[SIESTA-L] Structure of Sodalime Glass

[Younas Khan]

Hi all. I want to design structure of amorphous sodalime glass for
simulation using SIESTA. Can anybody help me with this?

Younas Khan

Re: [SIESTA-L] Research Articles on Bandstucture

[Younas Khan]

Yeah sure, but since many researchers who are working in this field are in
this group as well. So, I thought it would be a good idea if I can have a
first-hand information from them If I have some doubt in the way they have
carried out the calculations.


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On Wed, Aug 24, 2016 at 8:30 PM, Riccardo Rurali  wrote:

>
> > Thank You, I am actually doing DFT study of the bandstructure of
> Semiconductors such as CdS, CdTe etc.
>
> Dear Younas,
> What does exactly stop you from searching these articles yourself?
>
> I believe a quick search on Google will solve easily your problem.
>
> Good luck!
> Riccardo
>
>

Re: [SIESTA-L] Research Articles on Bandstucture

[Younas Khan]

Thank You, I am actually doing DFT study of the bandstructure of
Semiconductors such as CdS, CdTe etc. I need some articles which I can use
as a prototype to convert my findings into a publication. So, a good
article or two using the SIESTA method would suffice.

On Wed, Aug 24, 2016 at 7:55 PM, Matías Soto C. 
wrote:

> Dear Younas, which materials are you researching? There are many articles
> on bandstructure calculations using DFT, so if you could be more specific
> that way we can try to help you more efficiently.
>
> Thanks,
> -- Matias
>
> Matias Soto C.
> Ph.D. Canditate
> Materials Science and NanoEngineering
> Rice University
>
> On Wed, Aug 24, 2016 at 9:45 AM, Younas Khan  > wrote:
>
>> Dear All, I urgently need some articles on the bandstructure of
>> materials, calculated using SIESTA (preferably), or any other DFT method.
>> Help in this regard will be appreciated.
>>
>> Younas Khan
>>
>>
>> <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail&utm_term=icon>
>>  Virus-free.
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>> <#m_-8462786957954063402_m_-3506282493426732620_DDB4FAA8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
>>
>
>

[SIESTA-L] Research Articles on Bandstucture

[Younas Khan]

Dear All, I urgently need some articles on the bandstructure of materials,
calculated using SIESTA (preferably), or any other DFT method. Help in this
regard will be appreciated.

Younas Khan

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Re: [SIESTA-L] MD simulation

[Younas Khan]

This is a typical MD problem in SIESTA. It has been discussed several time
here. Kindly go through the old threads, you will find an answer. Best of
Luck.



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On Wed, Jun 1, 2016 at 6:25 PM, ZARA NBSH  wrote:

> Dear all,
> I am new in siesta and would like to perform molecular dynamics
> calculation on graphene sheet with periodic boundary conditions and the
> total number of C atoms  200.
>
> I set the temperature to 300K, but in the output the temperature
> fluctuations are very large between 230 to 360 K.
> I copy the input file here.
> Would any one help me what is wrong in my calculations?
>
>
>
> # fdf file
>
> SystemName  graphene
> SystemLabel c
>
> NumberOfAtoms   200
> NumberOfSpecies 1
>
> %block ChemicalSpeciesLabel
>  1  6  C
> %endblock ChemicalSpeciesLabel
>
> XC.functional GGA
> XC.authorsPBE
>
>
> LatticeConstant 2.471763457 Ang
>
> %block LatticeParameters
>  10   8.66025404 890.  90. 90.
> %endblock LatticeParameters
>
> AtomicCoordinatesFormat Ang
> AtomicCoordinatesAndAtomicSpecies < xyz
>
>
> %block kgrid_Monkhorst_Pack
>   1000.0
>   0100.0
>   0010.0
> %endblock kgrid_Monkhorst_Pack
>
> MeshCutoff  300.0 Ry
>
> # SCF options
> MaxSCFIterations  100   # Maximum number of SCF iter
> DM.NumberPulay 3# One Pulay every 3 iter
> DM.MixingWeight   0.25  # New DM amount for next SCF cycle
> DM.Tolerance  5.d-4 # Tolerance in maximum difference
>
> SolutionMethoddiagon# OrderN or Diagon
> ElectronicTemperature  25 meV   # Temp. for Fermi smearing
>
>
> # structural infomation
> AtomCoorFormatOut Ang
> WriteCoorXmol T
> WriteMDXmol T
> WriteForces T
>
> # options for MD
> MD.MaxForceTol  0.01 eV/Ang
> MD.TypeOfRunNose
> MD.VariableCell T
> MD.NumCGSteps   400
> MD.Broyden.History.Steps 6
> MD.Broyden.Initial.Inverse.Jacobian 1.0
>
>
> MD.InitialTimeStep 1
> MD.FinalTimeStep 2000
> MD.LengthTimeStep 1 fs
> MD.InitialTemperature 300 K
> MD.TargetTemperature 300 K
> MD.AnnealOption TemperatureAndPressure
> MD.TauRelax 100.0 fs
>
>

Re: [SIESTA-L] how can i find powerfull system

[Younas Khan]

Please elaborate what sort of calculations you are interested in and what
is the nature of your system?

regards

Younas Khan

On Mon, Jan 11, 2016 at 9:21 PM, Mads Engelund 
wrote:

> Dear Zahra,
>
> It depends very much on your situation what is best, whether you are a
> student, employee, boss, independent
>
> First of all, ask your supervisor if (s)he has access to a cluster - no
> point in buying this if you already have it available.
> Otherwise, if you have the budget for it, many companies these day are
> offering machines over the internet, for instance Google, Amazon and
> SableCore to name a few. You would need to install SIESTA yourself on such
> machines.
> Or you could contact a (nearby) university and ask if they could get you
> access. Then you would probably have to get someone interested in your
> project.
>
> Mads Engelund
>
> PS: The number of valence electrons is a better number to quote than
> number of atoms. 300 hydrogen atoms is very different from 300 iron atoms.
>
> On 11/01/16 10:21, Zahra Talebi wrote:
>
> hi every body,
> I am going to do a siesta run for a system with about 300 atom. so I need
> a power full system,
> Is there any online powerfull system which  I can connect and put my run
> on it to be done
> thanks
> have good time
> zahra
>
>
>

Re: [SIESTA-L] Transiesta Convergence problem in zigzag nanoribbon of Graphene

[Younas Khan]

My Pleasure.

Younas

On Sun, Dec 13, 2015 at 1:17 PM, Riya Rogers 
wrote:

> thank you so much
>
> Regards
> Riya
>
> On Mon, Dec 7, 2015 at 10:29 AM, Younas Khan  > wrote:
>
>> Well I think You have not specified the type of run in your input file.
>> Put 'MD.TypeOfRun=CG' and try again.
>> Best of luck.
>>
>> Younas Khan
>>
>> On Wed, Dec 2, 2015 at 5:30 PM, Riya Rogers 
>> wrote:
>>
>>> Here is my fdf file.
>>>
>>> Regards
>>> Riya
>>>
>>> On Mon, Nov 23, 2015 at 9:20 PM, Younas Khan <
>>> younaskhan.phys...@gmail.com> wrote:
>>>
>>>> Kindly share your input file so that it becomes easy to find out where
>>>> you are making a mistake.
>>>>
>>>> Thanks
>>>>
>>>>
>>>> On Mon, Nov 23, 2015 at 4:52 PM, Riya Rogers 
>>>> wrote:
>>>>
>>>>>
>>>>> Hello everyone
>>>>>
>>>>> I am trying to simulate the Zigzag Graphene Nanoribbon (hydrogen
>>>>> passivated)with boron doping for my project work. But transiesta won't
>>>>> converge.
>>>>>
>>>>> Which parameters should I vary to achieve convergence?
>>>>> Can anyone help me in converging transiesta?
>>>>>
>>>>> Thanks
>>>>>
>>>>> Regards
>>>>>
>>>>>
>>>>
>>>
>>
>

Re: [SIESTA-L] Transiesta Convergence problem in zigzag nanoribbon of Graphene

[Younas Khan]

Well I think You have not specified the type of run in your input file. Put
'MD.TypeOfRun=CG' and try again.
Best of luck.

