM, Alberto Garcia <alber...@icmab.es>
>>>>> wrote:
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> Please note that the gnubands program is intended to plot band
>>>>>> structures, i.e., energy values along *lines* in the BZ. The relevant 
>>>>>> data
>>>>>> is obtained with the "BandLines" option in Siesta. If you use the
>>>>>> "BandPoints" option you get information about a set of *points* in the 
>>>>>> BZ,
>>>>>> which is not appropriate for a band structure plot.
>>>>>>
>>>>>> It is perhaps unfortunate that the file extension is the same for
>>>>>> both cases. We make a note to change it.
>>>>>>
>>>>>>  Regards,
>>>>>>
>>>>>>   Alberto
>>>>>>
>>>>>> On 09 Sep 2016, at 12:27, Uttam Paliwal <uttam...@gmail.com> wrote:
>>>>>>
>>>>>> > hi
>>>>>> > I am using siesta-4.1-b1 and running the si_bandpoints.bands files
>>>>>> with gnubands. Then i found following error message on cygwin (windows 7)
>>>>>> terminal
>>>>>> >
>>>>>> > 
>>>>>> ---
>>>>>> >
>>>>>> > hp@jks /cygdrive/f/siesta-4.1-b1/util/bands
>>>>>> > $ ./gnubands < si_bandpoints.bands > up.dat
>>>>>> >
>>>>>> > At line 143 of file gnubands.f90 (unit = 5, file = 'stdin')
>>>>>> > Fortran runtime error: Bad integer for item 1 in list input
>>>>>> >
>>>>>> > -- 
>>>>>> --
>>>>>> >
>>>>>> > i am attetching the gnubands.f90, makefile, si_bandpoints files
>>>>>> herewith.
>>>>>> >
>>>>>> > kindly provide suggestions
>>>>>> > Uttam Paliwal
>>>>>> > Assistant Professor
>>>>>> > Department of Physics
>>>>>> > J.N.V. University
>>>>>> > Jodhpur (India)
>>>>>> > Phone- 7597908441
>>>>>> > 
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Uttam Paliwal
>>>>> *Assistant Professor*
>>>>> Department of Physics
>>>>> J.N.V. University
>>>>> Jodhpur (India)
>>>>> Phone- 7597908441
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>>
>>>>
>>>>
>>>> *Senior research fellow Dept. of Physics, University of
>>>> Calcutta Kolkata- 79, West Bengal, India.*
>>>> * Ph no-+91-9830512232*
>>>>
>>>>
>>>
>>>
>>> --
>>> Uttam Paliwal
>>> *Assistant Professor*
>>> Department of Physics
>>> J.N.V. University
>>> Jodhpur (India)
>>> Phone- 7597908441
>>>
>>
>>
>>
>> --
>>
>>
>>
>> *Senior research fellow Dept. of Physics, University of Calcutta Kolkata-
>> 79, West Bengal, India.*
>> * Ph no-+91-9830512232*
>>
>>
>
>
> --
> Uttam Paliwal
> *Assistant Professor*
> Department of Physics
> J.N.V. University
> Jodhpur (India)
> Phone- 7597908441
>

Re: [SIESTA-L] problem with gnubands

[Suman Chowdhury]

For that you need to provide two quantities. The lattice vectors and the
unit cell coordinate. That is all to specify the crystal structure.

On Sat, Sep 10, 2016 at 12:10 PM, Uttam Paliwal <uttam...@gmail.com> wrote:

> then how to specify the crystal structures
>
> On Sat, Sep 10, 2016 at 12:00 PM, Suman Chowdhury <
> sumanchowdhur...@gmail.com> wrote:
>
>> Dear Uttam,
>>
>> In SIESTA there is no option to provide space group number as far as I
>> know.
>>
>> On Sat, Sep 10, 2016 at 11:57 AM, Uttam Paliwal <uttam...@gmail.com>
>> wrote:
>>
>>> thanks prof Alberto
>>>
>>> Kindly clear my another small doubt. In siesta where we provide the
>>> space group number eg for Si the space group is #216 zinc blende type
>>> crystal structure.
>>>
>>> thanks and regards
>>>
>>> On Fri, Sep 9, 2016 at 6:16 PM, Alberto Garcia <alber...@icmab.es>
>>> wrote:
>>>
>>>> Hi,
>>>>
>>>> Please note that the gnubands program is intended to plot band
>>>> structures, i.e., energy values along *lines* in the BZ. The relevant data
>>>> is obtained with the "BandLines" option in Siesta. If you use the
>>>> "BandPoints" option you get information about a set of *points* in the BZ,
>>>> which is not appropriate for a band structure plot.
>>>>
>>>> It is perhaps unfortunate that the file extension is the same for both
>>>> cases. We make a note to change it.
>>>>
>>>>  Regards,
>>>>
>>>>   Alberto
>>>>
>>>> On 09 Sep 2016, at 12:27, Uttam Paliwal <uttam...@gmail.com> wrote:
>>>>
>>>> > hi
>>>> > I am using siesta-4.1-b1 and running the si_bandpoints.bands files
>>>> with gnubands. Then i found following error message on cygwin (windows 7)
>>>> terminal
>>>> >
>>>> > 
>>>> ---
>>>> >
>>>> > hp@jks /cygdrive/f/siesta-4.1-b1/util/bands
>>>> > $ ./gnubands < si_bandpoints.bands > up.dat
>>>> >
>>>> > At line 143 of file gnubands.f90 (unit = 5, file = 'stdin')
>>>> > Fortran runtime error: Bad integer for item 1 in list input
>>>> >
>>>> > -- 
>>>> --
>>>> >
>>>> > i am attetching the gnubands.f90, makefile, si_bandpoints files
>>>> herewith.
>>>> >
>>>> > kindly provide suggestions
>>>> > Uttam Paliwal
>>>> > Assistant Professor
>>>> > Department of Physics
>>>> > J.N.V. University
>>>> > Jodhpur (India)
>>>> > Phone- 7597908441
>>>> > 
>>>>
>>>>
>>>
>>>
>>> --
>>> Uttam Paliwal
>>> *Assistant Professor*
>>> Department of Physics
>>> J.N.V. University
>>> Jodhpur (India)
>>> Phone- 7597908441
>>>
>>
>>
>>
>> --
>>
>>
>>
>> *Senior research fellow Dept. of Physics, University of Calcutta Kolkata-
>> 79, West Bengal, India.*
>> * Ph no-+91-9830512232*
>>
>>
>
>
> --
> Uttam Paliwal
> *Assistant Professor*
> Department of Physics
> J.N.V. University
> Jodhpur (India)
> Phone- 7597908441
>



-- 



*Senior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

Re: [SIESTA-L] problem with gnubands

[Suman Chowdhury]

Dear Uttam,

In SIESTA there is no option to provide space group number as far as I know.

On Sat, Sep 10, 2016 at 11:57 AM, Uttam Paliwal  wrote:

> thanks prof Alberto
>
> Kindly clear my another small doubt. In siesta where we provide the space
> group number eg for Si the space group is #216 zinc blende type crystal
> structure.
>
> thanks and regards
>
> On Fri, Sep 9, 2016 at 6:16 PM, Alberto Garcia  wrote:
>
>> Hi,
>>
>> Please note that the gnubands program is intended to plot band
>> structures, i.e., energy values along *lines* in the BZ. The relevant data
>> is obtained with the "BandLines" option in Siesta. If you use the
>> "BandPoints" option you get information about a set of *points* in the BZ,
>> which is not appropriate for a band structure plot.
>>
>> It is perhaps unfortunate that the file extension is the same for both
>> cases. We make a note to change it.
>>
>>  Regards,
>>
>>   Alberto
>>
>> On 09 Sep 2016, at 12:27, Uttam Paliwal  wrote:
>>
>> > hi
>> > I am using siesta-4.1-b1 and running the si_bandpoints.bands files with
>> gnubands. Then i found following error message on cygwin (windows 7)
>> terminal
>> >
>> > ---
>> >
>> > hp@jks /cygdrive/f/siesta-4.1-b1/util/bands
>> > $ ./gnubands < si_bandpoints.bands > up.dat
>> >
>> > At line 143 of file gnubands.f90 (unit = 5, file = 'stdin')
>> > Fortran runtime error: Bad integer for item 1 in list input
>> >
>> > -- 
>> --
>> >
>> > i am attetching the gnubands.f90, makefile, si_bandpoints files
>> herewith.
>> >
>> > kindly provide suggestions
>> > Uttam Paliwal
>> > Assistant Professor
>> > Department of Physics
>> > J.N.V. University
>> > Jodhpur (India)
>> > Phone- 7597908441
>> > 
>>
>>
>
>
> --
> Uttam Paliwal
> *Assistant Professor*
> Department of Physics
> J.N.V. University
> Jodhpur (India)
> Phone- 7597908441
>



-- 



*Senior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

[SIESTA-L] interband or intraband

[Suman Chowdhury]

> Dear Users,
> I am really confused about one issue. While calculating optical
properties through SIESTA, what we get. Are these obtained data due to
interband transition or intraband transition. In one paper I have seen they
have separately calculate intraband and interband optical properties by
using siesta. Can anyone please help me to clear this confusion.
>
> From
>
> Suman
>
> --
> Senior research fellow
>  Dept. of Physics,
>  University of Calcutta
>  Kolkata- 79, West Bengal, India.
>  Ph no-+91-9830512232
>

[SIESTA-L] interband or intraband

[Suman Chowdhury]

Dear Users,
I am really confused about one issue. While calculating optical properties
through SIESTA, what we get. Are these obtained data due to interband
transition or intraband transition. In one paper I have seen they have
separately calculate intraband and interband optical properties by using
siesta. Can anyone please help me to clear this confusion.

From

Suman

-- 



*Senior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

Re: [SIESTA-L] Real and imaginary part of the wavefunction as a function of energy

[Suman Chowdhury]

Dear Prof. Junquera,

Thank you sooo much for your reply. Sir can I get your email id.
Because "javier.junquera
-- unican es" one is not working. I want to ask you some siesta related
question and also some post doc related questions. If you do not have any
problem, can you please provide me your email id..

Thanking you

On Sat, Jun 4, 2016 at 4:57 PM, Javier Junquera 
wrote:

>
>  Dear Suman:
>
>  Take a look to the self-explained exercise at:
>
>  http://personales.unican.es/junqueraj
>
>  and follow the links:
>
>  - A self-explained Siesta tutorial
>  - Set of self-explained Siesta exercises
>  - Computing structural and electronic properties of materials
>  - Exercise 2: analysis of the charge density in real space
>
>  Pay special attention to the variables:
>
>  WriteWaveFunctions
>  %block WaveFuncKPoints
>
>  Read their meaning and other related variables in the Siesta User Guide.
>
>  Hope this helps,
>
> Javier
>
>
>
>
>
> Dear siesta user.
>
> I need the real and imaginary part of the wavefunction as a function of
> energy. Is it possible to retrieve separately the real and imaginary part
> of the wavefucntion from siesta. Please look into the following paper for
> this:
>
> Raymond Atta Fynn et al PRB 69 085207 (2004)
>
> --
>
>
>
> *Senior research fellow Dept. of Physics, University of Calcutta Kolkata-
> 79, West Bengal, India.*
> * Ph no-+91-9830512232*
>
>
>


-- 



*Senior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

[SIESTA-L] Real and imaginary part of the wavefunction as a function of energy

[Suman Chowdhury]

Dear siesta user.

