Re: [SIESTA-L] Problem with Transiesta

[Pasan Henadeera]

Hello Haidar,
Thank you for the kind response.

In my case, I am using two similar electrodes at both ends. This is why I
defined the electrode.fdf in the following way.
1. Relaxed the structure of the 80 electrode atoms using a SIESTA run.
2. Since the electrode is similar to the scattering region for my case, I
used the ASE library to repeat the relaxed structure in the transport
direction 9 times.
3. I used the relaxed structure from step 1 for the electrode calculation.
4. In the case of the scattering region, the structure from step 2 was used
where the 80 leftmost and rightmost atoms were each specified as the
electrodes.

Further, I agree that the 400Ry energy cutoff is massive. I shall decrease
this to around 100Ry.  Also, the k-points were not the converged case. I
wanted to get a working tbtrans run before checking for the convergence of
k-points. Should I increase this and check?

As mentioned by you, should I change my steps as follows?
1. Relax the structure of the 80 atoms using a SIESTA run.
2. Since the electrode is similar to the scattering region for my case, use
the ASE library to repeat the relaxed structure in the transport direction
9 times.
3. Use the first 80 atoms to define the left electrode.
4. Use the last 80 atoms to define the right electrode. In this case, do I
leave a vacuum in the left side of the cell? As I am aware, the simulation
box in siesta always starts from 0,0,0 coordinates. However since the first
640 atoms should not be included in the electrode calculation, how do I
account for periodicity while maintaining the same coordinates as in the
scattering.fdf?
4. Use the Left and Right TSHS files to do the scattering region
calculation.


Thank you

On Thu, 16 Dec 2021 at 02:35, El-abed Haidar 
wrote:

> Hi Pasan,
>
> From the error and by looking at the electrode.fdf, I would say the right
> electrode and electrode.fdf are not the same.
>
> I would take the longer but safer approach and define left.fdf and
> right.fdf with the exact coordinates as the scattering.fdf (which showed
> some discrepancies).
>
>
>
> So in your case use the first 80 atoms in left.fdf and the last 80 atoms
> into a right.fdf file. Then use left.TSHS and right.TSHS in the scattering
> region.
>
>
>
> Another thing is that you might want to look at your parameters for the
> rest of the calculations. For example, I feel the 400 Ry cut off energy is
> massive no? Is the number of K pts chosen 1  20 50 the converged case?
>
>
>
> Hope that helps.
>
>
>
> Cheers,
>
> EL-Abed
>
>
>
> El-Abed Haidar | Doctor of Philosophy (Science)
> Condensed Matter Theory (CMT) Group| School of Physics
> THE UNIVERSITY OF SYDNEY | NSW | 2006
>
>
>
> *From: *Pasan Henadeera 
> *Sent: *Wednesday, 15 December 2021 8:06 AM
> *To: *siesta-l@uam.es
> *Subject: *[SIESTA-L] Problem with Transiesta
>
>
>
> Dear developers and users
>
>
>
> I have been trying to learn the Transiesta package to study
> current-voltage characteristics of a Si slab. During my scattering region
> calculation, the SIESTA run detects the positions of the electrodes and the
> scattering region properly as,
>
>
>
> transiesta: Regions of atoms:
>## (80): Elec.Left
>  [ 1 -- 80 ]
>## (80): Elec.Right
>  [ 641 -- 720 ]
>-- (560): Device
>  [ 81 -- 640 ]
>
>
>
> Although so, the SIESTA run does not complete and display the "Job
> completed" message, and I have been unable to find an error printed either.
>
>
>
> Following this, I attempted to conduct the Tbtrans calculation anyway, and
> was surprised to see that the atomic positions are not properly detected at
> this stage.
>
>
>
> Electrode position does not exist
> Stopping Program from Node:0
>  641  80
> Electrode position does not exist
>
>
>
> Does anyone have any advice or experience regarding this? I have attached
> my electrode and scattering region calculation files as well.
>
>
>
> elec.fdf  -> Input file for electrode run (80 atoms)
>
> scat.fdf  -> Input file for scattering region calculation (720 atoms, with
> first and last 80 atoms being the electrodes at the two ends of the
> structure)
>
> scat.out  -> Output of the scattering region calculation
>
>
>
> Thank you
>
> --
>
> Best regards
>
> Pasan Henadeera
>
>
>
> --
> SIESTA is supported by the Spanish Research Agency (AEI) and by the
> European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
>


-- 
Best regards
Pasan Henadeera

-- 
SIESTA is supported by the Spanish Research Agency (AEI) and by the European 
H2020 MaX Centre of Excellence (http://www.max-centre.eu/)

Re: [SIESTA-L] Problem restarting transiesta job

[Nick Papior]

Transiesta restart is based on whether or not the TSDE file exists and only
if the following flag is true.