Younas Khan

On Wed, Dec 2, 2015 at 5:30 PM, Riya Rogers  wrote:

> Here is my fdf file.
>
> Regards
> Riya
>
> On Mon, Nov 23, 2015 at 9:20 PM, Younas Khan  > wrote:
>
>> Kindly share your input file so that it becomes easy to find out where
>> you are making a mistake.
>>
>> Thanks
>>
>>
>> On Mon, Nov 23, 2015 at 4:52 PM, Riya Rogers 
>> wrote:
>>
>>>
>>> Hello everyone
>>>
>>> I am trying to simulate the Zigzag Graphene Nanoribbon (hydrogen
>>> passivated)with boron doping for my project work. But transiesta won't
>>> converge.
>>>
>>> Which parameters should I vary to achieve convergence?
>>> Can anyone help me in converging transiesta?
>>>
>>> Thanks
>>>
>>> Regards
>>>
>>>
>>
>

Re: [SIESTA-L] Transiesta Convergence problem in zigzag nanoribbon of Graphene

[Younas Khan]

Kindly share your input file so that it becomes easy to find out where you
are making a mistake.

Thanks


On Mon, Nov 23, 2015 at 4:52 PM, Riya Rogers 
wrote:

>
> Hello everyone
>
> I am trying to simulate the Zigzag Graphene Nanoribbon (hydrogen
> passivated)with boron doping for my project work. But transiesta won't
> converge.
>
> Which parameters should I vary to achieve convergence?
> Can anyone help me in converging transiesta?
>
> Thanks
>
> Regards
>
>

Re: [SIESTA-L] Temperature control

[Younas Khan]

A very valid question. Me too looking for the solution. The seniors on this
group should extend some help in this regard.

Younas Khan


On Mon, Nov 9, 2015 at 5:39 AM, Kausala Mylvaganam  wrote:

>
> Hi All,
> Herewith I have attached the file that I used to run MD simulation at 825
> K. Even after running the simulation for 2000 steps, I find that the
> temperature fluctuates by over 200 K.
> Is there a way to fix the temperature fluctuation within 5 - 10 K? Else
> please let me know the ways of  reducing the temperature fluctuation.
>
> Best Regards
> Kausala
>

[SIESTA-L] MD scheme in SIESTA

[Younas Khan]

Hi all. I wanted to know which scheme of Molecular Dynamics is implemented
in SIESTA? is it classical (MM), Quantum mechanical (QM) or hybrid
(QM/MM)??
Your comments on this will be appreciated.

Re: [SIESTA-L] Error in band structure calculations

[Younas Khan]

It would be better if You can share your input file.

Younas


On Thu, Oct 22, 2015 at 3:23 PM, Razie Mohebbi 
wrote:

> I am trying to calculate the bandgap energy of GaP, after convergence I
> receive this message at the end of output file
>
> "Wrong number of atoms in existing NC set!!
> Stopping Program from Node:"
>
> would you please help me solve this problem.
>
>

Re: [SIESTA-L] Crystal structure formats

[Younas Khan]

Thanks Camps. So it means it is equivalent to use either the 8 atoms
co-ordinates (the conventional cell) or the primitive cell (2 atoms)
co-ordinates i.e. both should give similar results.


On Wed, Oct 21, 2015 at 2:59 PM, I. Camps  wrote:

> As professor Gul explained, the xyz format lack the crystal information,
> so you only will see "the molecule". For me, the image you send is ok:
> showing the atoms position with its bonds (but without the crystal
> periodicity). Take a look at the files using common text editor program.
>
>
> []'s,
>
> @mps
>
> On Wed, Oct 21, 2015 at 7:48 AM, Younas Khan  > wrote:
>
>> Thank You sir for your kind reply. However, there are still some issues
>> which need to be clarified. For example when I take the conventional unit
>> cell, the xyz file consists of 8 co-ordinates. When I again visualize this
>> xyz file, it does not look like a conventional unit cell;it looks strange.
>> I have attached an image for clarity.
>>
>> On Wed, Oct 21, 2015 at 12:39 AM, Gul Rahman 
>> wrote:
>>
>>> Younas,
>>> It is very simple
>>> 2 atoms cell is the primitive cell of bulk ZnS.
>>> 8 atoms cell is the conventional cell of bulk ZnS.
>>> 18 atoms will be the molecular/cluster (Zn14S4) structure of ZnS. xyz
>>> formate is for molecular, and you can also see the boundary conditions in
>>> all these structures.
>>> I will expect the same results from 2 and 8 atoms bulk ZnS, but  will
>>> expect different results from Zn14S4  due to charge neutrality of ZnS.
>>> Gul
>>>
>>> Dr. Gul Rahman
>>> Assistant Professor,
>>> Department of Physics,
>>> Quaid-i-Azam University,
>>> Islamabad, Pakistan
>>> http://www.qau.edu.pk/profile.php?id=818020
>>>
>>>
>>>
>>> On Tuesday, 20 October 2015, 22:45, Younas Khan <
>>> younaskhan.phys...@gmail.com> wrote:
>>>
>>>
>>> Hi all. My question is not siesta-specific, however its a good forum to
>>> discuss it. After designing a structure in a specific software (say
>>> materials studio) we can save it in various formats such as Pdb, .vasp or
>>> .xyz, however all these formats show different number of atoms for the same
>>> structure. For example, when we save a ZnS unit cell (zinc blend) structure
>>> in pdb it gives us co-ordinates of two atoms i.e Zn and S, in case of xyz I
>>> have 18 atoms (4 S and 14 Zn) and in case of .vasp I get 8 atoms (4 S and 4
>>> Z). My question is: are these formats equally valid and will lead to same
>>> results??? What is the difference between them, if any.
>>>
>>> Thanks
>>>
>>>
>>>
>>>
>>>
>>
>

[SIESTA-L] Crystal structure formats

[Younas Khan]

Hi all. My question is not siesta-specific, however its a good forum to
discuss it. After designing a structure in a specific software (say
materials studio) we can save it in various formats such as Pdb, .vasp or
.xyz, however all these formats show different number of atoms for the same
structure. For example, when we save a ZnS unit cell (zinc blend) structure
in pdb it gives us co-ordinates of two atoms i.e Zn and S, in case of xyz I
have 18 atoms (4 S and 14 Zn) and in case of .vasp I get 8 atoms (4 S and 4
Z). My question is: are these formats equally valid and will lead to same
results??? What is the difference between them, if any.

Thanks

[SIESTA-L] MD simulations

[Younas Khan]

Hi. I wanted to ask when an MD run comes to an end? I mean in CG
optimization if the force tolerance is reached, the run terminates. The MD
run must complete it specified steps to complete or is there another
criteria?
regards
Younas

[SIESTA-L] Nose MD

[Younas Khan]

Hi all. I am doing nose MD simulation for the diffusion of silver ion in
silica. I am not sure how to set the following two parameters:

MD.LengthTimeStep   
MD.InitialTimeStep 
MD.FinalTimeStep 

The confusion is that should the length of time step and number of time
steps be chosen in accordance with the actual phenomena which is silver
diffusion in my case.


Regards


Younas Khan

Re: [SIESTA-L] error during pseudopotential generation

[Younas Khan]

You can easily find the input file for Eu Psf on siesta website. Modify the
inp file a little bit i.e. add or remove electrons
from the required orbitals and then use ATOM program to generate ionic
pseudopotential files.

Younas Khan

On Sat, Oct 3, 2015 at 6:20 PM, Durga Banchhor 
wrote:

> Dear all,
> I am a new user of siesta and i am interested to study Eu2+ and Eu3+
> doped systems for which I am trying to generate the pseudopotential
> for Eu.  I have tried to
> create this file several time using examples for Oxegen and others.  I
> get the following error message.
>
> cp: cannot stat `VPSOUT': No such file or directory
> cp: cannot stat `VPSFMT': No such file or directory
> ==> Output data in directory Eu
> ==> Pseudopotential in Eu.
>
> Any other suggestions on what I am doing wrong?
>
>  pg Europium
>  tm2 2.0
>  n=Eu c=ca
>  0.000 0.000 0.000 0.000 0.000 0.000
>114
>6 0 2.00  0.00
>6 1 0.00  0.00
>5 2 0.00  0.00
>4 3 7.00  0.00
> 3.2000   3.2000   3.2000   3.2000
>
> If any one have psf file of Eu kindly i request to share
>
> Thanking You.
>

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

[Younas Khan]

Hello and welcome to siesta community.


On Fri, Oct 2, 2015 at 8:51 PM, Riya Rogers  wrote:

> Hello everyone
>

Re: [SIESTA-L] optic

[Younas Khan]

Yes you can. You can use the block for optical properties. The details are
mentioned in the manual.

Thanks

On Sun, Sep 20, 2015 at 2:47 AM, Soumaia Djaadi 
wrote:

>
>
>   Hi Younnas khan
> Can i calculate the optical properties  for  Germanium clusters using
> siesta ? How ?
>
>
>   Regards
>
>Soumaia DJAADI
>
>
>
>
>
>

Re: [SIESTA-L] Ghost states in psf files

[Younas Khan]

Thank You Mostafa. I will try these.