I need the real and imaginary part of the wavefunction as a function of
energy. Is it possible to retrieve separately the real and imaginary part
of the wavefucntion from siesta. Please look into the following paper for
this:

Raymond Atta Fynn et al PRB 69 085207 (2004)

-- 



*Senior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

Re: [SIESTA-L] How to get simple stm images from plstm.f

[Suman Chowdhury]

It is very easy..it is absolutely applicable to linux...you have to
download it by a software called wine...
First install wine then install the .exe file thorugh wine...

On Wed, Nov 11, 2015 at 2:49 PM, Sukanya Ghosh <ghosh.sukanya1...@gmail.com>
wrote:

> Dear Suman,
> I have downloaded WSxM using the link you have sent. Can you please tell
> me how to install it ?
>
> On Wed, Nov 11, 2015 at 2:42 PM, Sukanya Ghosh <
> ghosh.sukanya1...@gmail.com> wrote:
>
>> Dear Suman,
>> Is WSxM applicable to linux ? I thought its is useful for Windows
>>
>> On Wed, Nov 11, 2015 at 1:49 PM, Suman Chowdhury <
>> sumanchowdhur...@gmail.com> wrote:
>>
>>> Dear Sukanya,
>>> For this please download this software from the following link. It is
>>> very easy to download and install and also very easy to visualize STM
>>> images from the RHO file generated by SIESTA.
>>>
>>> http://www.wsxmsolutions.com/
>>>
>>> On Wed, Nov 11, 2015 at 1:17 PM, Sukanya Ghosh <
>>> ghosh.sukanya1...@gmail.com> wrote:
>>>
>>>> Dear all,
>>>>
>>>> I want to plot stm images using siesta. I want to plot simple stm
>>>> images. Can any of you please tell me how to run the executable from
>>>> plstm.f to get the out files.
>>>>
>>>> Any suggestion is highly appreciated.
>>>>
>>>>
>>>> Thanking you,
>>>>
>>>> SUKANYA GHOSH
>>>>
>>>
>>>
>>>
>>> --
>>>
>>>
>>>
>>> *Senior research fellow Dept. of Physics, University of
>>> Calcutta Kolkata- 79, West Bengal, India.*
>>> * Ph no-+91-9830512232*
>>>
>>>
>>
>


-- 



*Senior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

[SIESTA-L] layers is charge density plot

[Suman Chowdhury]

Dear siesta user,
I am trying to plot the charge density of a monolayer system by using
rho2xsf utility and then visualize by using xcrysden. I have observed that
depending on the spanning vector, the layer number depends. I know the
extra atoms are the mirror images of the original structure. But among all
the layers, one structure is different from rest of the structures. I am
now confused which one is the original. Can anyone help me...

-- 



*Senior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

[SIESTA-L] MD Visualize in Linux machine

[Suman Chowdhury]

Dear SIESTA User,
I want to do molecular dynamics simulation. I have found that after the
simulation the program generates three files,
SystemLabel.MD,SystemLabel.MDE and SystemLabel.ANI.Can you tell me how
to visualize these files. I am unable to find any suitable software for
this in linux...

-- 



*Senior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

Re: [SIESTA-L] Problem using gnubands

[Suman Chowdhury]

Try this one
./gnubands si_bandpoints.bands si_bands.dat

On Thu, Jul 23, 2015 at 1:47 PM, jv sharma jvnano...@gmail.com wrote:

 I get like this:

 jv@jv-desktop:~$ cd siesta-trunk-462/Util/Bands
 jv@jv-desktop:~/siesta-trunk-462/Util/Bands$ ./gnubands
 si_bandpoints.bands si_bands.dat
 At line 27 of file gnubands.f (unit = 5, file = 'stdin')
 Fortran runtime error: Bad integer for item 1 in list input
 jv@jv-desktop:~/siesta-trunk-462/Util/Bands$

 I get like this, after trying with ./new.gnubands :

 jv@jv-desktop:~/siesta-trunk-462/Util/Bands$ ./new.gnubands
 si_bandpoints.bands si_bands.dat
 At line 128 of file new.gnubands.f90 (unit = 5, file = 'stdin')
 Fortran runtime error: Bad integer for item 1 in list input
 jv@jv-desktop:~/siesta-trunk-462/Util/Bands$


 On Thu, Jul 23, 2015 at 12:55 PM, Nick Papior nickpap...@gmail.com
 wrote:

 Try ./gnubands instead of gnubands.
  On 23 Jul 2015 06:28, jv sharma jvnano...@gmail.com wrote:

 Attached here the output. Thanks for the link on basics of linux.

 Regards,
 JVN.

 On Thu, Jul 23, 2015 at 2:06 AM, Nick Papior nickpap...@gmail.com
 wrote:

 Do this in the Bands directory (and supply the output to us).

 $ ls -l
 $ which gnubands
 $ make
 $ which gnubands

 Consider using the new.gnubands executable which can do several new
 things.

 Please read this:
 http://www.linfo.org/path_env_var.html and the links therein to get a
 basic grasp of linux.
 As you are a basic user of unix, this might shed some light of why
 things goes wrong, as well as providing some basic insights.


 2015-07-22 3:56 GMT+00:00 jv sharma jvnano...@gmail.com:

 Sorry, I could not catch your point, could you please elaborate?

 On Tue, Jul 21, 2015 at 11:13 PM, Nick Papior nickpap...@gmail.com
 wrote:

 It does not look like you are using the gnubands program in
 siesta-trunk-462, please assert you are...
 Line 27 is empty in siesta-trunk-462.

 2015-07-21 16:52 GMT+00:00 jv sharma jvnano...@gmail.com:

 Dear Users and Experts,

 I am new to Ubuntu and Siesta.
 I have installed siesta-trunk-462. While trying to convert
 si_bandpoints.bands from the Test, I get the following Fortran runtime
 error:

 jv@jv-desktop:~/siesta-trunk-462/Util/Bands$ gnubands
 si_bandpoints.bands si_bands.dat
 At line 27 of file gnubands.f (unit = 5, file = 'stdin')
 Fortran runtime error: Bad integer for item 1 in list input
 jv@jv-desktop:~/siesta-trunk-462/Util/Bands$

 I really don't know what to do. Could someone please suggest a
 working solution?
 Many thanks.

 Best regards,
 JVN Sarma.




 --
 Kind regards Nick





 --
 Kind regards Nick






-- 



*Senior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

Re: [SIESTA-L] Problem using gnubands

[Suman Chowdhury]

Don't give  after ./gnubands.

On Thu, Jul 23, 2015 at 2:01 PM, jv sharma jvnano...@gmail.com wrote:

 Got like this:

 jv@jv-desktop:~/siesta-trunk-462/Util/Bands$ make clean
 rm -f *.o *.mod new.gnubands eigfat2plot gnubands
 jv@jv-desktop:~/siesta-trunk-462/Util/Bands$ make
 f95  -c -g -O2   -DFC_HAVE_FLUSH -DFC_HAVE_ABORT -UMPI
 f2kcli.F90
 f95  -c -g -O2 m_getopts.f90
 f95  -c -g -O2 eigfat2plot.f90
 f95  -o eigfat2plot  m_getopts.o f2kcli.o  eigfat2plot.o
 f95  -c -g -O2 new.gnubands.f90
 f95  -o new.gnubands  m_getopts.o f2kcli.o  new.gnubands.o
 f95  -c -g -O2 gnubands.f
 f95  -o gnubands   gnubands.o
 jv@jv-desktop:~/siesta-trunk-462/Util/Bands$ ./gnubands
 si_bandpoints.bands si_bands.dat
 At line 37 of file gnubands.f (unit = 5, file = 'stdin')
 Fortran runtime error: Bad integer for item 1 in list input
 jv@jv-desktop:~/siesta-trunk-462/Util/Bands$

 Attached here the .bands file.

 On Thu, Jul 23, 2015 at 1:53 PM, Nick Papior nickpap...@gmail.com wrote:

 Do make clean, make, retry.
 Attach the band file.
 On 23 Jul 2015 10:19, jv sharma jvnano...@gmail.com wrote:

 I get like this:

 jv@jv-desktop:~$ cd siesta-trunk-462/Util/Bands
 jv@jv-desktop:~/siesta-trunk-462/Util/Bands$ ./gnubands
 si_bandpoints.bands si_bands.dat
 At line 27 of file gnubands.f (unit = 5, file = 'stdin')
 Fortran runtime error: Bad integer for item 1 in list input
 jv@jv-desktop:~/siesta-trunk-462/Util/Bands$

 I get like this, after trying with ./new.gnubands :

 jv@jv-desktop:~/siesta-trunk-462/Util/Bands$ ./new.gnubands
 si_bandpoints.bands si_bands.dat
 At line 128 of file new.gnubands.f90 (unit = 5, file = 'stdin')
 Fortran runtime error: Bad integer for item 1 in list input
 jv@jv-desktop:~/siesta-trunk-462/Util/Bands$


 On Thu, Jul 23, 2015 at 12:55 PM, Nick Papior nickpap...@gmail.com
 wrote:

 Try ./gnubands instead of gnubands.
  On 23 Jul 2015 06:28, jv sharma jvnano...@gmail.com wrote:

 Attached here the output. Thanks for the link on basics of linux.

 Regards,
 JVN.

 On Thu, Jul 23, 2015 at 2:06 AM, Nick Papior nickpap...@gmail.com
 wrote:

 Do this in the Bands directory (and supply the output to us).

 $ ls -l
 $ which gnubands
 $ make
 $ which gnubands

 Consider using the new.gnubands executable which can do several new
 things.

 Please read this:
 http://www.linfo.org/path_env_var.html and the links therein to get
 a basic grasp of linux.
 As you are a basic user of unix, this might shed some light of why
 things goes wrong, as well as providing some basic insights.


 2015-07-22 3:56 GMT+00:00 jv sharma jvnano...@gmail.com:

 Sorry, I could not catch your point, could you please elaborate?

 On Tue, Jul 21, 2015 at 11:13 PM, Nick Papior nickpap...@gmail.com
 wrote:

 It does not look like you are using the gnubands program in
 siesta-trunk-462, please assert you are...
 Line 27 is empty in siesta-trunk-462.

 2015-07-21 16:52 GMT+00:00 jv sharma jvnano...@gmail.com:

 Dear Users and Experts,

 I am new to Ubuntu and Siesta.
 I have installed siesta-trunk-462. While trying to convert
 si_bandpoints.bands from the Test, I get the following Fortran runtime
 error:

 jv@jv-desktop:~/siesta-trunk-462/Util/Bands$ gnubands
 si_bandpoints.bands si_bands.dat
 At line 27 of file gnubands.f (unit = 5, file = 'stdin')
 Fortran runtime error: Bad integer for item 1 in list input
 jv@jv-desktop:~/siesta-trunk-462/Util/Bands$

 I really don't know what to do. Could someone please suggest a
 working solution?
 Many thanks.

