Re: [SIESTA-L] kpoints inside Gamma-M-K-Gamma

[sauluck]

Sym points are governed by the lattice vectors. Please read kittel' book
on solid state physics chapters 1 and 2


> Thank you for your response. I see but in this references, the high
> symmetry points are provided just in term of lattice vectors now, my
> question is how kx, ky, and kz are vary along this pathes? I have found a
> file with some data (below) but I can't find my understood relation
> (mensioned in my previous email) between these data for Hexagonal lattice.
>
> 0.500 0.2887000 0
>
> 0.4930556 0.28469027778 0
>
> 0.486 0.2806806 0
>
> 0.4791667 0.2766708 0
>
> 0.472 0.2726611 0
>
> 0.4652778 0.26865138889 0
>
> 0.458 0.2646417 0
>
> 0.4513889 0.2606319 0
>
> 0.444 0.2566222 0
>
> 0.4375000 0.2526125 0
>
> 0.4305556 0.2486028 0
>
> 0.4236111 0.24459305556 0
>
> 0.417 0.2405833 0
>
> 0.4097222 0.2365736 0
>
> 0.4027778 0.2325639 0
>
> 0.3958333 0.22855416667 0
>
> 0.389 0.2245444 0
>
> 0.3819444 0.2205347 0
>
> 0.375 0.2165250 0
>
> 0.3680556 0.21251527778 0
>
> 0.361 0.2085056 0
>
> 0.3541667 0.2044958 0
>
> 0.347 0.2004861 0
>
> 0.3402778 0.19647638889 0
>
> 0.333 0.1924667 0
>
> 0.3263889 0.1884569 0
>
> 0.319 0.1844472 0
>
> 0.3125000 0.1804375 0
>
> 0.306 0.1764278 0
>
> 0.2986111 0.17241805556 0
>
> 0.2916667 0.1684083 0
>
> 0.2847222 0.1643986 0
>
> 0.278 0.1603889 0
>
> 0.2708333 0.15637916667 0
>
> 0.2638889 0.1523694 0
>
> 0.2569444 0.1483597 0
>
> 0.250 0.1443500 0
>
> 0.2430556 0.14034027778 0
>
> 0.236 0.1363306 0
>
> 0.2291667 0.1323208 0
>
> 0.222 0.1283111 0
>
> 0.2152778 0.12430138889 0
>
> 0.208 0.1202917 0
>
> 0.2013889 0.1162819 0
>
> 0.194 0.1122722 0
>
> 0.1875000 0.1082625 0
>
> 0.1805556 0.1042528 0
>
> 0.1736111 0.10024305556 0
>
> 0.167 0.0962  0
>
> 0.1597222 0.09222361  0
>
> 0.1527778 0.08821389  0
>
> 0.1458333 0.08420417  0
>
> 0.139 0.08019444  0
>
> 0.1319444 0.07618472  0
>
> 0.125 0.07217500  0
>
> 0.1180556 0.06816528  0
>
> 0.111 0.06415556  0
>
> 0.1041667 0.06014583  0
>
> 0.0973  0.05613611  0
>
> 0.09027778  0.05212639  0
>
> 0.0834  0.04811666  0
>
> 0.07638889  0.04410694  0
>
> 0.0695  0.04009722  0
>
> 0.0625  0.03608750  0
>
> 0.0556  0.03207778  0
>
> 0.04861112  0.02806805  0
>
> 0.0417  0.02405833  0
>
> 0.03472223  0.02004861  0
>
> 0.0278  0.01603889  0
>
> 0.02083334  0.01202916  0
>
> 0.0139  0.0080194410
>
> 0.006980.0040097180
>
> 0  0  0
>
> 0.009661836231884060  0
>
> 0.0193236724637681  0  0
>
> 0.0289855086956522  0  0
>
> 0.0386473449275362  0  0
>
> 0.0483091811594203  0  0
>
> 0.0579710173913043  0  0
>
> 0.0676328536231884  0  0
>
> 0.0772946898550725  0  0
>
> 0.0869565260869565

Re: [SIESTA-L] << avoid SIESTA terminal ouput >>

[sauluck]

Try
nohup siesta.x &
for serial run


> Hi SIESTers,
>
> I would like to know how to avoid the output from SIESTA that is directed
> to the terminal window.
>
> After sending a calculation to run in background, I am getting message
> like
> these:
>
> Gamma-point calculation with multiply-connected orbital pairs
> Folding of H and S implicitly performed
>
> I am using siesta_4.1-b4. In previous versions and with the same system I
> did not get such messages.
>
> Regards,
>
> Camps
>


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Re: [SIESTA-L] cell vector not converged

[sauluck]

Your volume changes are too small.
However point 20 has lowest energy.


> Dear experts,
>
> I am trying to converge my system unitcell structure for k - mesh values.
> Even though the Free Energy value has converged for less denser mesh, the
> unit cell parameter has not converged for even 21x21x1 k mesh. The system
> is a 2D one with 3 atoms in the unit cell. I am attaching the file
> containing the k values and the corresponding free energy and cell
> parameter values along with the plotted graph.
>
> please have a look and help me. Is the free energy convergence enough? I
> have used systems before where I have checked if both the parameters have
> converged for a given k mesh.
>
> Thank you.
>
> Regards,
> Sunetra Das
>


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Re: [SIESTA-L] Question about output of total spin in spin-orbit calculation

[sauluck]

You must be having 2 atoms in unit cell which have spin. Hence double.