On Thu, Sep 10, 2015 at 11:47 AM, Mostafa Shabani <
mostafa.nanophys...@gmail.com> wrote:

> Dear Younas Khan
> *Try this pseudo potentials*
> *Best regards   *
>
> On Tue, Sep 8, 2015 at 10:16 PM, Younas Khan  > wrote:
>
>> thank You dear
>>
>> On Tue, Sep 8, 2015 at 10:34 PM, azar ostovan 
>> wrote:
>>
>>> I have just S.psf , and it's working for my calculations.
>>>
>>> regards
>>> azar
>>>
>>> On Tue, Sep 8, 2015 at 6:48 AM, Younas Khan <
>>> younaskhan.phys...@gmail.com> wrote:
>>>
>>>> Hi all. Can anybody send me GGA pseudopotentials for Zn,S,Cd,Te,Se. I
>>>> have downloaded from siesta webpage but they are showing ghost states, so
>>>> not working.
>>>> I shall be grateful.
>>>>
>>>> Thanks
>>>>
>>>> Younas Khan
>>>>
>>>
>>>
>>
>

Re: [SIESTA-L] Ghost states in psf files

[Younas Khan]

thank You dear

On Tue, Sep 8, 2015 at 10:34 PM, azar ostovan  wrote:

> I have just S.psf , and it's working for my calculations.
>
> regards
> azar
>
> On Tue, Sep 8, 2015 at 6:48 AM, Younas Khan 
> wrote:
>
>> Hi all. Can anybody send me GGA pseudopotentials for Zn,S,Cd,Te,Se. I
>> have downloaded from siesta webpage but they are showing ghost states, so
>> not working.
>> I shall be grateful.
>>
>> Thanks
>>
>> Younas Khan
>>
>
>

Re: [SIESTA-L] fedora 20

[Younas Khan]

So you have no fortran in your system. Please use the command *sudo apt-get
install gfortran *to install gfortran, then use the command
*gfortran optical.f -o optical *compile the optical utility. Hope this will
work.

Younas Khan

On Tue, Sep 8, 2015 at 2:34 AM, Soumaia Djaadi  wrote:

>
>  Hi Younnas khan
> I used the command: which fortran
> [dell-inspiron@localhost ~]$ which fortran
> /usr/bin/which: no fortran in
> (/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/home/dell-inspiron/.local/bin:/home/dell-inspiron/bin)
> [dell-inspiron@localhost ~]$
> Do  must install the Fortran my system
>
>
>
>  Regards
>
>   Soumaia DJAADI
>
>
>
>
>
>

[SIESTA-L] Ghost states in psf files

[Younas Khan]

Hi all. Can anybody send me GGA pseudopotentials for Zn,S,Cd,Te,Se. I have
downloaded from siesta webpage but they are showing ghost states, so not
working.
I shall be grateful.

Thanks

Younas Khan

Re: [SIESTA-L] fedora 20

[Younas Khan]

Please use the command: *which fortran* to know the version of your fortran
compiler.

thanks

On Mon, Sep 7, 2015 at 5:44 PM, Soumaia Djaadi  wrote:

>
>
> Hi Younnas khan
>  no results, this is erreur message and fortran compiler installed in my
> system
>
> [dell-inspiron@localhost Optical]$ gfortran  optical.f -o optical
> bash: gfortran: command not found...
> [dell-inspiron@localhost Optical]$ man -k fortran
> ctags (1p)   - create a tags file (DEVELOPMENT, FORTRAN)
> fort77 (1p)  - FORTRAN compiler (FORTRAN)
> [dell-inspiron@localhost Optical]$
> Regards
>  Soumaia DJAADI
>
>

[SIESTA-L] Time Scale for MD Simulation

[Younas Khan]

Hi all. I am performing MD simulation of silver diffusion in silica.
Experimentally, the diffusion process has been studied for a time scale of
few hours. What number of time steps should i choose to model the process
accurately?


Regards

Younas Khan

Re: [SIESTA-L] fedora 20

[Younas Khan]

Can you tell which fortran compiler is installed on your system. If it is
gfortran then use: gfortran  optical.f -o optical
You must know which fortran compiler you are using.

Younas

On Sun, Sep 6, 2015 at 7:10 PM, Soumaia Djaadi  wrote:

> This is error message :
> [dell-inspiron@localhost Optical]$ f77  optical.f -o optical
> bash: f77: command not found...
>
>

Re: [SIESTA-L] linux fedora 20

[Younas Khan]

what error message are you getting when you enter the commands?

On Sat, Sep 5, 2015 at 10:13 PM, Soumaia Djaadi 
wrote:

> Thanks for help me Younas Khan
> I have tried but without result. What to do ?
> Soumaia DJAADI
>

Re: [SIESTA-L] linux fedora 20

[Younas Khan]

Issue the commands:





*  f77 input.f -o input f77  optical.f -o optical*
use your own compiler if it is different than f77.

Younas Khan


On Fri, Sep 4, 2015 at 12:16 AM, Soumaia Djaadi 
wrote:

>
>
>  hi, how to compile
> input.f and optical.f in linux fedora 20 ?
>
>
>  can any one help me?
>
>  soumaia djaadi
>

[SIESTA-L] Optical Properties Calculations

[Younas Khan]

Hi all. I want to calculate optical properties for CdS semiconductor. Now
there are two possible approaches:

1) I optimize the structure and then include the block for optical
properties calculation and the relaxed co-ordinates in the input file and
again run siesta with single point energy this time.

2) I include the block for optical calculation and the initial co-ordinates
(un-relaxed) and perform both the optimization and optical calculation at
the same time.

Kindly tell me which approach is right and correct me please if both the
approaches mentioned are wrong.


Thanks

Re: [SIESTA-L] I am new to siesta

[Younas Khan]

Sure

On Sun, Aug 9, 2015 at 1:07 PM, Fida Ullah  wrote:

> I want to discuss some problem with siesta user
>

Re: [SIESTA-L] The energy band gap of LiF

[Younas Khan]

Hi. How did you shift the fermi level to zero? I mean did you make any
changes in the input file or something else???

On Sat, Aug 8, 2015 at 1:42 PM, Mayuri Vaghela 
wrote:

> hi siesta users i am calculating band structure for HgNa i will get Fermi
> energy -2.0617 ev.
> is it proper or i am going in wrong direction. i have taken triclinic
> structure for HgNa alloy.
>
>
> On Sat, Aug 8, 2015 at 9:16 AM, 毛飞 <200921220...@mail.bnu.edu.cn> wrote:
>
>> Dear Zhen and Rahman
>>
>>
>>
>> Yes, I have had shifted the Fermi energy to 0 eV, but I did not mark the
>> Fermi energy at 0 eV. Then the obtained energy gap of LiF is 8.43 eV.
>>
>>
>>
>> Thank you.
>>
>> Regards,
>>
>>
>>
>> Fei
>>
>> 在2015-08-08，grnphysics  写道:
>>
>> -原始邮件-
>> *发件人:* grnphysics 
>> *发送时间:* 2015年8月8日 星期六
>> *收件人:* siesta-l@uam.es
>> *主题:* Re: [SIESTA-L] The energy band gap of LiF
>>
>> In my test calculation the Fermi enrgy was -7.33 eV.
>>
>>
>>
>> Sent from Samsung Mobile
>>
>>
>>  Original message 
>> From: 毛飞 <200921220...@mail.bnu.edu.cn>
>> Date:2015/08/07 2:59 PM (GMT+05:00)
>> To: siesta-l@uam.es
>> Cc: zhn...@gmail.com,grnphys...@yahoo.com
>> Subject: Re:[SIESTA-L] The energy band gap of LiF
>>
>> Dear Zhen and Rahman
>>
>>
>>
>> It can be seen from the E(k), the bangap at the Gamma point is 19.5 eV,
>> it is a little larger than anywhere else (see attachment). Does it strange?
>> The Fermi energy is at -7.44 eV, which is read from the *.bands file.
>>
>>
>>
>> Rahman, do you test the LiF calculation with the same input file with me,
>> if not, can you show me the input file? I want to know what is the
>> difference between them, and obtain the correct band structure of LiF.
>>
>>
>>
>> Thank you in advance.
>>
>>
>>
>> Regards,
>>
>>
>>
>> Fei
>>
>>
>> 在2015-08-07，Zhen Zhu  写道:
>>
>> -原始邮件-
>> *发件人:* Zhen Zhu 
>> *发送时间:* 2015年8月7日 星期五
>> *收件人:* Gul Rahman 
>> *抄送:* "siesta-l@uam.es" 
>> *主题:* Re: [SIESTA-L] The energy band gap of LiF
>>
>> Hi Fei,
>>
>> are you sure your Fermi level is correct?
>>
>> --Zhen
>>
>> On Thu, Aug 6, 2015 at 11:43 PM, Gul Rahman  wrote:
>>
>>> Are you calculating the bandgap at the Gamma Point?
>>> It is around 8.40 eV at Gamma point (my test calculation). Sure, this
>>> will be different at the other symmetry points in the BZ.
>>> Gul
>>>
>>> Dr. Gul Rahman
>>> Assistant Professor,
>>> Department of Physics,
>>> Quaid-i-Azam University,
>>> Islamabad, Pakistan
>>> http://www.qau.edu.pk/profile.php?id=818020
>>>
>>>
>>>
>>> On Thursday, 6 August 2015, 16:36, 毛飞 <200921220...@mail.bnu.edu.cn>
>>> wrote:
>>>
>>>
>>> Dear Zhen and Rahman
>>>
>>> Thank you for your useful suggestions. Please excuse me to bother you
>>> again.
>>>
>>> I calculate the band structure of LiF again, and I think I have already
>>> corrected the errors in the new input file, but the result is still
>>> unreasonable, the band gap of LiF is 15.8 eV (it is too large). You are
>>> right, the structure of LiF is the same with NaCl. I define the primitive
>>> cell as the simulation cell (see block LatticeVectors) in the input file.
>>>
>>> Regards,
>>>
>>> Fei
>>>
>>>  Input file ###
>>> SystemName  bulk.LiF
>>> SystemLabel bulk_LiF
>>>
>>> NumberOfAtoms   2
>>> NumberOfSpecies 2
>>>
>>> %block ChemicalSpeciesLabel
>>>  13Li
>>>  29F
>>> %endblock ChemicalSpeciesLabel
>>>
>>> # basis
>>> PAO.BasisSize   DZP
>>> PAO.EnergyShift 200 meV
>>>
>>> LatticeConstant4.08  Ang  # Lattice constant alat
>>> %block LatticeVectors # primitive cell
>>>   0.000  0.500  0.500
>>>   0.500  0.000  0.500
>>>   0.500  0.500  0.000
>>> %endblock LatticeVectors
>>>
>>> %block kgrid_Monkhorst_Pack
>>>  10 0 0   0.0
>>>  0 10 0   0.0
>>>  0 0 10   0.0
>>> %endblock kgrid_Monkhorst_Pack
>>>
>>>
>>> BandLinesScale  ReciprocalLatticeVectors
>>> %block BandLines
>>> 1 0.0   0.0   0.0 # Gamma-point
>>> 200.5   0.0   0.5 # X-point
>>> 300.5   0.25  0.75# W-point
>>> 300.375 0.375 0.75# K-point
>>> 300.0   0.0   0.0 # Gamma-point
>>> %endblock BandLines
>>>
>>>
>>> %block  ProjectedDensityOfStates
>>>  -20 10 0.1  300eV
>>> %endblock ProjectedDensityOfStates
>>>
>>> MeshCutoff  300.0 Ry
>>>
>>> # SCF options
>>> MaxSCFIterations  100   # Maximum number of SCF iter
>>> DM.NumberPulay 3# One Pulay every 3 iter
>>> DM.MixingWeight   0.35 # New DM amount for next SCF cycle
>>> DM.Tolerance  5.d-4 # Tolerance in maximum difference
>>>
>>> SolutionMethoddiagon# OrderN or Diagon
>>> OccupationFunctionFD
>>> ElectronicTemperature  25 meV   # Temp. for Fermi smearing
>>>
>>> # exchange-correlation functional
>>>
>>
>>
>

Re: [SIESTA-L] convert file .xv to xsf

[Younas Khan]

I have transferred the .XV file to my directory but the problem remains
same.


On Fri, Aug 7, 2015 at 11:15 AM, Zhen Zhu  wrote:

> Hi Younas,
>
> *.XV file is also an output of SIESTA. You should put it in the same
> folder as *.RHO. rho2xsf will read both files at the same time.
>
> --Zhen
>
> On Thu, Aug 6, 2015 at 10:44 PM, Younas Khan  > wrote:
>
>> I am having similar problem with rho2xsf utility. When I enter the system
>> label, I get the following error:
>>
>> *"Error opening file polyacetyline.RHO.XV as old formatted"*
>> Note that my system label is polyacetyline.RHO. I dont know how I get
>> polyacetyline.RHO.XV in the error message.
>>
>> Any clue?
>>
>> Younas
>>
>> On Mon, Aug 3, 2015 at 9:13 AM, Jeetu Donderiya <
>> jeetudonderiya2...@gmail.com> wrote:
>>
>>> Thanks for best suggestion.
>>>
>>> On Sun, Aug 2, 2015 at 9:48 AM, Altaf Ur Rahman 
>>> wrote:
>>>
>>>> For examle there is file CH.XV when you give the command " ~/bin/xv2xsf
>>>> then press enter and it will demand *SystemLabel *which can be read
>>>> from your input file. so in this example your System Label as CH
>>>>
>>>>
>>>> On Sat, Aug 1, 2015 at 2:19 PM, Jeetu Donderiya <
>>>> jeetudonderiya2...@gmail.com> wrote:
>>>>
>>>>> Hello SIESTA user
>>>>>
>>>>> I am trying to view crystal structure with the help of xcrysden
>>>>> software which reads file in xsf formate.so I want to convert .xv file
>>>>> generated by siesta to xsf  formate by using xv2xsf siesta utility. But
>>>>> there is some error -
>>>>>   Specify  SystemLabel (or 'siesta' if none):   Error opening file
>>>>> 37.927574328.XV as old formatted
>>>>> Please suggest me, where should i define system lavel?
>>>>>
>>>>
>>>>
>>>
>>
>
>
> --
> Zhen Zhu,
> Postdoctoral Researcher
> Materials Department
> University of California
> Santa Barbara, CA 93106-5050 U.S.A.
> Tel:  +1-517-488-2298
> Email: zhn...@gmail.com
>   zhuz...@engineering.ucsb.edu
>

Re: [SIESTA-L] convert file .xv to xsf

[Younas Khan]

I am having similar problem with rho2xsf utility. When I enter the system
label, I get the following error:

*"Error opening file polyacetyline.RHO.XV as old formatted"*
Note that my system label is polyacetyline.RHO. I dont know how I get
polyacetyline.RHO.XV in the error message.

Any clue?

Younas

On Mon, Aug 3, 2015 at 9:13 AM, Jeetu Donderiya <
jeetudonderiya2...@gmail.com> wrote:

> Thanks for best suggestion.
>
> On Sun, Aug 2, 2015 at 9:48 AM, Altaf Ur Rahman 
> wrote:
>
>> For examle there is file CH.XV when you give the command " ~/bin/xv2xsf
>> then press enter and it will demand *SystemLabel *which can be read from
>> your input file. so in this example your System Label as CH
>>
>>
>> On Sat, Aug 1, 2015 at 2:19 PM, Jeetu Donderiya <
>> jeetudonderiya2...@gmail.com> wrote:
>>
>>> Hello SIESTA user
>>>
>>> I am trying to view crystal structure with the help of xcrysden software
>>> which reads file in xsf formate.so I want to convert .xv file generated by
>>> siesta to xsf  formate by using xv2xsf siesta utility. But there is some
>>> error -
>>>   Specify  SystemLabel (or 'siesta' if none):   Error opening file
>>> 37.927574328.XV as old formatted
>>> Please suggest me, where should i define system lavel?
>>>
>>
>>
>

Re: [SIESTA-L] Calculating Charge Density Using saverho Option

[Younas Khan]

Thank You Zhen

On Wed, Aug 5, 2015 at 10:37 AM, Zhen Zhu  wrote:

> It is straight forward. Just use the flag SAVERHO = .TRUE.. Then you will
> get nametag.RHO file. That is what you want.
>
> You need some scripts to convert *.RHO to cube files that could be viewed
> by softwares like XCRYSDEN and so on.
>
> --Zhen
>
> On Tue, Aug 4, 2015 at 10:26 PM, Younas Khan  > wrote:
>
>> Hi all.
>>
>> How I can calculate the charge density using the saverho option? Can
>> anybody help?
>>
>> Younas
>>
>>
>
>
> --
> Zhen Zhu,
> Postdoctoral Researcher
> Materials Department
> University of California
> Santa Barbara, CA 93106-5050 U.S.A.
> Tel:  +1-517-488-2298
> Email: zhn...@gmail.com
>   zhuz...@engineering.ucsb.edu
>

[SIESTA-L] Calculating Charge Density Using saverho Option

[Younas Khan]

Hi all.