DM.AllowReuse

Transiesta will then try to read the TSDE file, and then transiesta
restarts. If it does not exist it will read the DM file and restart siesta
part, if that file does not exist, then it will start from scratch.

2017-10-31 7:45 GMT+01:00 Ankita Joshi :

> Dear all,
>
> I am facing problem in restarting a transiesta job. The last few lines of
> my output file are:
>
>
> **  WELCOME TO TRANSIESTA  *
> 
> *ts-Vha: -0.54939E-01 eV*
>
>
> *Created the TranSIESTA H,S sparsity pattern:   T T sparsity for geom step 0))nrows_g=9048 nrows=9048 sparsity=.0291
> nnzs=2378948, refcount: 1>*
>
>
> *Created the TranSIESTA global update sparsity pattern:   (M of: T T T sparsity for geom step 0))nrows_g=9048 nrows=9048
> sparsity=.0178 nnzs=1455804, refcount: 2>*
>
>
>
>
> *transiesta: Determining an optimal tri-matrix using: atom+Lefttransiesta:
> Established a near-optimal partition for the tri-diagonal matrix.BTD
> partitions (6):  [ 1508, 1508, 1508, 1508, 1508, 1508 ]transiesta: Matrix
> elements in tri / full: 36385024 / 81866304*
>
>
>
> *transiesta: mem of electrodes (static):
> 277.60MBtransiesta: mem of global update arrays (static):
> 58.51MBtransiesta: mem of tri-diagonal matrices:
> 1110.38MBtransiesta: Total memory usage:  1446.49MB*
>
>
>
>
>
>
>
> *transiesta: Charge distribution, target =   2784.0Total
> charge  [Q]  :  2784.0Device
> [D]  :   896.03886Left  [E1] :
> 896.03886Left / device [C1] :
> 31.96114Right [E2] :
> 896.03886Right/ device [C2] :
> 31.96114Other [O]  :31.96114*
>
>
> *ts-q: DE1C1E2C2dQts-q:
> 896.049   896.03931.961   896.03931.961  1.011E-2ts-Vha:
> -0.56101E-01 eV*
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> *siesta: Program's energy decomposition (eV):siesta: Ebs =
> -36268.197880siesta: Eions   =220029.598995siesta: Ena =
> 72066.314806siesta: Ekin= 77484.914325siesta: Enl =
> -1380.840883siesta: Eso = 0.00siesta: Eldau   =
> 0.00siesta: DEna= -2614.918169siesta: DUscf   =
> 180.455572siesta: DUext   = 0.00siesta: Exc =
> -33788.081311siesta: eta*DQ  = 0.00siesta: Emadel  =
> 0.00siesta: Emeta   = 0.00siesta: Emolmec =
> 0.00siesta: Ekinion = 0.00siesta: Eharris =
> -108081.874431siesta: Etot=   -108081.754654siesta: FreeEng =
> -108081.754654*
>
> *iscf Eharris(eV)E_KS(eV) FreeEng(eV) dDmax
> Ef(eV) dHmax(eV)ts-scf:1  -108081.874431  -108081.754654
> -108081.754654  0.000310 -3.855504  0.019581*
>
> Could anyone pls tell me whether I can restart this job or not? If yes,
> then how to restart?
>
> Thanks,
> Ankita
>
>
>


-- 
Kind regards Nick

Re: [SIESTA-L] Problem restarting transiesta job

[Ankita Joshi]