 Best regards,
 JVN Sarma.




 --
 Kind regards Nick





 --
 Kind regards Nick







-- 



*Senior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

Re: [SIESTA-L] Problem using gnubands

[Suman Chowdhury]

Attach the file
si_bands.dat

On Thu, Jul 23, 2015 at 2:06 PM, jv sharma jvnano...@gmail.com wrote:

 Hi,

 After giving this, nothing happened, just the cursor starts blinking in
 the next line:
 jv@jv-desktop:~$ cd siesta-trunk-462/Util/Bands
 jv@jv-desktop:~/siesta-trunk-462/Util/Bands$ ./gnubands
 si_bandpoints.bands si_bands.dat

 A blank si_bands.dat is also created in the directory.

 On Thu, Jul 23, 2015 at 1:56 PM, Suman Chowdhury 
 sumanchowdhur...@gmail.com wrote:

 Try this one
 ./gnubands si_bandpoints.bands si_bands.dat

 On Thu, Jul 23, 2015 at 1:47 PM, jv sharma jvnano...@gmail.com wrote:

 I get like this:

 jv@jv-desktop:~$ cd siesta-trunk-462/Util/Bands
 jv@jv-desktop:~/siesta-trunk-462/Util/Bands$ ./gnubands
 si_bandpoints.bands si_bands.dat
 At line 27 of file gnubands.f (unit = 5, file = 'stdin')
 Fortran runtime error: Bad integer for item 1 in list input
 jv@jv-desktop:~/siesta-trunk-462/Util/Bands$

 I get like this, after trying with ./new.gnubands :

 jv@jv-desktop:~/siesta-trunk-462/Util/Bands$ ./new.gnubands
 si_bandpoints.bands si_bands.dat
 At line 128 of file new.gnubands.f90 (unit = 5, file = 'stdin')
 Fortran runtime error: Bad integer for item 1 in list input
 jv@jv-desktop:~/siesta-trunk-462/Util/Bands$


 On Thu, Jul 23, 2015 at 12:55 PM, Nick Papior nickpap...@gmail.com
 wrote:

 Try ./gnubands instead of gnubands.
  On 23 Jul 2015 06:28, jv sharma jvnano...@gmail.com wrote:

 Attached here the output. Thanks for the link on basics of linux.

 Regards,
 JVN.

 On Thu, Jul 23, 2015 at 2:06 AM, Nick Papior nickpap...@gmail.com
 wrote:

 Do this in the Bands directory (and supply the output to us).

 $ ls -l
 $ which gnubands
 $ make
 $ which gnubands

 Consider using the new.gnubands executable which can do several new
 things.

 Please read this:
 http://www.linfo.org/path_env_var.html and the links therein to get
 a basic grasp of linux.
 As you are a basic user of unix, this might shed some light of why
 things goes wrong, as well as providing some basic insights.


 2015-07-22 3:56 GMT+00:00 jv sharma jvnano...@gmail.com:

 Sorry, I could not catch your point, could you please elaborate?

 On Tue, Jul 21, 2015 at 11:13 PM, Nick Papior nickpap...@gmail.com
 wrote:

 It does not look like you are using the gnubands program in
 siesta-trunk-462, please assert you are...
 Line 27 is empty in siesta-trunk-462.

 2015-07-21 16:52 GMT+00:00 jv sharma jvnano...@gmail.com:

 Dear Users and Experts,

 I am new to Ubuntu and Siesta.
 I have installed siesta-trunk-462. While trying to convert
 si_bandpoints.bands from the Test, I get the following Fortran runtime
 error:

 jv@jv-desktop:~/siesta-trunk-462/Util/Bands$ gnubands
 si_bandpoints.bands si_bands.dat
 At line 27 of file gnubands.f (unit = 5, file = 'stdin')
 Fortran runtime error: Bad integer for item 1 in list input
 jv@jv-desktop:~/siesta-trunk-462/Util/Bands$

 I really don't know what to do. Could someone please suggest a
 working solution?
 Many thanks.

 Best regards,
 JVN Sarma.




 --
 Kind regards Nick





 --
 Kind regards Nick






 --



 *Senior research fellow Dept. of Physics, University of Calcutta Kolkata-
 79, West Bengal, India.*
 * Ph no-+91-9830512232*





-- 



*Senior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

Re: [SIESTA-L] rho2xsf not working

[Suman Chowdhury]

Denchar also is not working..Instead of having the .DIM file in the working
directory the program is unable to read the .DIM file...

On Mon, Jul 6, 2015 at 4:42 PM, fariborz nemati fariborz.nem...@gmail.com
wrote:

 Need I a denchar output before use of the rho2xsf program?
 On 5 Jul 2015 13:01, Suman Chowdhury sumanchowdhur...@gmail.com wrote:

 Dear SIESTA User : Now another problem arises..While I am trying to plot
 the charge density using rho2xsf program it is showing Program received
 signal SIGFPE: Floating-point exception - erroneous arithmetic operation.

 Backtrace for this error:
 #0 0xB76B8163
 #1 0xB76B8800
 #2 0xB77C23FF
 #3 0x804CA75 in intpl04_ at intpl04.f:42
 #4 0x804AEEE in rho2xsf at rho2xsf.f:216
 Floating point exception
 Can anyone help me to solve this error..






-- 



*Senior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

[SIESTA-L] rho2xsf not working

[Suman Chowdhury]

Dear SIESTA User : Now another problem arises..While I am trying to plot
the charge density using rho2xsf program it is showing Program received
signal SIGFPE: Floating-point exception - erroneous arithmetic operation.

Backtrace for this error:
#0 0xB76B8163
#1 0xB76B8800
#2 0xB77C23FF
#3 0x804CA75 in intpl04_ at intpl04.f:42
#4 0x804AEEE in rho2xsf at rho2xsf.f:216
Floating point exception
Can anyone help me to solve this error..

[SIESTA-L] Unable to compile denchar

[Suman Chowdhury]

Dear SIESTA user : While I am trying to compile denchar by typing make
denchar it is giving me an error  No rule to make target
`../../../../Obj/arch.make'. Stop. . Can anyone help me in this regard to
solve the problem

-- 



*Senior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

[SIESTA-L] Dielectric function

[Suman Chowdhury]

Dear User,
I have a question. By definition the imaginary part of the dielectric
function is positive and also it can be seen from its mathematical
expression that at zero frequency it should be zero. Right now I am
studying some structure where sometimes I am getting 0 at 0 frequency and
sometimes I am not getting 0 at 0 frequency. It is coming of the order of
10. Do any of you know what is the reason behind it.

-- 



*Senior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

Re: [SIESTA-L] partial band structure

[Suman Chowdhury]

Thanks a lot Prof Artacho..I will now work very hard to learn the fatband..

On Mon, Apr 27, 2015 at 1:02 PM, Emilio Artacho ea...@cam.ac.uk wrote:

 fatbands gives you that kind of information

 E

 On Apr 27, 2015, at 9:24 AM, Suman Chowdhury wrote:

 My question is, is it possible to identify the bands arising out due to
 transition of electron from a particular orbital..Suppose I want to
 identify the bands due to the pi bonded p_z orbital of graphene. Is it
 possible in siesta..

 On Mon, Apr 27, 2015 at 12:41 PM, Emilio Artacho ea...@cam.ac.uk wrote:

 Not sure what you mean, maybe you are talking about the
 utility fatbands in the Util directory?

 Emilio

 On Apr 27, 2015, at 8:25 AM, Suman Chowdhury wrote:

 I am not talking about partial DOS...I want to know about partial band
 structure...I know how to calculate partial DOS by using fmpdos.f...

 On Mon, Apr 27, 2015 at 11:42 AM, fthe...@iesl.forth.gr wrote:

 Yes. It is easy to be done, thanks to Andrei Postnikov's utility
 fmpdos.f.
 You have to use as input the .PDOS output file of SIESTA and another
 file where you include details on which partial DOS you want (atom and/or
 orbitals).


  Dear User
  As we all know partial density of states can be calculated easily by
 using
  SIESTA...But in many papers I have seen partial band structure that is
  which band is due to which orbital...is there any way to do that in
  SIESTA..
 
  --
 
 
 
  *Senior research fellow Dept. of Physics, University of Calcutta
 Kolkata-
  79, West Bengal, India.*
  * Ph no-+91-9830512232*
 


 *
 Dr Zacharias G. Fthenakis
 Research Associate
 Institute of Electronic Structure and Laser (I.E.S.L.)
 Foundation for Research and Technology Hellas (FO.R.T.H.)
 Vassilika Vouton P.O. Box 1527 71003 Heraklion Crete Greece
 Phone +30 2810 391824
 FAX   +30 2810 391305
 webpage: http://esperia.iesl.forth.gr/~fthenak
 **




 --



 *Senior research fellow Dept. of Physics, University of Calcutta Kolkata-
 79, West Bengal, India.*
 * Ph no-+91-9830512232*


 --
 Emilio Artacho

 CIC nanoGUNE Consolider, and Cavendish Laboratory, University of Cambridge
 Tolosa Hiribidea 76, E-20018 Donostia - San Sebastián, Spain,
 e.arta...@nanogune.eu, +34 943 574039, http://theory.nanogune.eu




 --



 *Senior research fellow Dept. of Physics, University of Calcutta Kolkata-
 79, West Bengal, India.*
 * Ph no-+91-9830512232*


 --
 Emilio Artacho

 CIC nanoGUNE Consolider, and Cavendish Laboratory, University of Cambridge
 Tolosa Hiribidea 76, E-20018 Donostia - San Sebastián, Spain,
 e.arta...@nanogune.eu, +34 943 574039, http://theory.nanogune.eu




-- 



*Senior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

Re: [SIESTA-L] partial band structure

[Suman Chowdhury]

I am not talking about partial DOS...I want to know about partial band
structure...I know how to calculate partial DOS by using fmpdos.f...

On Mon, Apr 27, 2015 at 11:42 AM, fthe...@iesl.forth.gr wrote:

 Yes. It is easy to be done, thanks to Andrei Postnikov's utility fmpdos.f.
 You have to use as input the .PDOS output file of SIESTA and another
 file where you include details on which partial DOS you want (atom and/or
 orbitals).


  Dear User
  As we all know partial density of states can be calculated easily by
 using
  SIESTA...But in many papers I have seen partial band structure that is
  which band is due to which orbital...is there any way to do that in
  SIESTA..
 
  --
 
 
 
  *Senior research fellow Dept. of Physics, University of Calcutta Kolkata-
  79, West Bengal, India.*
  * Ph no-+91-9830512232*
 


 *
 Dr Zacharias G. Fthenakis
 Research Associate
 Institute of Electronic Structure and Laser (I.E.S.L.)
 Foundation for Research and Technology Hellas (FO.R.T.H.)
 Vassilika Vouton P.O. Box 1527 71003 Heraklion Crete Greece
 Phone +30 2810 391824
 FAX   +30 2810 391305
 webpage: http://esperia.iesl.forth.gr/~fthenak
 **




-- 



*Senior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

Re: [SIESTA-L] partial band structure

[Suman Chowdhury]

My question is, is it possible to identify the bands arising out due to
transition of electron from a particular orbital..Suppose I want to
identify the bands due to the pi bonded p_z orbital of graphene. Is it
possible in siesta..