> Dear all,
>
> I am performing my first spin-orbit calculations for a Fe atom over a
> Cu2N/Cu(100) slab. By the end of the calculation, Siesta prints a table
> with sqrt^2 for each of the atom in the supercell, the sum of all
> sqrt^2, and at the end of the calculation, the total spin.
>
> What I get is, for the sum of all sqrt^2 : 1.357
>
> Sum   792. 1.357-0.001 -0.001  1.357   0.017
> 0.000  0.000  0.017
>
> and, for the total spin:
>
> siesta: S , {S} = 2.714558   -0.002637   -0.0025712.714556
>
> So, according to the table of S and L, the total spin would be 1.357 Bohr
> magneton, but the final output shows double that value (2.714). Am I
> missing something here? Which value should I take for the total spin of
> the
> system, that of the table, or the final one?
>
> Best regards,
>
> Marcos
>


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

[sauluck]

For energy gap look at TDOS not PDOS


> 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*
>


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Re: [SIESTA-L] error with siesta-4.1-b3

[sauluck]

Hi,
This could a mpi problem. Submit job again.
S Auluck


> Dear Siesta users,
>
>  I have compiled the latest version of siesta-4.1-b3.
> The non polarized calculations run without problem.
> However, when I try a spin polarized calculation it
> crashes with the following error:
>
> ===
> =   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
> =   PID 22581 RUNNING AT argos1
> =   EXIT CODE: 7
> =   CLEANING UP REMAINING PROCESSES
> =   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
> ===
> YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Bus error (signal 7)
> This typically refers to a problem with your application.
> Please see the FAQ page for debugging suggestions
>
> Has anybody faced this problem?
>
> Many thanks in advance,
>
>   Pablo
>
>


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Re: [SIESTA-L] change DOS as increasing supercell size

[sauluck]

you have to consider zone folding2x2x2 BZ is 1/8 of 1x1x1 BZ


> Dear Sonu and Sushil,
>
> Thank you for your reply. But the point is that the position of states in
> the energy spectrum changes as I increase the supercell size!!! What do
> you
> think of that?
>
>
> Best regards
> Mohammad
>
>
> On Sat, Aug 12, 2017 at 4:16 PM, Sonu Kumar <1009uku...@gmail.com> wrote:
>
>> Increasing supercell size changes the concentration of defects, that is
>> why you see
>> changes in DOS.
>>
>> bests,
>> sonu
>>
>>
>> *===*
>> With kind regards,
>> Dr. S Kumar, Post doctoral fellow
>> Physical Sciences and Engineering  Divison,
>> IBN Sina Building, KAUST,
>> Thuwal, KSA
>> *===*
>>
>> On Tue, Aug 8, 2017 at 3:55 PM, MB MB  wrote:
>>
>>> Dear SIESTA users,
>>>
>>> I really need your help. I am studying defects in MoS2 2D structures.
>>> As I increase the size of the supercell from 5*5 to 8*8, the position
>>> of
>>> defects states changes in DOS diagram
>>>
>>> I use DZP basis set and default values to create orbitals.
>>> Is there any suggestion why this happens and how to fix it?
>>>
>>> Best regards
>>> Mohammad Bahmani
>>>
>>
>>
>


-- 
Prof. Sushil Auluck  Phone:+91-512-6797092/6148
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Re: [SIESTA-L] change DOS as increasing supercell size

[sauluck]

suppose you do a calculation with 1x1x1 and then 2x2x2. in the second case
dos will be almost 8 times the first case. dos should be written as
states/eV/unitcell which will be 1/8 of states/eV/supercell


> Increasing supercell size changes the concentration of defects, that is
> why
> you see
> changes in DOS.
>
> bests,
> sonu
>
>
> *===*
> With kind regards,
> Dr. S Kumar, Post doctoral fellow
> Physical Sciences and Engineering  Divison,
> IBN Sina Building, KAUST,
> Thuwal, KSA
> *===*
>
> On Tue, Aug 8, 2017 at 3:55 PM, MB MB  wrote:
>
>> Dear SIESTA users,
>>
>> I really need your help. I am studying defects in MoS2 2D structures.
>> As I increase the size of the supercell from 5*5 to 8*8, the position of
>> defects states changes in DOS diagram
>>
>> I use DZP basis set and default values to create orbitals.
>> Is there any suggestion why this happens and how to fix it?
>>
>> Best regards
>> Mohammad Bahmani
>>
>


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Re: [SIESTA-L] Plotting Bandstructure in Siesta

[sauluck]

fold2Bloch



> Hello All,
> In regard to the ongoing discussion about band structure, I have a query
> since I am newly working in this field of computational solid state
> physics.
> While calculating band structure, Is it absolutely necessary that I
> calculate the band structure of a unit cell and not of a supercell?
> If during structural relaxation I am using a supercell, will the
> calculated
> band structure of a supercell be the same as that of a unit cell band
> structure in that case? How do I get the unit cell parameters from the
> supercell relaxation output? Is there any code to extract the unit cell
> data from the SIESTA output files for a supercell?
>
> Any hints in this regard is highly appreciated.
> Thank you in advance.
>
> Sunetra Das
> Dept. of Physics,
> MMC College,
> Kolkata,
> India.
>
> On 6 July 2017 at 01:40, Ritwik Vatsyayan 
> wrote:
>
>> Dear Aakanksha,
>>   I am using XCrysDen version 1.5.60.
>>
>>
>> Regards,
>> Ritwik
>>
>> On Mon, Jul 3, 2017 at 1:53 AM, AAKANKSHA SUD
>> > > wrote:
>>
>>> Dear Ritwik
>>> I am happy that  my suggestions  were helpful to you. I was just
>>> wondering that how did you open .xyz file in xcrysden because such
>>> files
>>> cannot be opened in it.  Perhaps you are using some other version.I
>>> would
>>> really appreciate if you could tell me that which version of xcrysden
>>> are
>>> you using that supports .xyz file.
>>>
>>> Thanks
>>> Aakanksha
>>> --
>>> From: Ritwik Vatsyayan 
>>> Sent: ‎7/‎3/‎2017 1:30 AM
>>>
>>> To: siesta-l@uam.es
>>> Subject: Re: [SIESTA-L] Plotting Bandstructure in Siesta
>>>
>>> Dear Aakanksha,
>>> Thank you so much for that tip. I was
>>> normally using the .xyz file generated from siesta run after optimizing
>>> the
>>> geometry, but I guess that will not give the information about the
>>> k-points.
>>> I really appreciate your time and effort in this.
>>>
>>> Best Regards,
>>> Ritwik
>>>
>>> On Sat, Jul 1, 2017 at 7:24 AM, AAKANKSHA SUD <
>>> aakankshasood0...@gmail.com> wrote:
>>>
 Hi ritwik
 Could you please elaborate the steps you followed. First you have to
 optimise the geometry . So after optimisation you will get .xv file.
 There
 is a utility in siesta xv2xsf . Use that to generate .xsf file.Now
 open
 that file in xcrysden and generate the kpoints. After that do the
 calculation for bandstructure. Hope it helps.