> Dear all,> > I am facing problem in restarting a transiesta job. The last few 
> lines of my output file are: * WELCOME TO TRANSIESTA * 
> ***ts-Vha: -0.54939E-01 eVCreated the TranSIESTA H,S 
> sparsity pattern:  nrows_g=9048 nrows=9048 sparsity=.0291 nnzs=2378948, refcount: 1>Created the 
> TranSIESTA global update sparsity pattern:  sparsity for geom step 0)) nrows_g=9048 nrows=9048 sparsity=.0178 
> nnzs=1455804, refcount: 2>transiesta: Determining an optimal tri-matrix 
> using: atom+Lefttransiesta: Established a near-optimal partition for the 
> tri-diagonal matrix.BTD partitions (6): [ 1508, 1508, 1508, 1508, 1508, 1508 
> ]transiesta: Matrix elements in tri / full: 36385024 / 81866304transiesta: 
> mem of electrodes (static): 277.60MBtransiesta: mem of global update arrays 
> (static): 58.51MBtransiesta: mem of tri-diagonal matrices: 
> 1110.38MBtransiesta: Total memory usage: 1446.49MBtra
 nsiesta:

Re: [SIESTA-L] Problem in transiesta run

[Ankita Joshi]

Dear Nick,Thanks..I will follow these steps...Regards,AnkitaOn 23/09/17, Nick 
Papior   wrote:> From the provided information it is hard 
for us to pin down the problem.Could you please follow these steps:> > 
https://answers.launchpad.net/siesta/+faq/2779> > > > such that we can figure 
out what has gone wrong?> > > > 2017-09-20 15:20 GMT+02:00 Ankita Joshi 
:> > > > > > Dear SIESTA users,> > > > > I am using 
SIESTA version 4.0. I am getting the following error in the end of the output 
file for transiesta run. > > > > > > netCDF error: NetCDF: Invalid argument> > 
Stopping Program from Node: 0> > 
--> > 
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD> > with 
errorcode 1.> > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI 
processes.> > You may or may not see output from other processes, depending on> 
> exactly when Open MPI kills them.> > --
 

Re: [SIESTA-L] Problem in transiesta run

[Nick Papior]

>From the provided information it is hard for us to pin down the problem.
Could you please follow these steps:

https://answers.launchpad.net/siesta/+faq/2779

such that we can figure out what has gone wrong?

2017-09-20 15:20 GMT+02:00 Ankita Joshi :

> Dear SIESTA users,
>
> I am using SIESTA version 4.0.  I am getting the following error in the
> end of the output file for transiesta run.
>
>
>
>
>
> *netCDF error: NetCDF: Invalid argumentStopping Program from Node:
> 0--MPI_ABORT
> was invoked on rank 0 in communicator MPI_COMM_WORLDwith errorcode 1.*
>
>
> *NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.You
> may or may not see output from other processes, depending onexactly when
> Open MPI kills them.*
> --
>
> I think that the problem occur due to improper installation of transiesta
> as I faced the problem during its installation.
>
> After installing siesta (https://pelios.csx.cam.ac.uk/~mc321/siesta.html),
> I tried to install Transiesta but got the error "make: *** No rule to make
> target `libnetcdf_f90.a', needed by `transiesta'.  Stop."
>
> Then, I searched the mailing list and someone has suggested to comment the
> line NDF_INTERFACE in the arch.make file. I did that and successfully
> installed the transiesta but I don't know whether this is correct or not.
> Can anyone suggest something?
>
> Thanks,
>
> With regards
> Ankita
>
>
>


-- 
Kind regards Nick

Re: [SIESTA-L] problem converging transiesta

[Nick Papior]

There is not much to do other than trial an error.

Typically one can get a better convergence by increasing the number of
layers that separate the junction and the electrodes. I.e. if the
electrostatics are long-range.
Also, when you have vacuum regions as terminations of the buffer layers you
could also increase the number of layers "behind" the electrode to better
screen the surface.

Other than that it is difficult, it is purely trial and error.

You could try with siesta-4.1-b2 which has better convergence, and is
_much_ faster than the previous versions of transiesta.
4.1 also enables one to fix the DM in the electrodes to match that of the
pristine electrode (see flag: TS.Elecs.DM.Init). This _may_ improve a bit
the convergence.

2017-06-20 14:31 GMT+02:00 Leonardo Fonseca :

> Dear all, I have been converging transiesta 4.0 without problems for a
> number of systems, including graphene and gold chains. However, I recently
> tried to calculate the transmission function for Ti/HfO2/TiN and could not
> make it converge. The DM part converges fine, but the GF part oscillates. I
> tried longer buffer regions, more k-points and smaller mixing parameters
> (0.0002 right now), to no avail. Then I replaced TiN by Ti to simplify the
> problem. With that change the size of the system decreased from 258 to 120,
> by eliminating vacuum along z and and the necessary buffer layers. The GF
> part also oscillates. Finally, I also noticed that upon restarting the job
> in the GF part in case it has not converged, the progress obtained in the
> previous job is totally lost, and major oscillations in the total energy
> take place for several steps. Any ideas on how to improve the convergence
> in situations like this?
>



-- 
Kind regards Nick

Re: [SIESTA-L] problem writting Transiesta TSHS file as NetCDF format

[maryam jamaati]

Dear Nick,

Thank you for your kind helps. I will try new version of siesta and I am
hopeful to overcome the problem.