On Mon, Apr 27, 2015 at 12:41 PM, Emilio Artacho ea...@cam.ac.uk wrote:

 Not sure what you mean, maybe you are talking about the
 utility fatbands in the Util directory?

 Emilio

 On Apr 27, 2015, at 8:25 AM, Suman Chowdhury wrote:

 I am not talking about partial DOS...I want to know about partial band
 structure...I know how to calculate partial DOS by using fmpdos.f...

 On Mon, Apr 27, 2015 at 11:42 AM, fthe...@iesl.forth.gr wrote:

 Yes. It is easy to be done, thanks to Andrei Postnikov's utility fmpdos.f.
 You have to use as input the .PDOS output file of SIESTA and another
 file where you include details on which partial DOS you want (atom and/or
 orbitals).


  Dear User
  As we all know partial density of states can be calculated easily by
 using
  SIESTA...But in many papers I have seen partial band structure that is
  which band is due to which orbital...is there any way to do that in
  SIESTA..
 
  --
 
 
 
  *Senior research fellow Dept. of Physics, University of Calcutta
 Kolkata-
  79, West Bengal, India.*
  * Ph no-+91-9830512232*
 


 *
 Dr Zacharias G. Fthenakis
 Research Associate
 Institute of Electronic Structure and Laser (I.E.S.L.)
 Foundation for Research and Technology Hellas (FO.R.T.H.)
 Vassilika Vouton P.O. Box 1527 71003 Heraklion Crete Greece
 Phone +30 2810 391824
 FAX   +30 2810 391305
 webpage: http://esperia.iesl.forth.gr/~fthenak
 **




 --



 *Senior research fellow Dept. of Physics, University of Calcutta Kolkata-
 79, West Bengal, India.*
 * Ph no-+91-9830512232*


 --
 Emilio Artacho

 CIC nanoGUNE Consolider, and Cavendish Laboratory, University of Cambridge
 Tolosa Hiribidea 76, E-20018 Donostia - San Sebastián, Spain,
 e.arta...@nanogune.eu, +34 943 574039, http://theory.nanogune.eu




-- 



*Senior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

[SIESTA-L] partial band structure

[Suman Chowdhury]

Dear User
As we all know partial density of states can be calculated easily by using
SIESTA...But in many papers I have seen partial band structure that is
which band is due to which orbital...is there any way to do that in SIESTA..

-- 



*Senior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

Re: [SIESTA-L] negative PDOS

[Suman Chowdhury]

Can you provide us any reference..

On Sun, Apr 12, 2015 at 1:23 PM, fthe...@iesl.forth.gr wrote:

 This is a well known problem, but has not to do with SIESTA. It has to
 do with the physical meaning of the decomposition of DOS to PDOS. If you
 decompose to orbitals with different orientation you may probably not have
 those problems.

 Zacharias Fthenakis

  Dear siesta users,
  Has any one encountered the problem of negative value of projected DOS
  which is calculated with the mprop utility? It seems quite unreasonable
  for me, any ideas how this come out?
 
  Best regards,
  Bing


 *
 Dr Zacharias G. Fthenakis
 Research Associate
 Institute of Electronic Structure and Laser (I.E.S.L.)
 Foundation for Research and Technology Hellas (FO.R.T.H.)
 Vassilika Vouton P.O. Box 1527 71003 Heraklion Crete Greece
 Phone +30 2810 391824
 FAX   +30 2810 391305
 webpage: http://esperia.iesl.forth.gr/~fthenak
 **




-- 



*Senior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

Re: [SIESTA-L] negative PDOS

[Suman Chowdhury]

I got the negative values of the PDOS while using double zeta polarized
basis set implemented within the SIESTA...Are these basis sets
non-orthogonal?

On Sun, Apr 12, 2015 at 1:40 PM, Emilio Artacho ea...@cam.ac.uk wrote:

 The mentioned well-known problem is related with
 the use of non-orthogonal basis sets. For
 orthogonal ones the PDOS is definite positive,
 which is what people expect. But for
 non-orthogonal ones that is not the case
 (although negatve values tend to be small
 since the diagonal bit dominates and that one
 is positive)

 Emilio

 --
 Emilio Artacho
 CIC Nanogune Consolider, and Cavendish Laboratory, University of Cambridge
 Tolosa Hiribidea 76, E-20018 Donostia - San Sebastián, Spain,
 e.arta...@nanogune.eu, +34 943 574 4000, http://theory.nanogune.eu

 On 12 Apr 2015, at 09:53, fthe...@iesl.forth.gr wrote:

  This is a well known problem, but has not to do with SIESTA. It has to
  do with the physical meaning of the decomposition of DOS to PDOS. If you
  decompose to orbitals with different orientation you may probably not
 have
  those problems.
 
  Zacharias Fthenakis
 
  Dear siesta users,
  Has any one encountered the problem of negative value of projected DOS
  which is calculated with the mprop utility? It seems quite unreasonable
  for me, any ideas how this come out?
 
  Best regards,
  Bing
 
 
  *
  Dr Zacharias G. Fthenakis
  Research Associate
  Institute of Electronic Structure and Laser (I.E.S.L.)
  Foundation for Research and Technology Hellas (FO.R.T.H.)
  Vassilika Vouton P.O. Box 1527 71003 Heraklion Crete Greece
  Phone +30 2810 391824
  FAX   +30 2810 391305
  webpage: http://esperia.iesl.forth.gr/~fthenak
  **
 




-- 



*Senior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

Re: [SIESTA-L] negative PDOS

[Suman Chowdhury]

Thanks for the post...I have also encountered the same problem...Still I
don't understand what is the reason for this unreasonable PDOS...

On Sun, Apr 12, 2015 at 1:01 PM, BingHuang hbdft2...@gmail.com wrote:

 Dear siesta users,

 Has any one encountered the problem of negative value of projected DOS
 which is calculated with the mprop utility? It seems quite unreasonable for
 me, any ideas how this come out?


 Best regards,

 Bing




-- 



*Senior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

Re: [SIESTA-L] negative PDOS

[Suman Chowdhury]

In this situation my question is suppose I have obtained negative PDOS for
a particular structure. If I will give this values in the manuscript and
send to any journal for publication and if the referee will ask about this
then what should I do?

On Sun, Apr 12, 2015 at 3:05 PM, fthe...@iesl.forth.gr wrote:

 I fully agree with Emilio.
 The fact that you find negative PDOS even for s orbitals has to do with
 the interactions between those s-orbitals with the orbitals of the other
 atoms, which might give small negative contributions. If you select
 different orientations of the atoms, you may have different contributions
 from the atomic orbitals (since their orientation will not change) and
 those negative contributions could (hopefully) absorbed by other positive
 contributions. Thus, the PDOS will (hopefully) not be negative. Obviously,
 there is not any physical meaning for a negative PDOS.
 The problem comes from the physical meaning assigned to the PDOS, which is
 exactly the same with the physical meaning assigned to the Mullicken
 charges.
 Maybe you can get some answers in Roald Hoffmann's book Solids and
 Surfaces.

 Zacharias Fthenakis

  The mentioned well-known problem is related with
  the use of non-orthogonal basis sets. For
  orthogonal ones the PDOS is definite positive,
  which is what people expect. But for
  non-orthogonal ones that is not the case
  (although negatve values tend to be small
  since the diagonal bit dominates and that one
  is positive)
 
  Emilio
 
  --
  Emilio Artacho
  CIC Nanogune Consolider, and Cavendish Laboratory, University of
 Cambridge
  Tolosa Hiribidea 76, E-20018 Donostia - San Sebastián, Spain,
  e.arta...@nanogune.eu, +34 943 574 4000, http://theory.nanogune.eu
 
  On 12 Apr 2015, at 09:53, fthe...@iesl.forth.gr wrote:
 
  This is a well known problem, but has not to do with SIESTA. It has to
  do with the physical meaning of the decomposition of DOS to PDOS. If you
  decompose to orbitals with different orientation you may probably not
  have
  those problems.
 
  Zacharias Fthenakis
 
  Dear siesta users,
  Has any one encountered the problem of negative value of projected DOS
  which is calculated with the mprop utility? It seems quite unreasonable
  for me, any ideas how this come out?
 
  Best regards,
  Bing
 
 
  *
  Dr Zacharias G. Fthenakis
  Research Associate
  Institute of Electronic Structure and Laser (I.E.S.L.)
  Foundation for Research and Technology Hellas (FO.R.T.H.)
  Vassilika Vouton P.O. Box 1527 71003 Heraklion Crete Greece
  Phone +30 2810 391824
  FAX   +30 2810 391305
  webpage: http://esperia.iesl.forth.gr/~fthenak
  **
 
 


 *
 Dr Zacharias G. Fthenakis
 Research Associate
 Institute of Electronic Structure and Laser (I.E.S.L.)
 Foundation for Research and Technology Hellas (FO.R.T.H.)
 Vassilika Vouton P.O. Box 1527 71003 Heraklion Crete Greece
 Phone +30 2810 391824
 FAX   +30 2810 391305
 webpage: http://esperia.iesl.forth.gr/~fthenak
 **




-- 



*Senior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

[SIESTA-L] Symmetry from band structure

[Suman Chowdhury]

In siesta is it possible to identify the symmetry operations which give
rise to different bands from the band structure plot...
-- 



*Senior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

[SIESTA-L] atom contribution from pDOS

[Suman Chowdhury]

Dear user,
In one paper, the authors have used siesta and commented such that by
calculating pDOS we can conclude that the contribution to the DOS is mainly
due to the edge atoms My question is how can it be calculated? Because
pDOS gives us the information about orbital contribution but not atom by
atom contribution. Can anyone help me in this regard...
-- 



*Senior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

Re: [SIESTA-L] [***Posible SPAM***]

[Suman Chowdhury]

As far as I am concern it is not possible to calculate raman spectroscopy
by using siesta. You can calculate other DFT code such as quantum espresso
or Gaussian for this.

On Thu, Feb 26, 2015 at 9:51 PM, Mourad Boutahir mourad.bouta...@gmail.com
wrote:

 helo,
 i m phD in morocco i start to use the code siesta for dynamic calculations
 i would calculate the raman spectroscopy of some structures.
 so please if it was possible to indicate me how i can calculate the  raman
 polarisabity model using the code siesta.

 best regards

 --

 ---
 *Mr. Mourad BOUTAHIR* ;
 Doctorant à la Faculté des sciences MEKNES ;
 Laboratoire d'Etude des Matériaux Avancés et Applications (LEM2A)
 Université Moulay Ismail
 GSM : +212662770697;
 E-mail : *mourad.bouta...@gmail.com mourad.bouta...@gmail.com**
 ait_ta...@yahoo.fr;*

 
 -




-- 



*Senior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

[SIESTA-L] Time steps in MD

[Suman Chowdhury]

Dear user,
In the SIESTA manual it is written that, if I want to do molecular dynamics
simulation then I need to give the initial time steps and the final time
steps. The default values for initial time steps and the final time steps
are given as 1. But no unit of the time is mentioned. Do you know what is
the unit of time in this case, I think it should be femto-second (fs). But
I want to confirm with you.