How I can calculate the charge density using the saverho option? Can
anybody help?

Younas

Re: [SIESTA-L] The energy band gap of LiF

[Younas Khan]

I think you have incorrectly written the lattice vectors. Kindly check it,
they may not be in proper format.

Younas Khan

On Tuesday, August 4, 2015, 毛飞 <200921220...@mail.bnu.edu.cn> wrote:

> Dear Rahman
>
>
>
> Thank you for your reply, I will try the calculation with your suggestions.
>
>
>
> Fei
>
> 在2015-08-04，Gul Rahman  > 写道:
>
> -原始邮件-
> *发件人:* Gul Rahman  >
> *发送时间:* 2015年8月4日 星期二
> *收件人:* "siesta-l@uam.es "
> >
> *主题:* Re: [SIESTA-L] The energy band gap of LiF
>
> Dear Fei Mao,
> Yes, your band structure is strange, it has flat band (like molecules) and
> the band gap is very large, which is wrong.
> Plz, look carefully into your input file.
> First, try to reproduce the band structure and  lattice parameters of bulk
> (primitive) LiF, then you can generate the SuperCell either using your
> pencil in hands (:) or using the SIESTA or any other computer code. And
> then put the Atomic coordinates of the Supercell explicitly in your fdf
> file. You can see you have defined SuperCell (2x2x2) in your fdf file.
> Also, try to use fractional coordinates if you are dealing with a bulk
> system. Whenever you generate .XV file, you must visualise it to see what's
> going on.
> Also, your k-points sampling is not good for the bulk LiF system. You must
> use dense k-points. I will not use 1x1x1 for bulk. I have to converge it.
> I hope it may help.
> Regards,
> Gul
>
>
> Dr. Gul Rahman
> Assistant Professor,
> Department of Physics,
> Quaid-i-Azam University,
> Islamabad, Pakistan
> http://www.qau.edu.pk/profile.php?id=818020
>
>
>
> On Tuesday, 4 August 2015, 14:21, 毛飞 <200921220...@mail.bnu.edu.cn
> > wrote:
>
>
> Dear Rahman and Vaghela
>
> Thank you for kind replies.
> The Fermi energy level is at -5.9 eV in the calculation, I modify the fig
> and mark the Fermi energy by a black line (which is attached). Now, I am
> puzzled by two points in this fig.
>
> 1.  As shown in the fig, the conduction and valence band are both
> composed by many straight lines, it seems to me very strange. Generally,
> these energy levels evolves smoothly with changes in k, forming a smooth
> band of states, and there are conduction band bottom and valence band top.
> However, these typical characters are absence in the fig.
>
> 2.  It can be seen from the fig that, the energy gap of LiF is about
> 16 eV (the experimental one is 14 eV), but the LDA calculations usually
> underestimate the gap.
>
> Any comment is appreciated, and thank you in advance.
> Sincerely
>
> Fei Mao
> University of South China, China
>
>
>
>
>
> 在2015-08-04，Mayuri Vaghela  > 写道:
>
> -原始邮件-
> *发件人:* Mayuri Vaghela  >
> *发送时间:* 2015年8月4日 星期二
> *收件人:* siesta-l@uam.es 
> *主题:* Re: [SIESTA-L] The energy band gap of LiF
>
> first check systemlabel.EIG file,
> you will get fermi energy from that file.
> now draw clear line using set axis command of gnuplot at appropriate
> energy value
> from that you can distinguish band gap between CB &VB...
>
>
> On Tue, Aug 4, 2015 at 10:47 AM, Altaf Ur Rahman  > wrote:
>
> Dear when you calculate the band structure by using like gnuplot you must
> see the fermi energy from your band data file/EIG file and then when you
> plot the you can write in the gnuplot this sentence
> *set zero axis 3*
> gnuplot> plot './Band.data' u ($1)+3.23:2 w l
>
> here in above case your fermi energy is 3.23
>  and you can see the fermi line will appear that clearly distiguish the
> conduction and valance band
>
>
>
> On Mon, Aug 3, 2015 at 6:04 PM, 毛飞 <200921220...@mail.bnu.edu.cn
> > wrote:
>
> Dear siesta developers and users
>
> I am a newbie in band structure calculation. I calculate the band
> structure of LiF, and a 2*2*2 supercell of 64 atoms is selected. In this
> calculation, the local density approximation (LDA) is adopted for the
> exchange-correlation functional term, the band structure is obtained along
> the high symmetric line Γ->X->W->Γ, only gamma point is used for
> Brillouin zone sampling, more details can be found in the input file which
> is attached below.
>
> I can not understand the results of the E(k) (two figs are also attached),
> it seems there are two band gaps formed in the calculation (the Fermi
> energy is shifted to 0 eV), I want to know which one (gap 1 or gap 2) is
> the band gap in my calculation, and how does another gap come from?
>
> Is there anything wrong in the input file?
>
> Please help me, any suggestion or comment is appreciated.
> Sincerely
>
> Fei Mao
> University of South China, China
>
> #

Re: [SIESTA-L] Band Structure of ZnS

[Younas Khan]

No, the structures are different. I just want to know whether the lattice
vectors are for the primitive cell of MgO or for conventional cell?

Thanks

On Mon, Jul 27, 2015 at 11:46 AM,  wrote:

> The lattice vectors in Angstrom are
> 5.40930 0 0
> 0 5.40930 0
> 0 0 5.40930
>
>
> > Hi all. I am calculating the band structure of ZnS unit cell. I am
> > following an exercise for MgO given on SIESTA webpage. The attached Image
> > shows the lattice vectors for MgO. Can anybody explain to me in which
> > format the lattice vectors are written here? When I do my calculations
> for
> > the ZnS, the results look very odd. I am sure that I am writing the
> > lattice
> > vectors wrong.
> >
> > [image: Inline image 3]
> > (Lattice Vectors for MgO)
> >
> >
> >
> > The lattice vectors for ZnS designed in materials studio are:
> >
> >
> > LatticeConstant 5.40930 Ang
> > %block LatticeVectors
> >   1.000  0.000  0.000
> >   0.000  1.000  0.000
> >   0.000  0.000  1.000
> > %endblock LatticeVectors
> >
> >
> > Thanks
> >
>
>
> *
> 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
> **
>
>

Re: [SIESTA-L] Electric Field

[Younas Khan]

Actually I am not an expert. How can I know the bulk direction and
orthogonal direction? I have designed my structure in Materials studio.


On Mon, Jul 27, 2015 at 12:11 PM, Nick Papior  wrote:

> You should know which direction is the bulk one, if it becomes zero you
> have a fully bulk calculation. So my guess is that you have setup the fdf
> file incorrectly.
>
> --
>
> Kind regards Nick Papior
> On 27 Jul 2015 07:21, "Younas Khan"  wrote:
>
>> Thank You Nick, but I am still having difficulty in understanding this
>> paragraph. I lately tried E-field in all the three directions using:
>>
>>  %block ExternalElectricField
>> 0.0004 0.0004 0.0004 V/Ang
>>  %endblock ExternalElectricField
>>
>>
>> I think in this case we should have had at least one orthogonal component
>> because according to the manual the bulk components are
>> automatically suppressed. What do you suggest?
>>
>> Thank You
>>
>> On Mon, Jul 27, 2015 at 12:12 AM, Nick Papior 
>> wrote:
>>
>>> --
>>>
>>> Kind regards Nick Papior
>>> On 26 Jul 2015 20:59, "Younas Khan" 
>>> wrote:
>>> >
>>> > Hi all. I applied electric field to my system using the block:
>>> >
>>> > %block ExternalElectricField
>>> > 0. 0. 0.0004 V/Ang
>>> > %endblock ExternalElectricField
>>> >
>>> > However, in the output file I get the following error:
>>> >
>>> > efield: WARNING: Non zero bulk electric field.
>>> > efield: Input field (Ry/Bohr/e) =0.000.000.16
>>> > efield: Orthogonalized field=0.000.000.00
>>> >
>>> > The SIESTA manual has the following instructions on this issue:
>>> >
>>> > The electric field should be orthogonal to `bulk directions', like
>>> > those parallel
>>> > to a slab (bulk electric fields, like in dielectrics or
>>> > ferroelectrics, are not allowed). If it
>>> > is not, an error message is issued and the components of the field in
>>> > bulk directions are
>>> > suppressed automatically.
>>> This is why the orthogonal becomes 0. Please understand this paragraph.
>>> >
>>> >
>>> > I just wanted to know what mistake I may be making. I tried E-field in
>>> > all the three directions but i still get the warning. Anybody help me
>>> > please.
>>> >
>>> > Regards
>>> > Younas
>>>
>>
>>

[SIESTA-L] Band Structure of ZnS

[Younas Khan]

Hi all. I am calculating the band structure of ZnS unit cell. I am
following an exercise for MgO given on SIESTA webpage. The attached Image
shows the lattice vectors for MgO. Can anybody explain to me in which
format the lattice vectors are written here? When I do my calculations for
the ZnS, the results look very odd. I am sure that I am writing the lattice
vectors wrong.