Sincerely yours,

On Mon, Jun 12, 2017 at 12:41 AM, Nick Papior  wrote:

> Ah, yes, you should use siesta 4.1 or later versions (currently 4.1-b2 is
> the latest).
>
> 2017-06-11 15:52 GMT+02:00 maryam jamaati :
>
>> Dear Nick,
>>
>> Many thanks for your attention.
>> I have used "GNU Fortran (Ubuntu 4.8.4-2ubuntu1~14.04.1) 4.8.4
>> 2013 Free Software Foundation, Inc." as gfortran compiler.
>>
>> I attached make file and TSHS file for you.
>> May the siesta version I have used made this problem?(I have used
>> siesta3.2)
>>
>> Sincerely yours,
>>
>> On Sat, Jun 10, 2017 at 2:24 PM, Nick Papior 
>> wrote:
>>
>>> I am trying as best as I can.
>>>
>>> However, I cannot reproduce the error you find. Could you send me your
>>> TSHS file?
>>> Also, specify which compiler you have used to compile transiesta (your
>>> arch.make file).
>>>
>>>
>>> 2017-06-09 12:37 GMT+02:00 maryam jamaati :
>>>
 Dear Nick,

 I have uninstalled all the packages and installed them again.
 Then I downloded sisl-0.8.3.tar.gz and installed it by
 sudo python setup.py install
 as you said. It seems that everything is installed properly because I
 didn't recieve any error during installation.
 But unfortunately, code dose not run as before.
 I don't no where the log file has been saved. I copied what showed in
 terminal during installation into a text file.
 I attach this text file for you.
 I would be pleased if you could help me to solve this problem.

 Sincerely yours,


 On Thu, Jun 1, 2017 at 10:29 PM, Nick Papior 
 wrote:

> It seems like you re-ran the installation script in the same directory
> as before.
>
> First remove the build directory, then do
> sudo python setup.py install
>
> and send me the installation log from that.
>
> PS. Do you have a fortran compiler? I.e. try and install gfortran:
> sudo apt-get install gfortran (for Debian style distros)
>
> 2017-05-29 15:36 GMT+02:00 maryam jamaati :
>
>> Dear Nick,
>>
>> I have installed sisl manually by "$> python setup.py install" as
>> you said. But the mentioned error appeared again in the terminal. I 
>> attach
>> the installation log file.
>>
>> Best Regards,
>>
>>
>>
>>
>>
>> On Sun, May 28, 2017 at 12:41 AM, Nick Papior 
>> wrote:
>>
>>> It seems like you are installing using pip?
>>>
>>> As I mentioned in the previous mail, you should download the tarball
>>> and install sisl manually by using this command:
>>>
>>> $> python setup.py install
>>>
>>> If this is indeed what you did, could you please attach the entire
>>> installation log.
>>>
>>> 2017-05-27 7:54 GMT+02:00 maryam jamaati :
>>>
 Dear Nick,

 Thank you for your help.
 I have installed sisl package. It was installed completely and
 correctly as you can see in the below:


 " Installed /usr/local/lib/python2.7/dist-
 packages/sisl-0.8.3-py2.7-linux-i686.egg
 Processing dependencies for sisl==0.8.3
 Searching for netCDF4==1.2.7
 Best match: netCDF4 1.2.7
 Adding netCDF4 1.2.7 to easy-install.pth file
 Installing ncinfo script to /usr/local/bin
 Installing nc4tonc3 script to /usr/local/bin
 Installing nc3tonc4 script to /usr/local/bin

 Using /usr/local/lib/python2.7/dist-packages
 Searching for scipy==0.19.0
 Best match: scipy 0.19.0
 Adding scipy 0.19.0 to easy-install.pth file

 Using /usr/local/lib/python2.7/dist-packages
 Searching for numpy==1.12.1
 Best match: numpy 1.12.1
 Adding numpy 1.12.1 to easy-install.pth file