-- 



*Senior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

[SIESTA-L] Constraint adsorption

[Suman Chowdhury]

Dear siesta user,

Suppose I want to do some adsorption by using SIESTA...If I don't want to
change the xyz coordinate of the lattice on which the adatom is going to
adsorbed and also the x and y coordinate of the adatom only want to change
the z coordinate of the adatom..Then how can it be done by using siesta...

-- 



*Senior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

Re: [SIESTA-L] Spin Orbit Coupling

[Suman Chowdhury]

Dear Prof Ferrer,
You have written that the drawback of the serial version is that it cannot
 plot the SOC band, but you have also mentioned that it can be easily
done..Sir I am asking you can we do that..Because suppose I have done some
work and send it to a journal for publication, now suppose the referee ask
me to plot the band structure including the SOC effect, then I cannot do
anything. So I am requesting you if you do this easy task then I will
surely give your name as an author in my work..Hope to get a response from
you soon...

On Tue, Dec 9, 2014 at 10:49 PM, Jaime Ferrer j.fer...@cinn.es wrote:

 My apologies.
 This was intended to be sent to Suman only.
 Jaime Ferrer

 El 9/12/2014, a las 18:06, Jaime Ferrer j.fer...@cinn.es escribió:

 Sure. There goes, together with an afdf file. Cheers,
 Jaime
 Reservoir-18-Septiembre-2007.zip
 Ir copia.fdf

 El 9/12/2014, a las 17:54, Suman Chowdhury sumanchowdhur...@gmail.com
 escribió:

 Dear Prof. Ferrer,
 Can you share your serial version code with me..I am very much interested.

 On Tue, Dec 9, 2014 at 10:00 PM, Jaime Ferrer j.fer...@cinn.es wrote:

 Dear all,

 I guess that this string of emails calls for some clarification.

 The SIESTA team together with myself worked for some time to have the SOC
 facility implemented
 into the main trunk, but for a variety of reasons the project never
 reached the desired end.

 As a consequence, I have two private versions of SIESTA+SOC that I am
 happy to share
 with anyone having a SIESTA license. This comes under an old agreement
 between
 the SIESTA authors and me. I believe that perhaps these versions could be
 made publicly
 available in the SIESTA Web site, provided that there is a critical mass
 of plausible users,
 but this decision is beyond my reach.

 The two versions have each advantages and disadvantages, that I summarize:

 1. Serial version, based on siesta-1.4. This one is fully tested, and
 works with LDA and GGA,
 either non-magnetic, collinear magnetic and non-collinear magnetic. It
 also computes orbital moments.
 However, as far as I remember, it does not output SOC bands - although it
 would be easy to fix this.

 2. Parallel version, based on a beta release of siesta-3.0. This one is
 fully tested for LDA: non-magnetic
 and any sort of collinear and non-collinear magnetic systems. For GGA, it
 works only for
 non-magnetic systems. It provides wrong results for non-collinear
 magnetic systems. This version
 outputs also bands, DOS and I kind of remember that also wave-functions.
 Again orbital moments are
 computed and written.

 Two warnings are in order now:

 1. The SIESTA-SOC version converges slowly, and swallows more RAM
 resources than
 conventional simulations.

 2. You have to test carefully your pseudopotential parameters, because
 ghost states may appear.

 However, a new open-access paper has just appeared where Pablo Rivero,
 Salvador Barraza-Lopez, myself
 and collaborators have tested thoroughly the pseudo potentials of 20
 elements with focus on
 those having strong SOC -having in mind topological insulators -. We have
 used for testing the parallel
 SOC version. We have benchmarked the SIESTA results against VASP and in
 quite a few cases
 against an all-electrons code, and the pseudos work quite well.

 I would advise those interested in SOC to use any of the above two
 flavors together with the pseudos
 written down in the paper. The reference to the paper is:

  http://www.sciencedirect.com/science/article/pii/S0927025614007940#

 A last warning: I am no longer maintaining the SIESTA-SOC. What I can
 hand is what I wrote up to 2009.

 OK. I guess that this is all for now.

 With kind regards,

 Jaime Ferrer



 El 8/12/2014, a las 18:05, I. Camps ica...@gmail.com escribió:

 Hello,

 Since 2006, in the paper bellow there is an implementation of the
 spin-orbit coupling in SIESTA. Unfortunately, until now, I didn´t see this
 implemented in any version of the code.

 Paper: On-site approximation for spin–orbit coupling in linear
 combination of atomic orbitals density functional methods, L
 Fernandez-Seivane, M A Oliveira, S Sanvito and J Ferrer, J. Phys.: Condens.
 Matter 18 (2006) 7999–8013

 *Abstract*
 We propose a computational method that drastically simplifies the
 inclusion
 of the spin–orbit interaction in density functional theory when
 implemented
 over localized basis sets. Our method is based on a well-known procedure
 for obtaining pseudopotentials from atomic relativistic *ab initio *
 calculations
 and on an on-site approximation for the spin–orbit matrix elements.
 We have implemented the technique in the SIESTA (Soler J M *et al *2002
 *J. Phys.: Condens. Matter **14 *2745–79) code, and show that it
 provides accurate
 results for the overall band-structure and splittings of group IV and
 III–IV
 semiconductors as well as for 5d metals.

 DOI: http://dx.doi.org/10.1088/0953-8984/18/34/012


 []'s,

 @mps

 On Mon, Dec 8, 2014 at 2:52 PM, Suman Chowdhury

Re: [SIESTA-L] Spin Orbit Coupling

[Suman Chowdhury]

I want to thank Prof Ferrer and Prof Seivane for such an excellent
discussion on SO effect in SIESTA...

On Wed, Dec 10, 2014 at 3:13 PM, Lucas Fernandez Seivane queve...@gmail.com
 wrote:

 Dear All

 As Jaime said, the only drawback is the bigger memory and thus time
 requirements. And as you see in his link and former literature, bands can
 be perfectly plotted.

 I just want to point to you all to this reference which may be interesting
 in your case, where all the calculations were performed with SIESTA trying
 to match previous a previous ABINIT version of the calculations. While in
 the final paper we didn't do all the final calculations with SO, we also
 tested the SO in the bulk and monolayer, but it didn't affect what we were
 looking for in the initial calculations of the NWs in the cases we were
 interested, and as Prof. Ferrer said it makes the calculations slower, so
 we proceeded just with spin polarized. In any case, if you have problems
 reproducing literature I can look up the psf files we used for the MoS2.

 https://www.researchgate.net/publication/257247197_Atomic_and_electronic_properties_of_quasi-one-dimensional_MoS2_nanowires
 All the best




-- 



*Senior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

Re: [SIESTA-L] Spin Orbit Coupling

[Suman Chowdhury]

Dear Prof. Ferrer,
Can you share your serial version code with me..I am very much interested.

On Tue, Dec 9, 2014 at 10:00 PM, Jaime Ferrer j.fer...@cinn.es wrote:

 Dear all,

 I guess that this string of emails calls for some clarification.

 The SIESTA team together with myself worked for some time to have the SOC
 facility implemented
 into the main trunk, but for a variety of reasons the project never
 reached the desired end.

 As a consequence, I have two private versions of SIESTA+SOC that I am
 happy to share
 with anyone having a SIESTA license. This comes under an old agreement
 between
 the SIESTA authors and me. I believe that perhaps these versions could be
 made publicly
 available in the SIESTA Web site, provided that there is a critical mass
 of plausible users,
 but this decision is beyond my reach.

 The two versions have each advantages and disadvantages, that I summarize:

 1. Serial version, based on siesta-1.4. This one is fully tested, and
 works with LDA and GGA,
 either non-magnetic, collinear magnetic and non-collinear magnetic. It
 also computes orbital moments.
 However, as far as I remember, it does not output SOC bands - although it
 would be easy to fix this.

 2. Parallel version, based on a beta release of siesta-3.0. This one is
 fully tested for LDA: non-magnetic
 and any sort of collinear and non-collinear magnetic systems. For GGA, it
 works only for
 non-magnetic systems. It provides wrong results for non-collinear magnetic
 systems. This version
 outputs also bands, DOS and I kind of remember that also wave-functions.
 Again orbital moments are
 computed and written.

 Two warnings are in order now:

 1. The SIESTA-SOC version converges slowly, and swallows more RAM
 resources than
 conventional simulations.

 2. You have to test carefully your pseudopotential parameters, because
 ghost states may appear.

 However, a new open-access paper has just appeared where Pablo Rivero,
 Salvador Barraza-Lopez, myself
 and collaborators have tested thoroughly the pseudo potentials of 20
 elements with focus on
 those having strong SOC -having in mind topological insulators -. We have
 used for testing the parallel
 SOC version. We have benchmarked the SIESTA results against VASP and in
 quite a few cases
 against an all-electrons code, and the pseudos work quite well.

 I would advise those interested in SOC to use any of the above two flavors
 together with the pseudos
 written down in the paper. The reference to the paper is:

  http://www.sciencedirect.com/science/article/pii/S0927025614007940#

 A last warning: I am no longer maintaining the SIESTA-SOC. What I can hand
 is what I wrote up to 2009.

 OK. I guess that this is all for now.

 With kind regards,

 Jaime Ferrer



 El 8/12/2014, a las 18:05, I. Camps ica...@gmail.com escribió:

 Hello,

 Since 2006, in the paper bellow there is an implementation of the
 spin-orbit coupling in SIESTA. Unfortunately, until now, I didn´t see this
 implemented in any version of the code.

 Paper: On-site approximation for spin–orbit coupling in linear combination
 of atomic orbitals density functional methods, L Fernandez-Seivane, M A
 Oliveira, S Sanvito and J Ferrer, J. Phys.: Condens. Matter 18 (2006) 7999
 –8013

 *Abstract*
 We propose a computational method that drastically simplifies the inclusion
 of the spin–orbit interaction in density functional theory when implemented
 over localized basis sets. Our method is based on a well-known procedure
 for obtaining pseudopotentials from atomic relativistic *ab initio *
 calculations
 and on an on-site approximation for the spin–orbit matrix elements.
 We have implemented the technique in the SIESTA (Soler J M *et al *2002
 *J. Phys.: Condens. Matter **14 *2745–79) code, and show that it provides
 accurate
 results for the overall band-structure and splittings of group IV and
 III–IV
 semiconductors as well as for 5d metals.

 DOI: http://dx.doi.org/10.1088/0953-8984/18/34/012


 []'s,

 @mps

 On Mon, Dec 8, 2014 at 2:52 PM, Suman Chowdhury 
 sumanchowdhur...@gmail.com wrote:

 Yes, I completely agree with you. As far as I know, spin-orbit coupling
 is not included in siesta code. Even I posted about this issue in past in
 siesta forum.