[image: Inline image 3]
(Lattice Vectors for MgO)



The lattice vectors for ZnS designed in materials studio are:


LatticeConstant 5.40930 Ang
%block LatticeVectors
  1.000  0.000  0.000
  0.000  1.000  0.000
  0.000  0.000  1.000
%endblock LatticeVectors


Thanks

Re: [SIESTA-L] Electric Field

[Younas Khan]

Thank You Nick, but I am still having difficulty in understanding this
paragraph. I lately tried E-field in all the three directions using:

 %block ExternalElectricField
0.0004 0.0004 0.0004 V/Ang
 %endblock ExternalElectricField


I think in this case we should have had at least one orthogonal component
because according to the manual the bulk components are
automatically suppressed. What do you suggest?

Thank You

On Mon, Jul 27, 2015 at 12:12 AM, Nick Papior  wrote:

> --
>
> Kind regards Nick Papior
> On 26 Jul 2015 20:59, "Younas Khan"  wrote:
> >
> > Hi all. I applied electric field to my system using the block:
> >
> > %block ExternalElectricField
> > 0. 0. 0.0004 V/Ang
> > %endblock ExternalElectricField
> >
> > However, in the output file I get the following error:
> >
> > efield: WARNING: Non zero bulk electric field.
> > efield: Input field (Ry/Bohr/e) =0.000.000.16
> > efield: Orthogonalized field=0.000.000.00
> >
> > The SIESTA manual has the following instructions on this issue:
> >
> > The electric field should be orthogonal to `bulk directions', like
> > those parallel
> > to a slab (bulk electric fields, like in dielectrics or
> > ferroelectrics, are not allowed). If it
> > is not, an error message is issued and the components of the field in
> > bulk directions are
> > suppressed automatically.
> This is why the orthogonal becomes 0. Please understand this paragraph.
> >
> >
> > I just wanted to know what mistake I may be making. I tried E-field in
> > all the three directions but i still get the warning. Anybody help me
> > please.
> >
> > Regards
> > Younas
>

[SIESTA-L] Electric Field

[Younas Khan]

Hi all. I applied electric field to my system using the block:

%block ExternalElectricField
0. 0. 0.0004 V/Ang
%endblock ExternalElectricField

However, in the output file I get the following error:

efield: WARNING: Non zero bulk electric field.
efield: Input field (Ry/Bohr/e) =0.000.000.16
efield: Orthogonalized field=0.000.000.00

The SIESTA manual has the following instructions on this issue:

The electric field should be orthogonal to `bulk directions', like
those parallel
to a slab (bulk electric fields, like in dielectrics or
ferroelectrics, are not allowed). If it
is not, an error message is issued and the components of the field in
bulk directions are
suppressed automatically.


I just wanted to know what mistake I may be making. I tried E-field in
all the three directions but i still get the warning. Anybody help me
please.

Regards
Younas

[SIESTA-L] Problem with Nose MD

[Younas Khan]

Hi all. I am running nose MD for my system with same initial and final
temperature values i.e. i want to keep the temperature constant. However,
in the .MDE file, after each step, the temperature is shown to decrease
from the target value which i had set in the input. can someone explain
this behavior??

Thanks
Younas Khan

Re: [SIESTA-L] Silver ion

[Younas Khan]

Yes. But the output file still shows that the outermost shell contains 11
electrons as in the case of neutral atoms. Moreover I am calculating the
adsorption of silver ion on silica; the line "NetCharge" line does not
specify which specie should hold the net charge..

Regards

On Wed, May 27, 2015 at 12:56 PM, Jingxian Yu 
wrote:

>  HI Younas,
>
> Have you tried the line "NetCharge"? Cheers!
>
> Jin
>
>
>
> On 27-May-15 5:17 PM, Younas Khan wrote:
>
> Hi all I want to use Silver ion in my calculations i.e. a silver atom with
> +1 charge. Does anybody know how I can do this?
>
>  Regards
> Younas Khan
>
>
>

[SIESTA-L] Silver ion

[Younas Khan]

Hi all I want to use Silver ion in my calculations i.e. a silver atom with
+1 charge. Does anybody know how I can do this?

Regards
Younas Khan

Re: [SIESTA-L] How to plot graphs from given files

[Younas Khan]

Thank You Doctor sahab

On Sun, May 24, 2015 at 6:19 PM, Uma Shankar Sharma 
wrote:

> Dear Yonaus,
> No need to change format to plot adsorption coefficient etc.
>
> Yours
> DR U S SHARMA
> RJIT BSF TEKANPUR GWALIOR
> On May 24, 2015 6:45 PM, "Younas Khan" 
> wrote:
>
>> Thank You Dr. Sharma.
>>  I am particularly interested in calculating the absorption coefficient
>> from the file 'absorp_coef.out'. This file is in an obscure format. My
>> question is that do I have to make any changes in this file or use it
>> as-it-is?
>>
>>
>> Thanks
>>
>>
>> On Sun, May 24, 2015 at 6:01 PM, Uma Shankar Sharma <
>> ussharma...@gmail.com> wrote:
>>
>>> Dear Yonaus,
>>> Go through gnuplot and give command to plot e2.dat
>>>
>>> DR U S SHARMA
>>> RJIT BSF TEKANPUR GWALIOR
>>> On May 24, 2015 6:25 PM, "Younas Khan" 
>>> wrote:
>>>
>>>> Hi all.
>>>> I am learning siesta on self-help basis. currently I am trying to learn
>>>> optical calculations. I have got all the required files such as .EPSIMG,
>>>> e2.dat and those for the calculation of absorption co-efficient,
>>>> reflectance etc. Now I dont know how to plot the corresponding spectra from
>>>> these files. Do I have to make some changes in these files before I use any
>>>> standard plotting software. Kindly guide me.
>>>>
>>>>
>>>> Younas Khan
>>>>
>>>
>>

Re: [SIESTA-L] How to plot graphs from given files

[Younas Khan]

Thank You Dr. Sharma.
 I am particularly interested in calculating the absorption coefficient
from the file 'absorp_coef.out'. This file is in an obscure format. My
question is that do I have to make any changes in this file or use it
as-it-is?


Thanks


On Sun, May 24, 2015 at 6:01 PM, Uma Shankar Sharma 
wrote:

> Dear Yonaus,
> Go through gnuplot and give command to plot e2.dat
>
> DR U S SHARMA
> RJIT BSF TEKANPUR GWALIOR
> On May 24, 2015 6:25 PM, "Younas Khan" 
> wrote:
>
>> Hi all.
>> I am learning siesta on self-help basis. currently I am trying to learn
>> optical calculations. I have got all the required files such as .EPSIMG,
>> e2.dat and those for the calculation of absorption co-efficient,
>> reflectance etc. Now I dont know how to plot the corresponding spectra from
>> these files. Do I have to make some changes in these files before I use any
>> standard plotting software. Kindly guide me.
>>
>>
>> Younas Khan
>>
>

[SIESTA-L] How to plot graphs from given files

[Younas Khan]

Hi all.
I am learning siesta on self-help basis. currently I am trying to learn
optical calculations. I have got all the required files such as .EPSIMG,
e2.dat and those for the calculation of absorption co-efficient,
reflectance etc. Now I dont know how to plot the corresponding spectra from
these files. Do I have to make some changes in these files before I use any
standard plotting software. Kindly guide me.


Younas Khan

[SIESTA-L] Arch.make File for Siesta Parallel Compilation

[Younas Khan]

Hi all.
Like many others I am having serious problems in compiling siesta in
parallel mode. Can anybody share with me their arch.make file which
resulted in successful compilation? I just want to check where I may be
making the mistake.

Best regards

Younas Khan

[SIESTA-L] Adsorption of atom and Ion

[Younas Khan]

Hi all. I am trying to simulate the adsorption of Ag atom and ion on SiO2
surface, however I don't know how to distinguish atom from ion in the input
file.

Can anybody help?