 Using /usr/local/lib/python2.7/dist-packages
 Searching for setuptools==3.3
 Best match: setuptools 3.3
 Adding setuptools 3.3 to easy-install.pth file
 Installing easy_install script to /usr/local/bin
 Installing easy_install-2.7 script to /usr/local/bin

 Using /usr/lib/python2.7/dist-packages
 Searching for six==1.10.0
 Best match: six 1.10.0
 Adding six 1.10.0 to easy-install.pth file

 Using /home/sf/.local/lib/python2.7/site-packages
 Finished processing dependencies for sisl==0.8.3"

 *But unfortunately*, when I run the code the *below error *appears:

 /usr/lib/python2.7/dist-packages/pkg_resources.py:1031:
 UserWarning: /home/sf/.python-eggs is writable by group/others and
 vulnerable 

Re: [SIESTA-L] problem writting Transiesta TSHS file as NetCDF format

[Nick Papior]

Ah, yes, you should use siesta 4.1 or later versions (currently 4.1-b2 is
the latest).

2017-06-11 15:52 GMT+02:00 maryam jamaati :

> Dear Nick,
>
> Many thanks for your attention.
> I have used "GNU Fortran (Ubuntu 4.8.4-2ubuntu1~14.04.1) 4.8.4
> 2013 Free Software Foundation, Inc." as gfortran compiler.
>
> I attached make file and TSHS file for you.
> May the siesta version I have used made this problem?(I have used
> siesta3.2)
>
> Sincerely yours,
>
> On Sat, Jun 10, 2017 at 2:24 PM, Nick Papior  wrote:
>
>> I am trying as best as I can.
>>
>> However, I cannot reproduce the error you find. Could you send me your
>> TSHS file?
>> Also, specify which compiler you have used to compile transiesta (your
>> arch.make file).
>>
>>
>> 2017-06-09 12:37 GMT+02:00 maryam jamaati :
>>
>>> Dear Nick,
>>>
>>> I have uninstalled all the packages and installed them again.
>>> Then I downloded sisl-0.8.3.tar.gz and installed it by
>>> sudo python setup.py install
>>> as you said. It seems that everything is installed properly because I
>>> didn't recieve any error during installation.
>>> But unfortunately, code dose not run as before.
>>> I don't no where the log file has been saved. I copied what showed in
>>> terminal during installation into a text file.
>>> I attach this text file for you.
>>> I would be pleased if you could help me to solve this problem.
>>>
>>> Sincerely yours,
>>>
>>>
>>> On Thu, Jun 1, 2017 at 10:29 PM, Nick Papior 
>>> wrote:
>>>
 It seems like you re-ran the installation script in the same directory
 as before.

 First remove the build directory, then do
 sudo python setup.py install

 and send me the installation log from that.

 PS. Do you have a fortran compiler? I.e. try and install gfortran:
 sudo apt-get install gfortran (for Debian style distros)

 2017-05-29 15:36 GMT+02:00 maryam jamaati :