 On Mon, Dec 8, 2014 at 10:01 PM, Seyed Mohammad Tabatabaei 
 smt...@gmail.com wrote:

 Dear SIESTA Users,

 I want to implement spin orbit coupling for mono-layer MoS2 but as far
 as I know this is not implemented directly in the code. Any help or ideas
 in this regard is appreciated.

 Kind regards,
 Mohammad,




 --



 *Senior research fellow Dept. of Physics, University of Calcutta Kolkata-
 79, West Bengal, India.*
 * Ph no-+91-9830512232 %2B91-9830512232*






-- 



*Senior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

Re: [SIESTA-L] How to extract TB parameters from SIESTA

[Suman Chowdhury]

I think it cannot be done in siesta. Alternatively you can try LMTO.

On Wed, Dec 3, 2014 at 2:07 PM, 邵德喜 dxshao...@gmail.com wrote:

 Dear everyone:
 I'm now interested in formulating a TB Hamilton from SIESTA.
 Any ideas and comments will be appreciated.




-- 



*Senior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

Re: [SIESTA-L] How to extract TB parameters from SIESTA

[Suman Chowdhury]

Yes. LMTO is another ab inito software which uses tight binding
hamiltonian. From where you can get the TB parameter. LMTO is completely
free.

On Wed, Dec 3, 2014 at 2:32 PM, 邵德喜 dxshao...@gmail.com wrote:

 Thanks, is LMTO here also a software about ab initial?

 2014-12-03 16:42 GMT+08:00 Suman Chowdhury sumanchowdhur...@gmail.com:

 I think it cannot be done in siesta. Alternatively you can try LMTO.

 On Wed, Dec 3, 2014 at 2:07 PM, 邵德喜 dxshao...@gmail.com wrote:

 Dear everyone:
 I'm now interested in formulating a TB Hamilton from SIESTA.
 Any ideas and comments will be appreciated.




 --



 *Senior research fellow Dept. of Physics, University of Calcutta Kolkata-
 79, West Bengal, India.*
 * Ph no-+91-9830512232*





-- 



*Senior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

Re: [SIESTA-L] electronic and magnetic properties

[Suman Chowdhury]

You have to use Eig2dos in the Utils folder. After compilation of the
filename.EIG with the help of eig2dos you can have folder where there
will four coloumns. The first one will be the energy in eV. The next one
will be dos for spin up, then dos for spin down and the last one will be
the dos for spin up + spin down.

On Tue, Dec 2, 2014 at 1:03 PM, Nadia Salami nadiasala...@gmail.com wrote:

 I think that the density of states of spin up and down are same.

 On Tue, Dec 2, 2014 at 9:05 AM, Nadia Salami nadiasala...@gmail.com
 wrote:

 Dear Siesta users,

 I want to obtain the electronic and magnetic properties of my system. So
 I have used SpinPolarized true  option. But after DFT calculation
 by Siesta code, there aren't two files for density of states for up and
 down spins, but there are Mulliken Atomic and Orbital Populations for all
 species with up and down spins in the output file.
 It will be highly appreciated any help and comment.
 Thanks in advance,
 Best regards.
 Nadia Salami
 PhD student





-- 



*Senior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

[SIESTA-L] Hybridization

[Suman Chowdhury]

If I want to study some doped structure,how can I understand from siesta
data if there is some hybridization takes place or not between the dopant
atoms and the substrate..

-- 



*Senior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

[SIESTA-L] Contribution to the magnetism

[Suman Chowdhury]

Dear siesta user,
I have studied the magnetic property of some systems and found magnetism.
Is it possible from the siesta data to know which atoms are contributing in
this magnetism...It is very urgent...

-- 



*Senior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

Re: [SIESTA-L] Unrelaxed coordinates after siesta Optimization

[Suman Chowdhury]

Can you post your full .fdf file..

On Fri, Oct 10, 2014 at 3:07 PM, Manjeet Bhatia manjeetbhati...@gmail.com
wrote:

 Dear Siesta Users,

 After Siesta optimization i got forces as

 Tot0.0065550.016954   0.0022713

 and OutCoor: Final (Unrelaxed) atomic coordinates. Is that ok with the
 relaxation? if not then what parameter I have to change .

 Look forward to your reply.


 Manjeet




-- 



*Senior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

Re: [SIESTA-L] Unrelaxed coordinates after siesta Optimization

[Suman Chowdhury]

This .fdf file will never give relaxed structure. Because you have given
number of CG steps is 50, which not at all sufficient for this structure to
relax with the given relaxation criteria. Just increase the number of CG
steps to 1000, hopefully it will going to converge to within this..

On Fri, Oct 10, 2014 at 4:05 PM, Manjeet Bhatia manjeetbhati...@gmail.com
wrote:

 Attached...

 On Fri, Oct 10, 2014 at 3:33 PM, Suman Chowdhury 
 sumanchowdhur...@gmail.com wrote:

 Can you post your full .fdf file..

 On Fri, Oct 10, 2014 at 3:07 PM, Manjeet Bhatia 
 manjeetbhati...@gmail.com wrote:

 Dear Siesta Users,

 After Siesta optimization i got forces as

 Tot0.0065550.016954   0.0022713

 and OutCoor: Final (Unrelaxed) atomic coordinates. Is that ok with the
 relaxation? if not then what parameter I have to change .

 Look forward to your reply.


 Manjeet




 --



 *Senior research fellow Dept. of Physics, University of Calcutta Kolkata-
 79, West Bengal, India.*
 * Ph no-+91-9830512232*





-- 



*Senior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

[SIESTA-L] fatband

[Suman Chowdhury]

Dear user,
Can anyone clearly explain (step by step) how to plot fatband...I am unable
to understand from the siesta manual...Suppose I want to plot the band
structure of 2pz electrons...How to do that?

-- 



*Senior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

[SIESTA-L] Monkhorst Pack grid for structure relaxation

[Suman Chowdhury]

Dear user,
I want to know if I only want to relax the structure, without calculating
any other physical quantity from the siesta simulation, is it OK to define
the K point sampling i.e. Monkhorst Pack grid is simply
1 0 0
0 1 0
0 0 1
Because this will accelerate the convergence...I just want to relax the
structure..Will not use any data for calculation...
-- 



*Senior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

Re: [SIESTA-L] Monkhorst Pack grid for structure relaxation

[Suman Chowdhury]

Thanks to all of you for your reply...

On Wed, Oct 1, 2014 at 1:58 PM, Riccardo Rurali rrur...@icmab.es wrote:

 It depends on what your 'structure' is?

 If it is a non-periodic system not only you 'can', but you 'should' use
 only the Gamma point. If the system is periodic and the computational cell
 is not large enough, such a reduced sampling of the Brillouin zone could
 lead to an incorrect relaxed geometry.

 Riccardo


 On 10/1/14 9:53 AM, Suman Chowdhury wrote:

 Dear user,
 I want to know if I only want to relax the structure, without
 calculating any other physical quantity from the siesta simulation, is
 it OK to define the K point sampling i.e. Monkhorst Pack grid is simply
 1 0 0
 0 1 0
 0 0 1
 Because this will accelerate the convergence...I just want to relax the
 structure..Will not use any data for calculation...
 --
 /*Senior research fellow
   Dept. of Physics,
   University of Calcutta
   Kolkata- 79, West Bengal, India.*/
 /* Ph no-+91-9830512232*/
 /*
 */


 --

 Riccardo Rurali
 Institut de Cičncia de Materials de Barcelona (ICMAB-CSIC)
 Campus de Bellaterra
 08193 Bellaterra (Barcelona)
 Spain

 tel.: +34 935801853 ext. 347
 e-mail: rrur...@icmab.es
 http://www.researcherid.com/rid/D-3676-2011

 Man, the dope's that there's still hope




-- 



*Senior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

[SIESTA-L] SIESTA in FACEBOOK

[Suman Chowdhury]

Dear all SIESTA User,
Those users who has facebook account are requested to join the following
group for discussion:
https://www.facebook.com/groups/1482411542018575/

-- 



*Senior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

[SIESTA-L] Automatic Shut Down after simulation

[Suman Chowdhury]

Dear user,
Is it possible to configure one's PC or laptop in such a way that the PC or
laptop shut down automatically after the completion of the simulation.

-- 



*Senior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

Re: [SIESTA-L] Automatic Shut Down after simulation

[Suman Chowdhury]

Thanks, Can I run this command in my ubuntu PC?

On Tue, Sep 30, 2014 at 6:38 PM, Nick Papior Andersen nickpap...@gmail.com
wrote:

 Sure,

 Make shutdown a command exectuable by any user, (search around unix fora
 for this) then do:

 $ siesta  RUN.fdf  RUN.out ; shutdown -h now



 2014-09-30 12:56 GMT+00:00 Suman Chowdhury sumanchowdhur...@gmail.com:

 Dear user,
 Is it possible to configure one's PC or laptop in such a way that the PC
 or laptop shut down automatically after the completion of the simulation.

 --



 *Senior research fellow Dept. of Physics, University of Calcutta Kolkata-
 79, West Bengal, India.*
 * Ph no-+91-9830512232 %2B91-9830512232*




 --
 Kind regards Nick




-- 



*Senior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

[SIESTA-L] Problem with PBE Na pseudopotential

[Suman Chowdhury]

While I am running a simulation using GGA-PBE Na pseudopotential I am
getting the error. I am sure the problem is not with the .fdf file but with
the Na pseudopotential. I am attaching you the .out file. I also think the
problem lies in not including p shell in the pseudopotential. I don't know
how to include that in the pseudopotential. Please help to solve the
problem.

-- 



*Senior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*


Na1.out
Description: Binary data

Re: [SIESTA-L] How to restart Siesta?

[Suman Chowdhury]

Few weeks ago I had also posted a similar question in the forum..

On Sun, Sep 21, 2014 at 6:55 AM, Julio Henrique juliohenri...@msn.com
wrote:


 I had simulations interrupted by prolonged lack of electricity.
 How to restart from where it was interrupted?
 Is it possible?
 Thank's.
 Julio Henrique.











-- 



*Junior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

Re: [SIESTA-L] Force vs Iteration

[Suman Chowdhury]

I don't understand what you are saying...Can you please it clearly step by
step..

On Wed, Sep 17, 2014 at 8:50 PM, Irtaza Hassan irtazahassa...@gmail.com
wrote:

 grep 'constrained' outputfile  filename.ext

 use filename.ext file for plots.

 On Wed, Sep 17, 2014 at 8:08 PM, Suman Chowdhury 
 sumanchowdhur...@gmail.com wrote:

 Dear all,
 I need to produce a graph Force vs MD steps.Can you please tell me how to
 do that. IT is very urgent.?

 --



 *Junior research fellow Dept. of Physics, University of Calcutta Kolkata-
 79, West Bengal, India.*
 * Ph no-+91-9830512232 %2B91-9830512232*





-- 



*Junior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

[SIESTA-L] Force vs Iteration

[Suman Chowdhury]

Dear all,
I need to produce a graph Force vs MD steps.Can you please tell me how to
do that. IT is very urgent.?