 Regards
 Aakanksha
 --
 From: Ritwik Vatsyayan 
 Sent: ‎7/‎1/‎2017 1:31 AM
 To: siesta-l@uam.es
 Subject: Re: [SIESTA-L] Plotting Bandstructure in Siesta

 Dear Aakanksha,
Thank you for suggesting XCrysDen. I
 wanted to know that when you are using xcrysden to generate the
 k-points,
 what is the extension of the file you use as the input? I tried using
 the
 SystemLabel.xyz file, but it doesn't give me the option for making
 k-path.
 Is there some other file generated by Siesta which can be used?

 Regards,
 Ritwik Vatsyayan

 On Thu, Jun 29, 2017 at 1:59 AM, AAKANKSHA SUD <
 aakankshasood0...@gmail.com> wrote:

> Hi Ritwik
> It would be better if you use xcrysden to know the high symmetry pts.
> And using xcrysden you can easily generate the kpoints based on the
> brillouin zone.and its necessary to use a cyclic closed path. We are
> defining a region of brilliouin zone and by repeating it we can
> define
> whole zone so its necessary to specify the cyclic path. And
> specifying the
> number of intersections between two k points is also necessary.
> Regarding
> the reciprocal lattice vectors or fractional it depends like in which
> coordinates you are specifying the kpoints. I insist that you should
> use
> xcrysden or some other kpoint generating software .
>
> Hope it helps..
>
> Regards
> Aakanksha
> --
> From: Ritwik Vatsyayan 
> Sent: ‎6/‎29/‎2017 1:32 AM
> To: siesta-l@uam.es
> Subject: [SIESTA-L] Plotting Bandstructure in Siesta
>
> Dear Siesta Users,
>  I am working on a system with a
> hexagonal lattice, and I want to plot the bandstructure for the same.
> I read online at: https://lampx.tugraz.at/~hadle
> y/ss1/bzones/hexagonal.php
> that the high symmetry points of the first Brillouin zone of a simple
> hexagonal lattice are:
> Γ: (0,0,0)
> M: (1/2,0,0)
> K: (2/3,1/3,0)
> H: (2/3,1/3,1/2)
> A: (0,0,1/2)
> L: (1/2,0,1/2)
>  These points are in the fractional format. I want to plot the
> bandstructure using these points.
> In the fdf file, we must 

Re: [SIESTA-L] how to install Netcdf4 for compilation of tbtrans in siesta 4.1b2

[sauluck]

hi,
i think what you want to know is..how to install siesta WITHOUT netcdf.

s.auluck

> Hi. I am sorry my grammar mistakes. Actually I want to try asking  why
> have
> *not *siesta been coming with netcdf? Or why doesn't siesta include netcdf
> package?
>
> 2017-03-23 7:26 GMT+03:00 berna uyanık :
>
>> Hi. I wonder why have siesta been coming with netcdf?
>>
>> 23 Mar 2017 00:00 tarihinde "Nick Papior"  yazdı:
>>
>>> Please see this post which contains a script to install netcdf4.
>>>
>>> http://www.mail-archive.com/siesta-l@uam.es/msg09275.html
>>>
>>> If you have problems with it consult your local administrator or ask on
>>> the NetCDF mailing lists.
>>>
>>> 2017-03-21 10:00 GMT+01:00 Ankita Joshi :
>>>
 Dear SIESTA users,

 I want to compile tbtrans using netcdf4 in siesta 4.1b2. Can someone
 send me a link to install netcdf4 ?

 Thanks in advance,

 Ankita Joshi




>>>
>>>
>>> --
>>> Kind regards Nick
>>>
>>
>


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Re: [SIESTA-L] Error in Using PAO.SpliNorm

[sauluck]

Distance between these atoms is too small.
Perhaps an incorrect atom position or positions.

> Greetings Everyone, I'm wondering if someone can help me in correcting
> this
> warning
>
> siesta: WARNING: Atoms 11679 11979 too close: rij =0.402646 Ang
> siesta: WARNING: Atoms 11680 11963 too close: rij =0.516207 Ang
>
> I'm using PAO.SplitNorm 0.16 and varied it to 0.37
>  But still, I'm getting this warning. Can anybody please tell me what this
> warning about is?? and how can I correct this?
>
> Thank you.
> Ajay Khanna
> Student
>


-- 
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Department of Physics  +91-512-6798177(Home)
Indian Institute of Technology   Cell :+91-9305548667
Kanpur 208016 (UP)   Fax  :+91-512-6790914
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 ...:saul...@gmail.com
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~

Re: [SIESTA-L] Is relaxation is necessary during k-point optimization

[sauluck]

Simply take 20 k points. Then relax... increase to 50 k points relax
again. You will not see much change in atom positions.

> Dear Siesta Users
>
> I have a fairly large system of about 50 atoms of graphene ribbon. I want
> to optimize the same in terms of k-points and mesh cutoff.
>
> But if I relax my system at each k-point, It will cost too much time.
>
> My question is
>
> Can I skip the relaxation fr each k point??
> And plot Energies vs kpoint n evaluate optimized k-point??
>
> Please help me in this.
>
> Thank u so much...
>
> With Regarda
> Rajan
>


-- 
Prof. Sushil Auluck  Phone:+91-512-6797092/6148
Department of Physics  +91-512-6798177(Home)
Indian Institute of Technology   Cell :+91-9305548667
Kanpur 208016 (UP)   Fax  :+91-512-6790914
IndiaE-mail:saul...@iitk.ac.in
 ...:saul...@gmail.com
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...
~

Re: [SIESTA-L] Parallel compile and run

[sauluck]

hi,
just a simple thought...
do you have the same name for siesta serial & parallel excutables ?
try to name them siesta-s & siesta-p, so for mpirun use siesta-p
s.auluck