> Dear Nick,
>
> I have installed sisl manually by "$> python setup.py install" as you
> said. But the mentioned error appeared again in the terminal. I attach the
> installation log file.
>
> Best Regards,
>
>
>
>
>
> On Sun, May 28, 2017 at 12:41 AM, Nick Papior 
> wrote:
>
>> It seems like you are installing using pip?
>>
>> As I mentioned in the previous mail, you should download the tarball
>> and install sisl manually by using this command:
>>
>> $> python setup.py install
>>
>> If this is indeed what you did, could you please attach the entire
>> installation log.
>>
>> 2017-05-27 7:54 GMT+02:00 maryam jamaati :
>>
>>> Dear Nick,
>>>
>>> Thank you for your help.
>>> I have installed sisl package. It was installed completely and
>>> correctly as you can see in the below:
>>>
>>>
>>> " Installed /usr/local/lib/python2.7/dist-
>>> packages/sisl-0.8.3-py2.7-linux-i686.egg
>>> Processing dependencies for sisl==0.8.3
>>> Searching for netCDF4==1.2.7
>>> Best match: netCDF4 1.2.7
>>> Adding netCDF4 1.2.7 to easy-install.pth file
>>> Installing ncinfo script to /usr/local/bin
>>> Installing nc4tonc3 script to /usr/local/bin
>>> Installing nc3tonc4 script to /usr/local/bin
>>>
>>> Using /usr/local/lib/python2.7/dist-packages
>>> Searching for scipy==0.19.0
>>> Best match: scipy 0.19.0
>>> Adding scipy 0.19.0 to easy-install.pth file
>>>
>>> Using /usr/local/lib/python2.7/dist-packages
>>> Searching for numpy==1.12.1
>>> Best match: numpy 1.12.1
>>> Adding numpy 1.12.1 to easy-install.pth file
>>>
>>> Using /usr/local/lib/python2.7/dist-packages
>>> Searching for setuptools==3.3
>>> Best match: setuptools 3.3
>>> Adding setuptools 3.3 to easy-install.pth file
>>> Installing easy_install script to /usr/local/bin
>>> Installing easy_install-2.7 script to /usr/local/bin
>>>
>>> Using /usr/lib/python2.7/dist-packages
>>> Searching for six==1.10.0
>>> Best match: six 1.10.0
>>> Adding six 1.10.0 to easy-install.pth file
>>>
>>> Using /home/sf/.local/lib/python2.7/site-packages
>>> Finished processing dependencies for sisl==0.8.3"
>>>
>>> *But unfortunately*, when I run the code the *below error *appears:
>>>
>>> /usr/lib/python2.7/dist-packages/pkg_resources.py:1031:
>>> UserWarning: /home/sf/.python-eggs is writable by group/others and
>>> vulnerable to attack when used with get_resource_filename. Consider a 
>>> more
>>> secure location (set with .set_extraction_path or the PYTHON_EGG_CACHE
>>> environment variable).
>>> warnings.warn(msg, UserWarning)
>>> Traceback (most recent call last):
>>> File "convert-tshs-nc.py", line 5, in 
>>> H = sisl.get_sile(sys.argv[1]).read_es()

Re: [SIESTA-L] problem writting Transiesta TSHS file as NetCDF format

[Nick Papior]

I am trying as best as I can.

However, I cannot reproduce the error you find. Could you send me your TSHS
file?
Also, specify which compiler you have used to compile transiesta (your
arch.make file).


2017-06-09 12:37 GMT+02:00 maryam jamaati :

> Dear Nick,
>
> I have uninstalled all the packages and installed them again.
> Then I downloded sisl-0.8.3.tar.gz and installed it by
> sudo python setup.py install
> as you said. It seems that everything is installed properly because I
> didn't recieve any error during installation.
> But unfortunately, code dose not run as before.
> I don't no where the log file has been saved. I copied what showed in
> terminal during installation into a text file.
> I attach this text file for you.
> I would be pleased if you could help me to solve this problem.
>
> Sincerely yours,
>
>
> On Thu, Jun 1, 2017 at 10:29 PM, Nick Papior  wrote:
>
>> It seems like you re-ran the installation script in the same directory as
>> before.
>>
>> First remove the build directory, then do
>> sudo python setup.py install
>>
>> and send me the installation log from that.
>>
>> PS. Do you have a fortran compiler? I.e. try and install gfortran:
>> sudo apt-get install gfortran (for Debian style distros)
>>
>> 2017-05-29 15:36 GMT+02:00 maryam jamaati :
>>
>>> Dear Nick,
>>>
>>> I have installed sisl manually by "$> python setup.py install" as you
>>> said. But the mentioned error appeared again in the terminal. I attach the
>>> installation log file.
>>>
>>> Best Regards,
>>>
>>>
>>>
>>>
>>>
>>> On Sun, May 28, 2017 at 12:41 AM, Nick Papior 
>>> wrote:
>>>
 It seems like you are installing using pip?

 As I mentioned in the previous mail, you should download the tarball
 and install sisl manually by using this command:

 $> python setup.py install

 If this is indeed what you did, could you please attach the entire
 installation log.

 2017-05-27 7:54 GMT+02:00 maryam jamaati :