-- 



*Junior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

[SIESTA-L] Fwd: Forceful termination of the program

[Suman Chowdhury]

-- Forwarded message --
From: Suman Chowdhury sumanchowdhur...@gmail.com
Date: Fri, Aug 22, 2014 at 1:30 PM
Subject: Forceful termination of the program
To: siesta-l@uam.es


Dear user,
I have a question. Suppose I have made MD.UseSaveXV, MD.UseSaveCG and
DM.UseSaveDM flags true and run a simulation. Then suppose I have to
stopped the program forcefully before its completion.Then I will again run
the unfinished program. My question is will the program start from where I
have stopped it forcefully before the completion.

-- 



*Junior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*




-- 



*Junior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

Re: [SIESTA-L] why the result (lattice constant...etc.) of Siesta and Vasp can't compare?

[Suman Chowdhury]

Because they use different algorithm, different potential and different
basis set.


On Fri, Aug 22, 2014 at 11:15 AM, joyce79928cc . joyce79...@gmail.com
wrote:

 Dear:

 I have asked this similar question before.
 why the result (lattice constant...etc.) of Siesta and Vasp can't compare?
 because I have use this two software to calculate the example provided by
 Siesta
 and also create the input file for Vasp.
 Though I have tried my best to set the same flag.
 but the results are just very different.

 why the result (lattice constant...etc.) of Siesta and Vasp can't compare?
 Thank you!
 the file attached is my input for vasp and siesta
 --
 Best Regards

 邱芳瑜  Chiu Fang Yu
 國立成功大學 材料科學與工程學系碩一
 MOBILE：0930287221(中華)
 GMAIL：joyce79...@gmail.com wisdom4...@gmail.com





-- 



*Junior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

[SIESTA-L] Forceful termination of the program

[Suman Chowdhury]

Dear user,
I have a question. Suppose I have made MD.UseSaveXV, MD.UseSaveCG and
DM.UseSaveDM flags true and run a simulation. Then suppose I have to
stopped the program forcefully before its completion.Then I will again run
the unfinished program. My question is will the program start from where I
have stopped it forcefully before the completion.

-- 



*Junior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

Re: [SIESTA-L] lattice constant problem

[Suman Chowdhury]

No I don't think so..


On Fri, Aug 22, 2014 at 4:38 PM, Максим Арсентьев ars21031...@gmail.com
wrote:

 I believe cartesian coordinate is orthogonal
 http://en.wikipedia.org/wiki/Cartesian_coordinate_system
 It is better to use reduced?


 2014-08-22 7:23 GMT+04:00 Suman Chowdhury sumanchowdhur...@gmail.com:

 Yes I have corrected entered the coordinated, because when the make the
 supercell I am getting the structure which I want but with zero z
 coordinate and with much much longer lattice constant. Cartesian coordinate
 can be of any system not necessarily of orthogonal system.


 On Fri, Aug 22, 2014 at 1:28 AM, Максим Арсентьев ars21031...@gmail.com
 wrote:

 PLs give us the link of the literature. K point grid should be more
 dense. Did you properly entered coordinates (cartesian are for ortogonal
 system)?


 2014-08-21 21:04 GMT+04:00 Suman Chowdhury sumanchowdhur...@gmail.com:

 But after optimization the 2D sheet no longer remains 2D. It must have
 some non -zero buckling.


 On Thu, Aug 21, 2014 at 9:54 PM, Sergio Ferrari 
 lic.sergio.ferr...@gmail.com wrote:

 I simply notice that you said that you want to optimize a two
 dimensional sheet of germanium, so all atoms should be put in a plane (of
 your choice), of course 2 atoms are allways in a plane but I wonder if for
 simplicity it is preferable to write the coordinates of the atoms in the
 x-y plane. Also in your  kgrid_Monkhorst_Pack your k points are equal en
 all directions, that is clearly wrong if you want to simulate a 2D sheet.


 2014-08-15 5:27 GMT-03:00 Suman Chowdhury sumanchowdhur...@gmail.com
 :

 Dear siesta user,
 I am trying to optimize the two dimensional sheet of germanium. I am
 using the pp given in the siesta website. The lattice constant given in 
 the
 literature is within 3.97 to 4.01 A with buckling 0.6 to 0.7 A. But each
 time I run the siesta program I am getting the lattice constant just the
 double of this and with almost zero buckling. I started with lattice
 constant 3.97 and buckling 0.7 A. Can anyone help to solve the problem. I
 am attaching the .fdf file.

 --



 *Junior research fellow Dept. of Physics, University of
 Calcutta Kolkata- 79, West Bengal, India.*
 * Ph no-+91-9830512232*




 --
 
 Dr. Sergio Ferrari
 Depto. de Fí­sica-Fac. de Ingenierí­a
 INTECIN (UBA-CONICET)
 Av. Paseo Colón 850
 C1063ACV-Ciudad de Buenos Aires
 ARGENTINA

 Tel: +54 (11) 4342-1396 (Directo)
 4342-9184/4343-0891/4343-2775 (Int. 1021)

 http://intecin.fi.uba.ar
 




 --



 *Junior research fellow Dept. of Physics,  University of
 Calcutta Kolkata- 79, West Bengal, India.*
 * Ph no-+91-9830512232*




 --
 Best wishes,
 Maxim Arsent'ev, D.Sc.(Chemistry)
 Laboratory of research of nanostructures
 Institute of Silicate Chemistry of RAS




 --



 *Junior research fellow Dept. of Physics, University of Calcutta Kolkata-
 79, West Bengal, India.*
 * Ph no-+91-9830512232*




 --
 Best wishes,
 Maxim Arsent'ev, D.Sc.(Chemistry)
 Laboratory of research of nanostructures
 Institute of Silicate Chemistry of RAS




-- 



*Junior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

Re: [SIESTA-L] lattice constant problem

[Suman Chowdhury]

But after optimization the 2D sheet no longer remains 2D. It must have some
non -zero buckling.


On Thu, Aug 21, 2014 at 9:54 PM, Sergio Ferrari 
lic.sergio.ferr...@gmail.com wrote:

 I simply notice that you said that you want to optimize a two dimensional
 sheet of germanium, so all atoms should be put in a plane (of your choice),
 of course 2 atoms are allways in a plane but I wonder if for simplicity it
 is preferable to write the coordinates of the atoms in the x-y plane. Also
 in your  kgrid_Monkhorst_Pack your k points are equal en all directions,
 that is clearly wrong if you want to simulate a 2D sheet.


 2014-08-15 5:27 GMT-03:00 Suman Chowdhury sumanchowdhur...@gmail.com:

 Dear siesta user,
 I am trying to optimize the two dimensional sheet of germanium. I am
 using the pp given in the siesta website. The lattice constant given in the
 literature is within 3.97 to 4.01 A with buckling 0.6 to 0.7 A. But each
 time I run the siesta program I am getting the lattice constant just the
 double of this and with almost zero buckling. I started with lattice
 constant 3.97 and buckling 0.7 A. Can anyone help to solve the problem. I
 am attaching the .fdf file.

 --



 *Junior research fellow Dept. of Physics, University of Calcutta Kolkata-
 79, West Bengal, India.*
 * Ph no-+91-9830512232*




 --
 
 Dr. Sergio Ferrari
 Depto. de Fí­sica-Fac. de Ingenierí­a
 INTECIN (UBA-CONICET)
 Av. Paseo Colón 850
 C1063ACV-Ciudad de Buenos Aires
 ARGENTINA

 Tel: +54 (11) 4342-1396 (Directo)
 4342-9184/4343-0891/4343-2775 (Int. 1021)

 http://intecin.fi.uba.ar
 




-- 



*Junior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

Re: [SIESTA-L] lattice constant problem

[Suman Chowdhury]

Yes I have corrected entered the coordinated, because when the make the
supercell I am getting the structure which I want but with zero z
coordinate and with much much longer lattice constant. Cartesian coordinate
can be of any system not necessarily of orthogonal system.


On Fri, Aug 22, 2014 at 1:28 AM, Максим Арсентьев ars21031...@gmail.com
wrote:

 PLs give us the link of the literature. K point grid should be more dense.
 Did you properly entered coordinates (cartesian are for ortogonal system)?


 2014-08-21 21:04 GMT+04:00 Suman Chowdhury sumanchowdhur...@gmail.com:

 But after optimization the 2D sheet no longer remains 2D. It must have
 some non -zero buckling.


 On Thu, Aug 21, 2014 at 9:54 PM, Sergio Ferrari 
 lic.sergio.ferr...@gmail.com wrote:

 I simply notice that you said that you want to optimize a two
 dimensional sheet of germanium, so all atoms should be put in a plane (of
 your choice), of course 2 atoms are allways in a plane but I wonder if for
 simplicity it is preferable to write the coordinates of the atoms in the
 x-y plane. Also in your  kgrid_Monkhorst_Pack your k points are equal en
 all directions, that is clearly wrong if you want to simulate a 2D sheet.


 2014-08-15 5:27 GMT-03:00 Suman Chowdhury sumanchowdhur...@gmail.com:

 Dear siesta user,
 I am trying to optimize the two dimensional sheet of germanium. I am
 using the pp given in the siesta website. The lattice constant given in the
 literature is within 3.97 to 4.01 A with buckling 0.6 to 0.7 A. But each
 time I run the siesta program I am getting the lattice constant just the
 double of this and with almost zero buckling. I started with lattice
 constant 3.97 and buckling 0.7 A. Can anyone help to solve the problem. I
 am attaching the .fdf file.

 --



 *Junior research fellow Dept. of Physics, University of
 Calcutta Kolkata- 79, West Bengal, India.*
 * Ph no-+91-9830512232*




 --
 
 Dr. Sergio Ferrari
 Depto. de Fí­sica-Fac. de Ingenierí­a
 INTECIN (UBA-CONICET)
 Av. Paseo Colón 850
 C1063ACV-Ciudad de Buenos Aires
 ARGENTINA

 Tel: +54 (11) 4342-1396 (Directo)
 4342-9184/4343-0891/4343-2775 (Int. 1021)

 http://intecin.fi.uba.ar
 




 --



 *Junior research fellow Dept. of Physics, University of Calcutta Kolkata-
 79, West Bengal, India.*
 * Ph no-+91-9830512232*




 --
 Best wishes,
 Maxim Arsent'ev, D.Sc.(Chemistry)
 Laboratory of research of nanostructures
 Institute of Silicate Chemistry of RAS




-- 



*Junior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

Re: [SIESTA-L] Charge Transfer

[Suman Chowdhury]

Thanks a lot..


On Sun, Aug 17, 2014 at 3:14 AM, I. Camps ica...@gmail.com wrote:

 I Dear Suman,

 You have two different type of charge analysis. One is simple: to get the
 charge distribution. The second one is to get the charge transfer from/to
 your system.

 In the first case, your system is only one. In this case, you calculate
 the charge distribution (using one or different schemes) and you are set.

 In the second case, your system has an initial conformation/configuration,
 them it suffers some modification giving it a final
 conformation/configuration. In this case, you calculate the charge
 distribution BEFORE the fenomenum that alter the conformation/configuration
 and calculate again AFTER the fenomenum, so, you calculate the charges
 twice. After that, you calculate the charge transfer as the difference
 between the two situations.