> Good news!
> Finally I built parallel siesta
>
> root@cluster:ObjPar# ./siesta
> ./siesta: error while loading shared libraries: libscalapack.so.2: cannot
> open shared object file: No such file or directory
> root@cluster:ObjPar# export LD_LIBRARY_PATH=/usr/lib64/openmpi/lib
> root@cluster:ObjPar# ./siesta
> ./siesta: error while loading shared libraries: libmpi_f90.so.1: cannot
> open shared object file: No such file or directory
> root@cluster:ObjPar# export
> LD_LIBRARY_PATH=/usr/lib64/openmpi/lib:/opt/openmpi/lib
> root@cluster:ObjPar# ./siesta
> Siesta Version:siesta-3.2
> Architecture  : i686-pc-linux-gnu--unknown
> Compiler flags: mpif90 -O3
> PARALLEL version
> NetCDF support
>
> * Running in serial mode with MPI
>>> Start of run:   6-JUL-2016   0:53:28
>
>***
>*  WELCOME TO SIESTA  *
>***
>
> reinit: Reading from standard input
>
>
>
>
>
> As you can see it is saying PARALLEL version, but I see "Running in serial
> mode with MPI". What does that mean?
>
> More info:
> root@cluster:ObjPar# ldd siesta
> linux-vdso.so.1 =>  (0x7fffa960)
> libscalapack.so.2 => not found
> libnetcdf.so.7 => /usr/lib64/libnetcdf.so.7 (0x2b4af12b8000)
> libnetcdff.so.5 => /usr/lib64/libnetcdff.so.5 (0x2b4af15e)
> libmpi_f90.so.1 => /opt/openmpi/lib/libmpi_f90.so.1
> (0x2b4af184)
> libmpi_f77.so.1 => /opt/openmpi/lib/libmpi_f77.so.1
> (0x2b4af1a48000)
> libmpi.so.1 => /opt/openmpi/lib/libmpi.so.1 (0x2b4af1c8)
> libibverbs.so.1 => /usr/lib64/libibverbs.so.1 (0x003e43c0)
> libdat.so.1 => /usr/lib64/libdat.so.1 (0x2b4af2218000)
> librt.so.1 => /lib64/librt.so.1 (0x003e44c0)
> libnsl.so.1 => /lib64/libnsl.so.1 (0x003e5240)
> libutil.so.1 => /lib64/libutil.so.1 (0x003e5180)
> libgfortran.so.3 => /usr/lib64/libgfortran.so.3
> (0x2b4af2428000)
> libm.so.6 => /lib64/libm.so.6 (0x2b4af272)
> libdl.so.2 => /lib64/libdl.so.2 (0x003e4400)
> libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x0033c120)
> libpthread.so.0 => /lib64/libpthread.so.0 (0x003e4440)
> libc.so.6 => /lib64/libc.so.6 (0x003e4380)
> libcurl.so.4 => /usr/lib64/libcurl.so.4 (0x003d2840)
> libz.so.1 => /lib64/libz.so.1 (0x0033c0e0)
> /lib64/ld-linux-x86-64.so.2 (0x003e4340)
> libidn.so.11 => /lib64/libidn.so.11 (0x003e4880)
> libldap-2.4.so.2 => /lib64/libldap-2.4.so.2 (0x003d2780)
> libgssapi_krb5.so.2 => /lib64/libgssapi_krb5.so.2
> (0x003d2400)
> libkrb5.so.3 => /lib64/libkrb5.so.3 (0x003d2440)
> libk5crypto.so.3 => /lib64/libk5crypto.so.3 (0x003d23c0)
> libcom_err.so.2 => /lib64/libcom_err.so.2 (0x003e4f00)
> libssl3.so => /usr/lib64/libssl3.so (0x003d2680)
> libsmime3.so => /usr/lib64/libsmime3.so (0x003d2640)
> libnss3.so => /usr/lib64/libnss3.so (0x003d2600)
> libnssutil3.so => /usr/lib64/libnssutil3.so (0x003d2580)
> libplds4.so => /lib64/libplds4.so (0x003d25c0)
> libplc4.so => /lib64/libplc4.so (0x003d2540)
> libnspr4.so => /lib64/libnspr4.so (0x003d2500)
> libssh2.so.1 => /usr/lib64/libssh2.so.1 (0x003d2800)
> liblber-2.4.so.2 => /lib64/liblber-2.4.so.2 (0x003d2740)
> libresolv.so.2 => /lib64/libresolv.so.2 (0x003e4580)
> libsasl2.so.2 => /usr/lib64/libsasl2.so.2 (0x003d26c0)
> libkrb5support.so.0 => /lib64/libkrb5support.so.0
> (0x003d2480)
> libkeyutils.so.1 => /lib64/libkeyutils.so.1 (0x003e5040)
> libssl.so.10 => /usr/lib64/libssl.so.10 (0x003d24c0)
> libcrypto.so.10 => /usr/lib64/libcrypto.so.10 (0x0033c1e0)
> libcrypt.so.1 => /lib64/libcrypt.so.1 (0x003f8480)
> libselinux.so.1 => /lib64/libselinux.so.1 (0x003e4500)
> libfreebl3.so => /lib64/libfreebl3.so (0x003f8440)
>
>
>
>
>
>
> Then I run it along with mpirun command, but the output is buggy
>
>
> mahmood@cluster:~$ export
> LD_LIBRARY_PATH=/usr/lib64/openmpi/lib:/opt/openmpi/lib
> mahmood@cluster:~$ mpirun -np 2
> /export/apps/chemistry/siesta-3.2/ObjPar/siesta < file.fdf
> [cluster.scu.ac:17731] [[42189,0],0] mca_oob_tcp_recv_handler: invalid
> message type: 12
> [cluster.scu.ac:17731] [[42189,0],0] mca_oob_tcp_recv_handler: invalid
> message type: 12
> 