Younas

[SIESTA-L] Adsorption of Ag Cation on silica Surface

[Younas Khan]

Hi all.
I want to study the adsorption of Ag ion on silica surface. I have used
co-ordinates of Ag from pdb file to study the adsorption behaviour for Ag
atom but i am not sure how to do the same in case of Ag ion.
Can anyone suggest?
Thanks

Younas

[SIESTA-L] Fused quartz Structure

[Younas Khan]

Hi all. I want to generate amorphous SiO2 (fused quartz) structure for my
simulation. I searched it in materials studio but could not find it. any
suggestions from your side?

Younas Khan

[SIESTA-L] Properties Calculation

[Younas Khan]

Hi all. I am new to SIESTA. I just wanted to know that can we calculate
optical, structural, electronic and mechanical properties of a material
using SIESTA? If yes, then what blocks should be included in the input file.

Thanks in advance.

Younas Khan

Re: [SIESTA-L] Error in running parallel job

[Younas Khan]

Nick, I used the same fdf file as used in serial mode and it worked fine in
serial. Should I make changes in it for parallel mode? If yes, then what
sort of changes?

thanks

On Sun, Mar 22, 2015 at 6:06 AM, Nick Papior Andersen 
wrote:

> Please read in the manual on how to create an FDF file. You have not
> defined any species.
>
> 2015-03-21 19:13 GMT+00:00 Younas Khan :
>
>> Hi all. I get this error when try to run a parallel job. Can anybody
>> help? what mistake I may be making?
>>
>>
>>
>> *[abc_up@hpc test_siesta_parallel]$ No species found!!!*
>> *ERROR STOP from Node:0*
>> *No species found!!!*
>> *ERROR STOP from Node:0*
>> *No species found!!!*
>> *ERROR STOP from Node:0*
>>
>> *--*
>> *mpirun noticed that process rank 1 with PID 21533 on node
>> hpc.giki.edu.pk <http://hpc.giki.edu.pk> exited on signal 6 (Aborted).*
>> *---*
>>
>
>
>
> --
> Kind regards Nick
>

[SIESTA-L] Error in running parallel job

[Younas Khan]

Hi all. I get this error when try to run a parallel job. Can anybody help?
what mistake I may be making?



*[abc_up@hpc test_siesta_parallel]$ No species found!!!*
*ERROR STOP from Node:0*
*No species found!!!*
*ERROR STOP from Node:0*
*No species found!!!*
*ERROR STOP from Node:0*
*--*
*mpirun noticed that process rank 1 with PID 21533 on node hpc.giki.edu.pk
 exited on signal 6 (Aborted).*
*---*

[SIESTA-L] Job Submission in parallel SIESTA

[Younas Khan]

Dear all. Hope you are fine.
I have just installed SIESTA in parallel. Kindly let me know how can I
submit a job using parallel version of SIESTA. Please elaborate in detail.

Thanks.

Younas Khan

[SIESTA-L] SIESTA Parallel Compilation

[Younas Khan]

Hi all. Hope you are fine. I am trying to install SIESTA in parallel on an
HPC cluster. Can anybody  provide a comprehensive guide on compilation of
the required libraries and SIESTA.
Its an ardous task for me, I shall be grateful if anybody can help me in
this regard.

Thanks in advance.

Younas Khan

Re: [SIESTA-L] Designing of protein structure

[Younas Khan]

Thanks a lot jin

On Thu, Mar 19, 2015 at 3:17 AM, Jingxian Yu 
wrote:

>  Dear Younas,
>
> I reckon you need to find a template (not temple), for example searching
> collagen in Protein Data Bank. Or even you do a litereature survey and find
> out a crystal structure of collagen. With the initial crystal, you then do
> modifications that you want. Cheers!
>
> Jin
>
>
>
> On 19/03/2015 3:38 AM, Younas Khan wrote:
>
> Thanks jin but how should I design the structure, lets say in pdb or xyz
> format??
>
>
> On Wed, Mar 18, 2015 at 4:25 PM, Jingxian Yu 
> wrote:
>
>>  Dear Younas,
>>
>> I quote the following paragraph from wikipedia (
>> http://en.wikipedia.org/wiki/Collagen).
>>
>> "Collagen is composed of a triple helix, which generally consists of two
>> identical chains (α1) and an additional chain that differs slightly in its
>> chemical composition (α2).[27]
>> <http://en.wikipedia.org/wiki/Collagen#cite_note-SzpakJAS-27> The amino
>> acid composition of collagen is atypical for proteins, particularly with
>> respect to its high hydroxyproline
>> <http://en.wikipedia.org/wiki/Hydroxyproline> content. The most common
>> motifs in the amino acid sequence of collagen are glycine
>> <http://en.wikipedia.org/wiki/Glycine>-proline
>> <http://en.wikipedia.org/wiki/Proline>-X and glycine-X-hydroxyproline,
>> where X is any amino acid other than glycine, proline or hydroxyproline.
>> The average amino acid composition for fish and mammal skin is given.[27]
>> <http://en.wikipedia.org/wiki/Collagen#cite_note-SzpakJAS-27>"
>>
>> For me, your question is clearly answered by the paragraph.
>>
>> Cheers!
>>
>> Jin
>>
>>
>>
>>
>> On 18/03/15 21:35, Younas Khan wrote:
>>
>> Dear Jingxian Yu,
>> Actually I am working on collagen protein which has a long tiple helix
>> structure but I would like to have at least one tripeptide from each of the
>> three chains of collagen triple helix. The tripeptide should most probably
>> be GLY-PRO-HYP.
>>
>>  Regards
>>
>> On Wed, Mar 18, 2015 at 3:48 PM, Jingxian Yu 
>> wrote:
>>
>>>  Dear Younas,
>>>
>>> Sorry your question is not clear to me! Do you mean the "protein" is a
>>> tripeptide, or quite long but only contains three types of amino acids? I
>>> have been working with peptide design and synthesis for some time. I hope I
>>> could help you if your question is clearer. Cheers!
>>>
>>> Jin
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> On 18/03/15 20:19, Younas Khan wrote:
>>>
>>> Hi all.
>>> I want to design a protein structure from three amino acids.
>>> Unfortunately I am unable to find the structure of required protein or its
>>> constituent amino acids in materials studio. How can I design the
>>> structure? kindly help me.
>>>
>>>  thanks
>>> Younas Khan
>>>
>>>
>>>
>>
>>
>
>

Re: [SIESTA-L] Designing of protein structure

[Younas Khan]

Thanks jin but how should I design the structure, lets say in pdb or xyz
format??


On Wed, Mar 18, 2015 at 4:25 PM, Jingxian Yu 
wrote:

>  Dear Younas,
>
> I quote the following paragraph from wikipedia (
> http://en.wikipedia.org/wiki/Collagen).
>
> "Collagen is composed of a triple helix, which generally consists of two
> identical chains (α1) and an additional chain that differs slightly in its
> chemical composition (α2).[27]
> <http://en.wikipedia.org/wiki/Collagen#cite_note-SzpakJAS-27> The amino
> acid composition of collagen is atypical for proteins, particularly with
> respect to its high hydroxyproline
> <http://en.wikipedia.org/wiki/Hydroxyproline> content. The most common
> motifs in the amino acid sequence of collagen are glycine
> <http://en.wikipedia.org/wiki/Glycine>-proline
> <http://en.wikipedia.org/wiki/Proline>-X and glycine-X-hydroxyproline,
> where X is any amino acid other than glycine, proline or hydroxyproline.
> The average amino acid composition for fish and mammal skin is given.[27]
> <http://en.wikipedia.org/wiki/Collagen#cite_note-SzpakJAS-27>"
>
> For me, your question is clearly answered by the paragraph.
>
> Cheers!
>
> Jin
>
>
>
>
> On 18/03/15 21:35, Younas Khan wrote:
>
> Dear Jingxian Yu,
> Actually I am working on collagen protein which has a long tiple helix
> structure but I would like to have at least one tripeptide from each of the
> three chains of collagen triple helix. The tripeptide should most probably
> be GLY-PRO-HYP.
>
>  Regards
>
> On Wed, Mar 18, 2015 at 3:48 PM, Jingxian Yu 
> wrote:
>
>>  Dear Younas,
>>
>> Sorry your question is not clear to me! Do you mean the "protein" is a
>> tripeptide, or quite long but only contains three types of amino acids? I
>> have been working with peptide design and synthesis for some time. I hope I
>> could help you if your question is clearer. Cheers!
>>
>> Jin
>>
>>
>>
>>
>>
>>
>>
>> On 18/03/15 20:19, Younas Khan wrote:
>>
>> Hi all.
>> I want to design a protein structure from three amino acids.
>> Unfortunately I am unable to find the structure of required protein or its
>> constituent amino acids in materials studio. How can I design the
>> structure? kindly help me.
>>
>>  thanks
>> Younas Khan
>>
>>
>>
>
>

Re: [SIESTA-L] Designing of protein structure

[Younas Khan]

Dear Jingxian Yu,
Actually I am working on collagen protein which has a long tiple helix
structure but I would like to have at least one tripeptide from each of the
three chains of collagen triple helix. The tripeptide should most probably
be GLY-PRO-HYP.