 An example: the water molecule.

 If you one to get the charges in each atom, you calculate the charge
 distribution for the atoms in the molecule only one time.

 If you want to calculate the charge modification in the O (the difference
 between the isolated and molecular atoms)  you must do the calculation
 twice: one for the isolated atom and one for the molecular atom.  Then,
 you calculate the transferred charge as
 Charge_O_isolated-Charge_O_molecular.

 Regards
 On 15 Aug, 2014 1:22 AM, Suman Chowdhury sumanchowdhur...@gmail.com
 wrote:

 Dear Camps,
 Twice means? Can you please explain clearly what should be the process.


 On Fri, Aug 15, 2014 at 3:23 AM, Bishal Bhattarai 
 bishalbhattarai...@gmail.com wrote:

 Can we get the wave functions out from the MULIKEN charge distribution ?
 I want to calculate IPR( Inverse Participation Ratio ) for my 648 silica
 atoms

 Bishal


 On Thu, Aug 14, 2014 at 4:11 PM, I. Camps ica...@gmail.com wrote:

 Hello Suman,

 If you want to calculate charge transfer you have to do your
 calculation twice and then calculate the difference of charges for the two
 calculations.  You can use the diferente charge scheme implemented in
 SIESTA such as Voroni,  Hirsfeld or Muliken (or all at the same time).
 Take a look in the manual for the wright keywords.

 Regards,
 On 14 Aug, 2014 6:50 AM, Suman Chowdhury sumanchowdhur...@gmail.com
 wrote:

 Dear siesta user,
 How I can estimate the charge transfer from atom to atom from SIESTA?

 --



 *Junior research fellow  Dept. of Physics, University of
 Calcutta Kolkata- 79, West Bengal, India.*
 * Ph no-+91-9830512232 %2B91-9830512232*





 --



 *Junior research fellow Dept. of Physics, University of Calcutta
  Kolkata- 79, West Bengal, India.*
 * Ph no-+91-9830512232 %2B91-9830512232*




-- 



*Junior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

[SIESTA-L] lattice constant problem

[Suman Chowdhury]

Dear siesta user,
I am trying to optimize the two dimensional sheet of germanium. I am using
the pp given in the siesta website. The lattice constant given in the
literature is within 3.97 to 4.01 A with buckling 0.6 to 0.7 A. But each
time I run the siesta program I am getting the lattice constant just the
double of this and with almost zero buckling. I started with lattice
constant 3.97 and buckling 0.7 A. Can anyone help to solve the problem. I
am attaching the .fdf file.

-- 



*Junior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*


germanene.fdf
Description: Binary data

[SIESTA-L] Charge Transfer

[Suman Chowdhury]

Dear siesta user,
How I can estimate the charge transfer from atom to atom from SIESTA?

-- 



*Junior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

Re: [SIESTA-L] Charge Transfer

[Suman Chowdhury]

Dear Camps,
Twice means? Can you please explain clearly what should be the process.


On Fri, Aug 15, 2014 at 3:23 AM, Bishal Bhattarai 
bishalbhattarai...@gmail.com wrote:

 Can we get the wave functions out from the MULIKEN charge distribution ? I
 want to calculate IPR( Inverse Participation Ratio ) for my 648 silica
 atoms

 Bishal


 On Thu, Aug 14, 2014 at 4:11 PM, I. Camps ica...@gmail.com wrote:

 Hello Suman,

 If you want to calculate charge transfer you have to do your calculation
 twice and then calculate the difference of charges for the two
 calculations.  You can use the diferente charge scheme implemented in
 SIESTA such as Voroni,  Hirsfeld or Muliken (or all at the same time).
 Take a look in the manual for the wright keywords.

 Regards,
 On 14 Aug, 2014 6:50 AM, Suman Chowdhury sumanchowdhur...@gmail.com
 wrote:

 Dear siesta user,
 How I can estimate the charge transfer from atom to atom from SIESTA?

 --



 *Junior research fellow  Dept. of Physics, University of
 Calcutta Kolkata- 79, West Bengal, India.*
 * Ph no-+91-9830512232 %2B91-9830512232*





-- 



*Junior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

Re: [SIESTA-L] unfolding formula

[Suman Chowdhury]

This paper is very interesting. In fact I have also been searching in
internet for this kind of methods. But how can I implement this method in
siesta. It is now not possible for me to implement your method in siesta by
writing programs, because I don't have so much time left for my phd. If you
can supply me your package then I can use it then definitely with proper
acknowledgement or citations of your papers in our all future works...So
can we collaborate..


On Tue, Aug 12, 2014 at 1:20 PM, Antonino LaMagna 
antonino.lama...@imm.cnr.it wrote:

  Dear SIESTA Users,
 I would like to annonce the
 pubblication of the manuscript
 Role of basis sets on the unfolding of supercell band structures:
 From tight-binding to density functional theory  Eur. Phys. Lett. 107
 27006 (2014)
 by I. Deretzis et al.

 http://iopscience.iop.org/0295-5075/107/2/27006/

 Here we propose a band unfolding method for supercell
 calculations which can be directly applied with the SIESTA outcomes.

 Kind Regards
 Antonino La Magna






-- 



*Junior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

[SIESTA-L] Huge stress tensor

[Suman Chowdhury]

 Dear all,
After running just 1 CG step, I got the following stress-tensor-voigt (kbar)
Stress-tensot-voigt (kbar) -10092.56  -61.77  5.74  -0.46  0.00  0.00..
My question is can said that the structure is relaxed after the CG step.


-- 



*Junior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

[SIESTA-L] charge density

[Suman Chowdhury]

Dear user,
Can anyone know how to plot charge density through siesta by using vmd
visualization tool.

-- 



*Junior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

[SIESTA-L] Magnetism from Charge Density

[Suman Chowdhury]

Dear all,
How to estimate magnetism from charge density in siesta?

-- 



*Junior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

[SIESTA-L] Xcrysden

[Suman Chowdhury]

Dear All,
I have tried thousand times to install Xcrysden in my machine, but I
failed.Can anyone tell me how to do it step by step?

-- 



*Junior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

[SIESTA-L] Band Structure

[Suman Chowdhury]

Dear all,
How can I get a good band structure when my unit cell is large?

-- 



*Junior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

[SIESTA-L] Band Structure

[Suman Chowdhury]

Dear all,
To plot the band structure which is to be set true, WriteBands or
WriteKBands or both.

-- 



*Junior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

[SIESTA-L] Energy window in siesta

[Suman Chowdhury]

Dear all,
When I calculate the optical properties of any system in SIESTA, the
imaginary part of the di electric constant which it gives as an output, the
difference between any two successive energy is always found to be constant
(0.01979).How can I change this energy window.

-- 



*Junior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

[SIESTA-L] Nanodisks

[Suman Chowdhury]

Dear all,
How do I calculate the electronic structure of graphene nano disks which do
not have any boundary condition by siesta?

-- 



*Junior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

Re: [SIESTA-L] Nanodisks

[Suman Chowdhury]

Thanks to all.Can you tell me how I put fake boundary condition i.e.
putting the nano disk in a large enough box..


On Fri, Feb 7, 2014 at 9:11 PM, Bailey, Steven s.bai...@lancaster.ac.ukwrote:

  Taking the isolated disc will give you the energy levels (flat). You
 need to connect the disc to periodic leads or make the discs periodic to
 obtain the band structure of your system.



 Dr S Bailey

 Department of Physics

 Lancaster University UK

 Email: s.bai...@lancaster.ac.uk

 Tel: +441524592844



 *From:* siesta-l-requ...@uam.es [mailto:siesta-l-requ...@uam.es] *On
 Behalf Of *Suman Chowdhury
 *Sent:* 07 February 2014 15:19
 *To:* siesta-l@uam.es
 *Subject:* [SIESTA-L] Nanodisks



 Dear all,

 How do I calculate the electronic structure of graphene nano disks which
 do not have any boundary condition by siesta?



 --




 *Junior research fellow  Dept. of Physics,  University of Calcutta
  Kolkata- 79, West Bengal, India.*

 * Ph no-+91-9830512232*






-- 



*Junior research fellow Dept. of Physics, University of Calcutta Kolkata-
79, West Bengal, India.*
* Ph no-+91-9830512232*

[SIESTA-L] Pseudo

[Suman Chowdhury]

Dear all,
How reliable are the pseudo potentials given in the siesta website?

Re: [SIESTA-L] atoms

[Suman Chowdhury]

thanks a lot


On Sat, Jan 25, 2014 at 2:50 AM, Abraham Hmiel abehm...@gmail.com wrote:

 Suman,

 I think the answer you're looking for is 42. Only 42-atom simulations are
 considered by peer review ;)

 But joking aside, you should look to previously-published ab-initio
 results in your system of interest or something close to it. Even if such
 results exist, you should perform methodological checks on system size,
 i.e. size-convergence simulations with respect to: the number of layers in
 a surface slab, or supercell dimensions if you're simulating a bulk
 compound (perhaps with a defect or other non-homogeneity), different sizes
 of nanowire, etc. Some of the most important current problems in
 nanoscience involve quantum size-effects, and you don't really know how
 many atoms a good simulation requires until you try it- the physics of a
 particular solid-state system can vary dramatically based on small size
 increments!

 So, to answer the question you posed, no real number of atoms guideline
 exists. Use what is feasible and timely for your computational setup while
 giving trustworthy, meaningful, repeatable results! By the way, the T in
 siesta stands for Thousands (but this only really makes sense with the
 order-N functional). The number of atoms in a SIESTA simulation could be
 anywhere in the range {10^0, 10^4}.

 --
 *Abraham Hmiel*
 Katherine Belz Groves Fellow in Nanoscience
 Xue Group, SUNY College of Nanoscale Science and Engineering
 http://abehmiel.net/about

 On Fri, Jan 24, 2014 at 8:21 AM, Suman Chowdhury 
 sumanchowdhur...@gmail.com wrote:

 Dear all,
 what is the typical number of atoms one should use for publishable
 results using SIESTA?

[SIESTA-L] Elastic Constant

[Suman Chowdhury]

Dear all,
How all the elastic constants can be calculated by using SIESTA?

[SIESTA-L] Graphene Band Lines

[Suman Chowdhury]

Dear all.
Can anyone provide me the correct band lines of a hexagonal lattice (like
graphene,silicene,germanene,stanene etc. sheet (not in terms of reciprocal
lattice vectors)

[SIESTA-L] Spin Orbit Coupling

[Suman Chowdhury]

Can anyone provide me the SIESTA code where the Spin Orbit coupling is
considered.

[SIESTA-L] Fwd: Convergence

[Suman Chowdhury]

-- Forwarded message --
From: Suman Chowdhury sumanchowdhur...@gmail.com
Date: Thu, Dec 19, 2013 at 12:10 PM
Subject: Convergence
To: siesta-l@uam.es


Dear all siesta user,
How do I know if my molecular dynamics simulation is converging or not?

[SIESTA-L] Convergence

[Suman Chowdhury]

Dear all siesta user,
How do I know if my molecular dynamics simulation is converging or not?