Re: [SIESTA-L] [***Posible SPAM***]2

[sauluck]

barnali,
send a ps or pdf fileof the band structure & name of compound.
s.auluck

> Thank you sir for your kind response. My system is a metallic one where
> the
> Fermi energy sifted towards conduction band due to doping. For details
> here
> I am attaching the band structure. Do you think should I include drude
> term? Kindly guide me to chose relaxation time for my system.
>
> I am waiting for your suggestion.
>
> Thanks in advance.
>
> Sincerely
> Barnali
>
>
> On Wed, Feb 17, 2016 at 6:02 PM,  wrote:
>
>> barnali,
>> drude term is to included only when a band/bands cut the fermi
>> energy...for
>> metals,semimetals..if you have an energy gap then you have only
>> interband contributions..no drde term.
>> s.auluck
>>
>> > Respected SIESTA users (Marty Blaber)
>> >
>> > I am calculating the optical properties of  a graphene like  2D sheet
>> > using
>> > SIESTA 3.2. The band structure confirms its metallic nature and  the
>> > *.EPSIMG (was generated after optical calculation) shows  W_p is
>> non-zero,
>> > i.e.  W_p =0.0013.  As I know that the  drude term is to be included
>> for
>> > metal, now my queries are -
>> > For calculating optical properties  using optical.f should I  include
>> > drude term?
>> >  Is it necessary to include drude term for my system? If it is
>> necessary,
>> > then how can I choose relaxation time?  I will be grateful if anyone
>> > guide
>> > me to choose relaxation time for graphene like 2D sheet? I am waiting
>> for
>> > any response.
>> >
>> > Thanks in advance.
>> >
>> > Sincerely
>> > Barnali Bhattacharya
>> > Ph.D. Student,
>> >  Assam University, Silchar, India
>> >
>>
>>
>> --
>> Prof. Sushil Auluck  Phone:+91-512-6797092/6148
>> Department of Physics  +91-512-6798177(Home)
>> Indian Institute of Technology   Cell :+91-9305548667
>> Kanpur 208016 (UP)   Fax  :+91-512-6790914
>> IndiaE-mail:saul...@iitk.ac.in
>>  ...:saul...@gmail.com
>> http://www.iitk.ac.in/phy/People/phy_facvis.html
>> http://www.iitk.ac.in/phy/New01/profile_SA.html
>> http://www.iitk.ac.in/phy/index.php/people/faculty
>>
>> http://www.iitk.ac.in/phy/index.php/people/faculty/12-people/faculty/profile/88-sushil-auluck
>> ...
>> ~
>>
>


-- 
Prof. Sushil Auluck  Phone:+91-512-6797092/6148
Department of Physics  +91-512-6798177(Home)
Indian Institute of Technology   Cell :+91-9305548667
Kanpur 208016 (UP)   Fax  :+91-512-6790914
IndiaE-mail:saul...@iitk.ac.in
 ...:saul...@gmail.com
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...
~

Re: [SIESTA-L] [***Posible SPAM***]2

[sauluck]

barnali,
drude term is to included only when a band/bands cut the fermi energy...for
metals,semimetals..if you have an energy gap then you have only
interband contributions..no drde term.
s.auluck

> Respected SIESTA users (Marty Blaber)
>
> I am calculating the optical properties of  a graphene like  2D sheet
> using
> SIESTA 3.2. The band structure confirms its metallic nature and  the
> *.EPSIMG (was generated after optical calculation) shows  W_p is non-zero,
> i.e.  W_p =0.0013.  As I know that the  drude term is to be included for
> metal, now my queries are -
> For calculating optical properties  using optical.f should I  include
> drude term?
>  Is it necessary to include drude term for my system? If it is necessary,
> then how can I choose relaxation time?  I will be grateful if anyone
> guide
> me to choose relaxation time for graphene like 2D sheet? I am waiting for
> any response.
>
> Thanks in advance.
>
> Sincerely
> Barnali Bhattacharya
> Ph.D. Student,
>  Assam University, Silchar, India
>


-- 
Prof. Sushil Auluck  Phone:+91-512-6797092/6148
Department of Physics  +91-512-6798177(Home)
Indian Institute of Technology   Cell :+91-9305548667
Kanpur 208016 (UP)   Fax  :+91-512-6790914
IndiaE-mail:saul...@iitk.ac.in
 ...:saul...@gmail.com
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...
~

Re: [SIESTA-L] Band Structure of ZnS

[sauluck]

hi,
do ZnS ans MgO have the same structure ?
s.auluck

 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



-- 
Prof. Sushil Auluck  Phone:+91-512-6797092/6148
Department of Physics  +91-512-6798177(Home)
Indian Institute of Technology   Cell :+91-9305548667
Kanpur 208016 (UP)   Fax  :+91-512-6790914
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 ...:saul...@gmail.com
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...
~

Re: [SIESTA-L] generate executable file

[sauluck]

Command is
gfortran -o eig2dos eig2dos.f

S. Auluck


 Respected Sir Nick Papior

 When I run gfortran -o eig2dos.f eig2dos from Util directory to create
 eig2dos executable file but command gives unexpected error

 gfortran: error: eig2dos: no such file or directory

 I can see this file by using ls -x command .I don't know how can it
 possible.


 On Fri, Jul 24, 2015 at 10:30 PM, Nick Papior nickpap...@gmail.com
 wrote:


 On 24 Jul 2015 17:08, jv sharma jvnano...@gmail.com wrote:
 
  Do this in the forlder where your .f is located:
 
  gfortran -o filename.f filename
 Swap the two last arguments and it should be fine.
 
  I got this from the below link, as rightly said by Dr. Nick:
 
  https://www.mail-archive.com/siesta-l@uam.es/msg05632.html
 
  Regards,
  JVN.
 
  On Fri, Jul 24, 2015 at 12:37 PM, Jeetu Donderiya 
 jeetudonderiya2...@gmail.com wrote:
 
  Hello SIESTA user
 
  I forget, how to generate executable file from .f file with the help
 of
 gfortran compiler. Please anyone can tell that command line.
 
  Thanks in advance
 
 




-- 
Prof. Sushil Auluck  Phone:+91-512-6797092/6148
Department of Physics  +91-512-6798177(Home)
Indian Institute of Technology   Cell :+91-9305548667
Kanpur 208016 (UP)   Fax  :+91-512-6790914
IndiaE-mail:saul...@iitk.ac.in
 ...:saul...@gmail.com
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...
~

Re: [SIESTA-L] TranSiesta Error after trying to run a fast example

[sauluck]

hi,
the computer cannot locate the executables siesta  transiesta.
you need to make entries in .bashrc or .cshrc files
a very simple fix is to copy the executables to /usr/bin/
s.auluck

 Dear Prof. Verma ji,

 Everything went well and transiesta is working now.
 But, I am now experiencing a new problem after doing this.