Regards

On Wed, Mar 18, 2015 at 3:48 PM, Jingxian Yu 
wrote:

>  Dear Younas,
>
> Sorry your question is not clear to me! Do you mean the "protein" is a
> tripeptide, or quite long but only contains three types of amino acids? I
> have been working with peptide design and synthesis for some time. I hope I
> could help you if your question is clearer. Cheers!
>
> Jin
>
>
>
>
>
>
>
> On 18/03/15 20:19, Younas Khan wrote:
>
> Hi all.
> I want to design a protein structure from three amino acids. Unfortunately
> I am unable to find the structure of required protein or its constituent
> amino acids in materials studio. How can I design the structure? kindly
> help me.
>
>  thanks
> Younas Khan
>
>
>

[SIESTA-L] Designing of protein structure

[Younas Khan]

Hi all.
I want to design a protein structure from three amino acids. Unfortunately
I am unable to find the structure of required protein or its constituent
amino acids in materials studio. How can I design the structure? kindly
help me.

thanks
Younas Khan

[SIESTA-L] Restarting a job

[Younas Khan]

Hi all. I am currently running a job. The job has terminated so many times
and every time I have restarted it in a new directory using the .XV, .CG
and .DM files from the previous runs. My questions are:

a) Why a job gets terminated?
b) If we restart a job many times using the mentioned files, will the final
result be reliable?
c) If I want to visualize the results, will I have to use the .ANI file
from the last run only?

Thanks in advance.

Younas Khan

[SIESTA-L] Modifications in certain files for restarting a job

[Younas Khan]

Hi all.
My question is that is there any modification required in the .XV, .MD
and/or .DM files when we use it to restart a job? if yes, then what sort of
changes do we have to make?

best regards
Younas Khan

[SIESTA-L] Adsorption and diffusion of Ag on quartz surface

[Younas Khan]

Hi all. Hope you are fine.
I am new to SIESTA. I am studying the adsorption and diffusion of Ag atom
on quartz surface, in the presence of electric field at high temperature .
As a first step I optimized the 60-atom quartz structure. I wanted to know
that what should I do next? I mean how should I proceed to include the Ag
atom to the surface and how should I bring the electric field and
temperature into play?

Kindly guide me please.

Younas Khan

Re: [SIESTA-L] Parameters for calculation

[Younas Khan]

Thank You Camp for such a detailed reply. It will certainly help me.


On Fri, Feb 13, 2015 at 8:33 PM, I. Camps  wrote:

> Hello Younas,
>
> Welcome to the SIESTA word!
>
> Regarding your questions:
>
> Type of run: it depends on you research. Do you need to optimize the atom
> positions only? Do you need to optimize the cell with some contrains (fix
> volume, free volume)? Do you want to do a dynamic simulation? Etc. etc. etc.
>
> Number of steps (for the geometry optimizations?): this parameter is
> "trial and error". You specify a number (30, for example) and look if the
> geometry calculation is converged. If ok, then you are set. If not
> converged, you can increase this number (this number is very related with
> other parameter you cite: force tolerance)
>
> Maximum SCF iteration: you used similar than "Number of steps". You use a
> number, and then look for the SCF convergence. If not converging, you
> increased it (this number is very related to the SCF convergence value).
>
> Mesh cut-off: in this case the recommendation is to do a convergence
> study. You have to select a parameter (for example the system energy) and
> calculate it for several different values of the mesh cut-off. Then, plot
> the data as energy vs mesh cut-off. From this graph, when the energy is
> converged, you select the value of the mesh cut-off. Then, you do all the
> "serious" calculation.
>
> Force-tolerance: is the valued used to accept that the structure is
> geometrically converged (the value of the force "felt" by the atoms, the
> lower the value, the atoms are more near the "equilibrium"). If you define
> a very low value, and your system is away from the equilibrium point, you
> might not get convergence. As said before, if you desire a given
> force-tolerance and the "number of steps" is low, you might not reach
> convergence, so you have then two choices: decrease the value of
> "force-tolerance" or increase the value of "Number of steps".
>
> My recommendation? Start with a simple system, and then go playing with
> this parameters to see how they affect the calculations.
>
> Good luck!
>
>
> On Friday, February 13, 2015, Younas Khan 
> wrote:
>
>> Hi all, hope you are fine.
>> I am new to SIESTA, therefor having problems in selection of parameters
>> for my calculation. My structure consists of silica_quartz (60 atoms)
>> supercell. I have tried many times but the job terminates automatically
>> without showing any error or warning. I want to ask:
>> 1) Is there any strategy to select correct parameters such as type of
>> run, number of steps, maximum SCF iterations, mesh cut-off, force tolerance
>> etc? currently I am proceeding on trial and error basis but it is
>> ineffective.
>>
>> Kindly help me in this regard.
>>
>> Younas Khan
>>
>
>
> --
>
> []'s,
>
> @mps
>
>

[SIESTA-L] Parameters for calculation

[Younas Khan]

Hi all, hope you are fine.
I am new to SIESTA, therefor having problems in selection of parameters for
my calculation. My structure consists of silica_quartz (60 atoms)
supercell. I have tried many times but the job terminates automatically
without showing any error or warning. I want to ask:
1) Is there any strategy to select correct parameters such as type of run,
number of steps, maximum SCF iterations, mesh cut-off, force tolerance etc?
currently I am proceeding on trial and error basis but it is ineffective.

Kindly help me in this regard.

Younas Khan

[SIESTA-L] How to estimate and reduce job completion time?

[Younas Khan]

Hi all. I am a postgraduate student. I am new to SIESTA and want to ask a
couple of questions.
1) How can we estimate the completion time for a specific job?
2) Which steps we should take so that our job takes minimum time to
complete, without affecting the quality of our results?

Regards
Younas Khan

Re: [SIESTA-L] How to restart an accidently closed job?

[Younas Khan]

Thank you Irtaza and Pu for your positive response.

On Sat, Dec 6, 2014 at 5:24 PM, Irtaza Hassan 
wrote:

> Dear,
>
> What you can do is in case when you running jobs got terminated.
>
> 1-add these tags in your FDF
>
> UseSaveData T
> DM.UseSaveDM   T
> MD.UseSaveXVT
>
> then run your job.
>
> 2- If first option gives an error
>
> then only use
>
> MD.UseSaveXVT
>
> 3-if both above options gives an error
>
> Use Atomic coordinates and box parameters from that last step of your
> output file in your FDF and restat your job.
>
> Best
> Irtaza
>
> On Sat, Dec 6, 2014 at 4:09 PM, Pu ZHANG  wrote:
>
>> In such situation, generally it's not possible to restart.
>>
>> Best regards, Pu Zhang
>> --
>> Postdoc
>> The group of Structured Electromagnetic Materials
>> Department of Photonics Engineering
>> Technical University of Denmark
>> Ørsteds Plads, Building 345v, 166
>> 2800, Kgs. Lyngby
>> E-mail: pu...@fotonik.dtu.dk
>> Homepage: http://www.dtu.dk/Service/Telefonbog/Person?id=91944&tab=0
>> Phone: 45 25 36 43
>> Fax: 45 93 65 81
>>
>> On Sat, Dec 6, 2014 at 11:57 AM, Younas Khan <
>> younaskhan.phys...@gmail.com> wrote:
>>
>>> Hi all,
>>> I am new to SIESTA. I recently encountered a problem while using SIESTA.
>>> I was running a job for the past several days. Unfortunately my computer
>>> was accidentally shut down and as a result the job got killed. Kindly tell
>>> me if I can restart my job from the same point where it was terminated? If
>>> yes, then how can i do this?
>>>
>>> Regards
>>> Younas Khan
>>>
>>>
>>
>

[SIESTA-L] How to restart an accidently closed job?

[Younas Khan]

Hi all,
I am new to SIESTA. I recently encountered a problem while using SIESTA. I
was running a job for the past several days. Unfortunately my computer was
accidentally shut down and as a result the job got killed. Kindly tell me
if I can restart my job from the same point where it was terminated? If
yes, then how can i do this?

Regards
Younas Khan