 Either siesta or transiesta, only one at a time is working. I mean, after
 doing make transiesta and so on..
 transiesta is working well, but when I try with siesta test, I get the
 following error:

 jv@jv-desktop:~/siesta-trunk-462/Obj/Tests/ag$ make
 Running ag test...
 == Copying pseudopotential file for Ag...
 == Running SIESTA as ../../../siesta
 /bin/sh: 1: ../../../siesta: not found
 make: *** [completed_work] Error 127
 jv@jv-desktop:~/siesta-trunk-462/Obj/Tests/ag$

 Same thing happens with transiesta, when I do make siesta and so on... and
 then try with a test run for transiesta.

 Please suggest me.

 Regards,
 JVN Sarma.



 On Sat, Jun 27, 2015 at 10:31 AM, Dr. Mohan L. Verma drmoha...@yahoo.com
 wrote:

 Dear Sharma ji

 Please read the manual carefully and  start from beginning i.e. from the
 compilation of transiesta. we are using siesta-trunk-462.
  In order to compile transiesta in series Use following steps :
 1. download siesta-trunk-462 from :
 http://departments.icmab.es/leem/siesta/CodeAccess/Code/downloads.html
 and extract it in home directory
 now go to Obj dir and configure using  :
 $ /home/drmohanlv/siesta-trunk-462/Obj/ sh ../Src/obj_setup.sh
 then
 $ /home/drmohanlv/siesta-trunk-462/Obj/ ../Src/configure
 finally compile transiesta using
 $ /home/drmohanlv/siesta-trunk-462/Obj/ make transiesta
 this will generate a transiesta binary file in this directory.
 copy binary file to /home/drmohanlv/bin/ directory by
 $ /home/drmohanlv/siesta-trunk-462/Obj/ cp transiesta ~/bin
 now for compilation of tbtrans go to
 $ /home/drmohanlv/siesta-trunk-462/Util/TBTrans_rep/
 and only type make this will generate tbtrans binary file for further
 use
 copy binary file to /home/drmohanlv/bin/ directory by
 $ /home/drmohanlv/siesta-trunk-462/Obj/ cp tbtrans ~/bin
 After above compilation of transiesta and tbtrans you can run the
 examples in the test directory.
 All the best.

 Dr Mohan L Verma
 Prof  Head
 Department of Applied Physics
 FET,SSGI Shri Shankaracharya Technical Campus-Junwani, Bhilai
 (Chhattisgrah) INDIA
 490020
 email : drmoha...@gmail.com




   On Friday, 26 June 2015 10:39 PM, Jaehwan Kweon janikw...@gmail.com
 wrote:


 that is probably because there is no executable transiesta file in
 /your_directory/siesta-3.2/Obj

 so, you need to check whether files are successfully compiled

 try this..

 $cd siesta-3.2/Obj/
 $make clean
 $make transiesta
 $cp /directory/siesta/Obj/transiesta /usr/local/bin

 good luck!

 On Sat, Jun 27, 2015 at 1:39 AM, jv sharma jvnano...@gmail.com wrote:

 I am still getting the same error, after doing this. That is, like this:

 jv@jv-desktop:~/siesta-3.2/Examples/TranSiesta/Elec/OUT_Test$ transiesta
  elec.fast.fdf  elec.fast.out
 transiesta: command not found
 jv@jv-desktop:~/siesta-3.2/Examples/TranSiesta/Elec/OUT_Test$

 On Fri, Jun 26, 2015 at 10:01 PM, Raha khalili
 khadije.khal...@gmail.com
 wrote:

 Hi,

 You can try this:
 export PATH= /your_directory/siesta-3.2/Obj:$PATH

 Best,
 Raha

 On Fri, Jun 26, 2015 at 6:05 PM, jv sharma jvnano...@gmail.com wrote:


 On Fri, Jun 26, 2015 at 9:18 PM, Jaehwan Kweon janikw...@gmail.com
 wrote:

 you would better install transiesta first

 $cd siesta-3.2/Obj/
 $make transiesta

 then
 $cp /directory/siesta/Obj/transiesta /usr/local/bin


 Now I get like this:

 jv@jv-desktop:~$ cp /directory/siesta-3.2/Obj/transiesta /usr/local/bin
 cp: cannot stat ‘/directory/siesta-3.2/Obj/transiesta’: No such file
 or
 directory
 jv@jv-desktop:~$



 On Sat, Jun 27, 2015 at 12:36 AM, jv sharma jvnano...@gmail.com wrote:



 On Fri, Jun 26, 2015 at 4:28 PM, 毛飞 200921220...@mail.bnu.edu.cn
 wrote:

  Hi, Sarma

 It seems that the transiesta can not be found by the system. Do you add
 the absolute path of the executable transiesta in the environment
 variable
 $PATH? You can test if it is added in the $PATH by typing “which
 transiesta” in the command line.


 I got like this:

 jv@jv-desktop:~$ which transiesta
 jv@jv-desktop:~$

 I do not understand this.


  Good luck.

 Fei Mao
 USC

 在2015-06-26，jv sharma jvnano...@gmail.com 写道:

 -原始邮件-
 *发件人:* jv sharma jvnano...@gmail.com
 *发送时间:* 2015年6月26日 星期五
 *收件人:* siesta-l@uam.es
 *抄送:* nickpap...@gmail.com
 *主题:* [SIESTA-L] TranSiesta Error after trying to run a fast example


 Dear Siesta Community,


 I get the following after trying to run a fast example in TranSiesta:

 jv@jv-desktop:~/siesta-3.2/Examples/TranSiesta/Elec/OUT_Test$ transiesta
  elec.fast.fdf  elec.fast.out
 transiesta: command not found

 Please help me to get out of this.
 Many thanks.

 

Re: [SIESTA-L] Drude term

[sauluck]

hi,

look at the DOS. if a gap (even a very very small one) is there at the
fermi energy use only inter,
if at the fermi level there is a finite dos value then add intra.

s.auluck

 Dear Sauluck,

 There is only interband contribution to eps for a system with energy
 gaps. However, for metal clusters with specific size, the energy gap is
 so small between the HOMO and LUMO energy levels. So, how to account the
 intraband contribution in this case in SIESTA?

 Kind regards,

 /Guangping

 On 04/28/2015 09:24 AM, saul...@iitk.ac.in wrote:
 hi,
 drude term is to be included for systems when fermi level cuts a
 band/bands.
 hence it is called intra band contribution.
 for systems with energy gaps there is no drude term.you have only inter
 band contributions.
 in general eps = eps_inter + eps_intra
 s.auluck

 Dear user

 I want to calculate real and imaginary parts of the permittivity for
 some
 metals
 (for cluster not bulk).
 How can I include Drude term for intarband transition of the
 permittivity?

 In the *.EPSIMG, (was generated after optical calculation) the value of
 W_p
 is written 0.000. I think this value should be non-zero, to include
 Drude
 term.
 How can I determinate W_p?

 Regards,
 Eliya







-- 
Prof. Sushil Auluck  Phone:+91-512-6797092/6148
Department of Physics  +91-512-6798177(Home)
Indian Institute of Technology   Cell :+91-9305548667
Kanpur 208016 (UP)   Fax  :+91-512-6790914
IndiaE-mail:saul...@iitk.ac.in
 ...:saul...@gmail.com
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...
~

Re: [SIESTA-L] Drude term

[sauluck]

hi,
drude term is to be included for systems when fermi level cuts a band/bands.
hence it is called intra band contribution.
for systems with energy gaps there is no drude term.you have only inter
band contributions.
in general eps = eps_inter + eps_intra
s.auluck

 Dear user

 I want to calculate real and imaginary parts of the permittivity for some
 metals
 (for cluster not bulk).
 How can I include Drude term for intarband transition of the permittivity?

 In the *.EPSIMG, (was generated after optical calculation) the value of
 W_p
 is written 0.000. I think this value should be non-zero, to include Drude
 term.
 How can I determinate W_p?

 Regards,
 Eliya



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Re: [SIESTA-L] Difference between Bulk and nanowire ?

[sauluck]

hi,
when lattice constant becomes infinite, then there is no periodicity.
so choose a large lattice constant so as to make periodicity as small as
possible.
s.auluck


 Hi siesta users, 
  I want to know:If the boundary conditions in SIESTA are always periodic
 then how to differentiate bulk and nanowire ?
 - To my knowledge,  the boundary conditions for bulk should be periodic
 in all directions (X,Y and Z) while for a  nanowire  with infinite
 length the periodicity is only along the Z-axis.
 Thanks in advance,B. Aouchenni




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Re: [SIESTA-L] Transmission doesn't change

[sauluck]

hi,
the 5 layer looks very different.
could you have reached saturation after 7 layers ?
s.auluck

 Dear all transiesta/tbtrans users,

 i am doing transport properties  of Fe/MgO junctions, at 0 bias you can
 see that the transmission
 coeffiecient doesn't change when increasing the thickness of the substrate
 (MgO) from 5
 to 11 monolayers, the same for 7, 9 and 11.

 i can not undersatand what happens
 any suggestions?

 bests
 taoufik



-- 
Prof. Sushil Auluck  Phone:+91-512-6797092/6148
Department of Physics  +91-512-6798177(Home)
Indian Institute of Technology   Cell :+91-9305548667
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RE: [SIESTA-L] Transmission doesn't change

[sauluck]

hi,

when you make a crystal by adding layers, then after some layers it
behaves like bulk...after that no change is there in the electronic
properties.

that means after 7 layers, results are same...rather similaron going
from 7 to 9 very small change9 to 11 even smaller changeyou can
call it saturation or say consistency has been achieved.
if results are EXACTLY same...that is the 2 curves overlap...then
something else may me going on..

s.auluck
 what do you mean by saturation?
 for 7, 9 and 11 layers i have exactally the same results

 Date: Tue, 10 Feb 2015 13:51:21 +0530
 From: saul...@iitk.ac.in
 To: siesta-l@uam.es
 Subject: Re: [SIESTA-L] Transmission doesn't change

 hi,
 the 5 layer looks very different.
 could you have reached saturation after 7 layers ?
 s.auluck

  Dear all transiesta/tbtrans users,
 
  i am doing transport properties  of Fe/MgO junctions, at 0 bias you
 can
  see that the transmission
  coeffiecient doesn't change when increasing the thickness of the
 substrate
  (MgO) from 5
  to 11 monolayers, the same for 7, 9 and 11.
 
  i can not undersatand what happens
  any suggestions?
 
  bests
  taoufik
 


 --
 Prof. Sushil Auluck  Phone:+91-512-6797092/6148
 Department of Physics  +91-512-6798177(Home)
 Indian Institute of Technology   Cell :+91-9305548667
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 IndiaE-mail:saul...@iitk.ac.in
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 ...
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Prof. Sushil Auluck  Phone:+91-512-6797092/6148
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Indian Institute of Technology   Cell :+91-9305548667
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Re: [SIESTA-L] why the result (lattice constant...etc.) of Siesta and Vasp can't compare?

[sauluck]

hi,
it is not clear what you mean by lattice constants from different codes
comparing.one should only look at rough comparsions. as the 2 codes
are different in terms of wave functions, psuedopotentails, # kpoints,
methodology, etc ( there are too many variables), so do not expect lattice
constants from any two codes to be same..perhaps simular is a better way
of comparing. sometimes they do come out to be same...that is a bonus..
lattice constants depend on PP used as also on XC used.
s.auluck


 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



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RE: [SIESTA-L] compiling Siesta in parallel with intelmpi

[sauluck]

hi,
did you do a make clean ..you may have leftovers *.mod *.o files from
a previous compilation...
s.auluck

 Thanks,

 I was able to compile without openmp now.
 The siesta-ldau bug I found is still there though (see next mail/thread).

 Giovanni
 
 De : siesta-l-requ...@uam.es [siesta-l-requ...@uam.es] de la part de
 Herbert Fruchtl [herbert.fruc...@st-andrews.ac.uk]
 Envoyé : mardi 13 mai 2014 14:55
 À : siesta-l@uam.es
 Objet : Re: [SIESTA-L] compiling Siesta in parallel with intelmpi

 You need the sequential mkl. Here's my BLAS line:

 BLAS_LIBS= -L/usr/local/intel/mkl/lib/intel64 -lmkl_intel_lp64
 -lmkl_sequential
 -lmkl_core

Herbert

 On 13/05/14 13:42, Borghi Giovanni wrote:
 Ok below an arch.make which works, and lets siesta run in parallel,
 apparently -openmp is required, otherwise I get errors of the type (full
 output included below the arch.make)

 /opt/intel/composer_xe_2011_sp1.6.233/mkl/lib/intel64/libmkl_intel_thread.so:
 undefined reference to `__kmpc_dispatch_fini_8'

 kmpc appears to be library coming with openmp.

 ***
 SIESTA_ARCH=x86_64-unknown-linux-gnu--Intel

 FPP=
 FPP_OUTPUT=
 FC=mpiifort
 RANLIB=ranlib

 SYS=nag

 SP_KIND=4
 DP_KIND=8
 KINDS=$(SP_KIND) $(DP_KIND)

 FFLAGS=-g -check all -traceback -openmp
 FPPFLAGS= -DMPI -DFC_HAVE_FLUSH -DFC_HAVE_ABORT
 LDFLAGS=-static-intel -openmp

 ARFLAGS_EXTRA=

 FCFLAGS_fixed_f=
 FCFLAGS_free_f90=
 FPPFLAGS_fixed_F=
 FPPFLAGS_free_F90=

 BLAS_LIBS=-lmkl_intel_lp64  -lmkl_intel_thread -lmkl_core
 LAPACK_LIBS=-lmkl_intel_lp64  -lmkl_intel_thread -lmkl_core
 BLACS_LIBS=-lmkl_blacs_lp64 -lmkl_blacs_intelmpi_lp64
 SCALAPACK_LIBS= -lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64

 COMP_LIBS=dc_lapack.a

 NETCDF_LIBS=
 NETCDF_INTERFACE=

 LIBS=$(SCALAPACK_LIBS) $(BLACS_LIBS) $(LAPACK_LIBS) $(BLAS_LIBS)
 $(NETCDF_LIBS)

 #SIESTA needs an F90 interface to MPI
 #This will give you SIESTA's own implementation
 #If your compiler vendor offers an alternative, you may change
 #to it here.
 #MPI_INTERFACE=/opt/intel/impi/4.0.3.008/intel64/lib/libmpiif.a
 MPI_INTERFACE=libmpi_f90.a
 MPI_INCLUDE=.

 *

 siesta.o: In function `siesta':
 /home/borghi/marzari/siesta/siesta-ldau/Src/siesta.F:1: undefined
 reference to `__kmpc_begin'
 /home/borghi/marzari/siesta/siesta-ldau/Src/siesta.F:37: undefined
 reference to `__kmpc_end'
 /opt/intel/composer_xe_2011_sp1.6.233/mkl/lib/intel64/libmkl_intel_thread.so:
 undefined reference to `__kmpc_ok_to_fork'
 /opt/intel/composer_xe_2011_sp1.6.233/mkl/lib/intel64/libmkl_intel_thread.so:
 undefined reference to `__kmpc_end_single'
 /opt/intel/composer_xe_2011_sp1.6.233/mkl/lib/intel64/libmkl_intel_thread.so:
 undefined reference to `__kmpc_ordered'
 /opt/intel/composer_xe_2011_sp1.6.233/mkl/lib/intel64/libmkl_intel_thread.so:
 undefined reference to `__kmpc_for_static_init_8'
 /opt/intel/composer_xe_2011_sp1.6.233/mkl/lib/intel64/libmkl_intel_thread.so:
 undefined reference to `omp_get_thread_num'
 /opt/intel/composer_xe_2011_sp1.6.233/mkl/lib/intel64/libmkl_intel_thread.so:
 undefined reference to `__kmpc_barrier'
 /opt/intel/composer_xe_2011_sp1.6.233/mkl/lib/intel64/libmkl_intel_thread.so:
 undefined reference to `omp_get_num_threads'
 /opt/intel/composer_xe_2011_sp1.6.233/mkl/lib/intel64/libmkl_intel_thread.so:
 undefined reference to `omp_get_num_procs'
 /opt/intel/composer_xe_2011_sp1.6.233/mkl/lib/intel64/libmkl_intel_thread.so:
 undefined reference to `__kmpc_dispatch_next_4'
 /opt/intel/composer_xe_2011_sp1.6.233/mkl/lib/intel64/libmkl_intel_thread.so:
 undefined reference to `__kmpc_end_reduce_nowait'
 /opt/intel/composer_xe_2011_sp1.6.233/mkl/lib/intel64/libmkl_intel_thread.so:
 undefined reference to `__kmpc_critical'
 /opt/intel/composer_xe_2011_sp1.6.233/mkl/lib/intel64/libmkl_intel_thread.so:
 undefined reference to `__kmpc_dispatch_fini_8'
 /opt/intel/composer_xe_2011_sp1.6.233/mkl/lib/intel64/libmkl_intel_thread.so:
 undefined reference to `__kmpc_atomic_cmplx8_add'
 /opt/intel/composer_xe_2011_sp1.6.233/mkl/lib/intel64/libmkl_intel_thread.so:
 undefined reference to `__kmpc_atomic_float4_add'
 /opt/intel/composer_xe_2011_sp1.6.233/mkl/lib/intel64/libmkl_intel_thread.so:
 undefined reference to `__kmpc_serialized_parallel'
 /opt/intel/composer_xe_2011_sp1.6.233/mkl/lib/intel64/libmkl_intel_thread.so:
 undefined reference to `__kmpc_end_critical'
 /opt/intel/composer_xe_2011_sp1.6.233/mkl/lib/intel64/libmkl_intel_thread.so:
 undefined reference to `__kmpc_dispatch_init_8'
 /opt/intel/composer_xe_2011_sp1.6.233/mkl/lib/intel64/libmkl_intel_thread.so:
 undefined reference to `ompc_set_nested'
 /opt/intel/composer_xe_2011_sp1.6.233/mkl/lib/intel64/libmkl_intel_thread.so:
 undefined reference to `omp_get_nested'