> Dear Nick,
>
> Thank you for your help.
> I have installed sisl package. It was installed completely and
> correctly as you can see in the below:
>
>
> " Installed /usr/local/lib/python2.7/dist-
> packages/sisl-0.8.3-py2.7-linux-i686.egg
> Processing dependencies for sisl==0.8.3
> Searching for netCDF4==1.2.7
> Best match: netCDF4 1.2.7
> Adding netCDF4 1.2.7 to easy-install.pth file
> Installing ncinfo script to /usr/local/bin
> Installing nc4tonc3 script to /usr/local/bin
> Installing nc3tonc4 script to /usr/local/bin
>
> Using /usr/local/lib/python2.7/dist-packages
> Searching for scipy==0.19.0
> Best match: scipy 0.19.0
> Adding scipy 0.19.0 to easy-install.pth file
>
> Using /usr/local/lib/python2.7/dist-packages
> Searching for numpy==1.12.1
> Best match: numpy 1.12.1
> Adding numpy 1.12.1 to easy-install.pth file
>
> Using /usr/local/lib/python2.7/dist-packages
> Searching for setuptools==3.3
> Best match: setuptools 3.3
> Adding setuptools 3.3 to easy-install.pth file
> Installing easy_install script to /usr/local/bin
> Installing easy_install-2.7 script to /usr/local/bin
>
> Using /usr/lib/python2.7/dist-packages
> Searching for six==1.10.0
> Best match: six 1.10.0
> Adding six 1.10.0 to easy-install.pth file
>
> Using /home/sf/.local/lib/python2.7/site-packages
> Finished processing dependencies for sisl==0.8.3"
>
> *But unfortunately*, when I run the code the *below error *appears:
>
> /usr/lib/python2.7/dist-packages/pkg_resources.py:1031: UserWarning:
> /home/sf/.python-eggs is writable by group/others and vulnerable to attack
> when used with get_resource_filename. Consider a more secure location (set
> with .set_extraction_path or the PYTHON_EGG_CACHE environment variable).
> warnings.warn(msg, UserWarning)
> Traceback (most recent call last):
> File "convert-tshs-nc.py", line 5, in 
> H = sisl.get_sile(sys.argv[1]).read_es()
> File "build/bdist.linux-i686/egg/sisl/io/siesta/binaries.py", line
> 89, in read_es
> File "build/bdist.linux-i686/egg/sisl/io/siesta/binaries.py", line
> 50, in read_geom
> File "build/bdist.linux-i686/egg/sisl/io/siesta/binaries.py", line
> 35, in read_sc
> ValueError: failed to create intent(cache|hide)|optional array— must
> have defined dimensions but got (3,0,)
>
> Best Regards,
>
> Maryam Jamaati
>
>
> On Wed, May 24, 2017 at 11:21 AM, Nick Papior 
> wrote:
>
>> I haven't tried the fortran extensions through pip.
>>
>> Could you please try and install sisl the manual way?
>> Download the tar-ball and issue:
>>
>> python setup.py install
>>
>>
>> 2017-05-23 10:09 GMT+02:00 maryam 

Re: [SIESTA-L] problem writting Transiesta TSHS file as NetCDF format

[maryam jamaati]

Dear Nick,

I have uninstalled all the packages and installed them again.
Then I downloded sisl-0.8.3.tar.gz and installed it by
sudo python setup.py install
as you said. It seems that everything is installed properly because I
didn't recieve any error during installation.
But unfortunately, code dose not run as before.
I don't no where the log file has been saved. I copied what showed in
terminal during installation into a text file.
I attach this text file for you.
I would be pleased if you could help me to solve this problem.

Sincerely yours,


On Thu, Jun 1, 2017 at 10:29 PM, Nick Papior  wrote:

> It seems like you re-ran the installation script in the same directory as
> before.
>
> First remove the build directory, then do
> sudo python setup.py install
>
> and send me the installation log from that.
>
> PS. Do you have a fortran compiler? I.e. try and install gfortran:
> sudo apt-get install gfortran (for Debian style distros)
>
> 2017-05-29 15:36 GMT+02:00 maryam jamaati :
>
>> Dear Nick,
>>
>> I have installed sisl manually by "$> python setup.py install" as you
>> said. But the mentioned error appeared again in the terminal. I attach the
>> installation log file.
>>
>> Best Regards,
>>
>>
>>
>>
>>
>> On Sun, May 28, 2017 at 12:41 AM, Nick Papior 
>> wrote:
>>
>>> It seems like you are installing using pip?
>>>
>>> As I mentioned in the previous mail, you should download the tarball and
>>> install sisl manually by using this command:
>>>
>>> $> python setup.py install
>>>
>>> If this is indeed what you did, could you please attach the entire
>>> installation log.
>>>
>>> 2017-05-27 7:54 GMT+02:00 maryam jamaati :
>>>
 Dear Nick,

 Thank you for your help.
 I have installed sisl package. It was installed completely and
 correctly as you can see in the below:


 " Installed /usr/local/lib/python2.7/dist-
 packages/sisl-0.8.3-py2.7-linux-i686.egg
 Processing dependencies for sisl==0.8.3
 Searching for netCDF4==1.2.7
 Best match: netCDF4 1.2.7
 Adding netCDF4 1.2.7 to easy-install.pth file
 Installing ncinfo script to /usr/local/bin
 Installing nc4tonc3 script to /usr/local/bin
 Installing nc3tonc4 script to /usr/local/bin

 Using /usr/local/lib/python2.7/dist-packages
 Searching for scipy==0.19.0
 Best match: scipy 0.19.0
 Adding scipy 0.19.0 to easy-install.pth file

 Using /usr/local/lib/python2.7/dist-packages
 Searching for numpy==1.12.1
 Best match: numpy 1.12.1
 Adding numpy 1.12.1 to easy-install.pth file

 Using /usr/local/lib/python2.7/dist-packages
 Searching for setuptools==3.3
 Best match: setuptools 3.3
 Adding setuptools 3.3 to easy-install.pth file
 Installing easy_install script to /usr/local/bin
 Installing easy_install-2.7 script to /usr/local/bin

 Using /usr/lib/python2.7/dist-packages
 Searching for six==1.10.0
 Best match: six 1.10.0
 Adding six 1.10.0 to easy-install.pth file

 Using /home/sf/.local/lib/python2.7/site-packages
 Finished processing dependencies for sisl==0.8.3"

 *But unfortunately*, when I run the code the *below error *appears:

 /usr/lib/python2.7/dist-packages/pkg_resources.py:1031: UserWarning:
 /home/sf/.python-eggs is writable by group/others and vulnerable to attack
 when used with get_resource_filename. Consider a more secure location (set
 with .set_extraction_path or the PYTHON_EGG_CACHE environment variable).
 warnings.warn(msg, UserWarning)
 Traceback (most recent call last):
 File "convert-tshs-nc.py", line 5, in 
 H = sisl.get_sile(sys.argv[1]).read_es()
 File "build/bdist.linux-i686/egg/sisl/io/siesta/binaries.py", line 89,
 in read_es
 File "build/bdist.linux-i686/egg/sisl/io/siesta/binaries.py", line 50,
 in read_geom
 File "build/bdist.linux-i686/egg/sisl/io/siesta/binaries.py", line 35,
 in read_sc
 ValueError: failed to create intent(cache|hide)|optional array— must
 have defined dimensions but got (3,0,)

 Best Regards,

 Maryam Jamaati


 On Wed, May 24, 2017 at 11:21 AM, Nick Papior 
 wrote:

> I haven't tried the fortran extensions through pip.
>
> Could you please try and install sisl the manual way?
> Download the tar-ball and issue:
>
> python setup.py install
>
>
> 2017-05-23 10:09 GMT+02:00 maryam jamaati :
>
>> Dear Nick,
>>
>> thanks for your attention.
>> I installed sisl via pip command. And it was successfully installed
>> without any errors.
>> Also i installed pre-requisite before installing sisl such as :
>> setuptools, numpy (>=1.9), scipy, netcdf4-python.
>>
>> ‌Best Regards,
>>
>> On Mon, May 22, 2017 at 5:44 PM, Nick Papior 

Re: [SIESTA-L] problem writting Transiesta TSHS file as NetCDF format

[Nick Papior]

It seems like you re-ran the installation script in the same directory as
before.

First remove the build directory, then do
sudo python setup.py install

and send me the installation log from that.

PS. Do you have a fortran compiler? I.e. try and install gfortran:
sudo apt-get install gfortran (for Debian style distros)

2017-05-29 15:36 GMT+02:00 maryam jamaati :

> Dear Nick,
>
> I have installed sisl manually by "$> python setup.py install" as you
> said. But the mentioned error appeared again in the terminal. I attach the
> installation log file.
>
> Best Regards,
>
>
>
>
>
> On Sun, May 28, 2017 at 12:41 AM, Nick Papior 
> wrote:
>
>> It seems like you are installing using pip?
>>
>> As I mentioned in the previous mail, you should download the tarball and
>> install sisl manually by using this command:
>>
>> $> python setup.py install
>>
>> If this is indeed what you did, could you please attach the entire
>> installation log.
>>
>> 2017-05-27 7:54 GMT+02:00 maryam jamaati :
>>
>>> Dear Nick,
>>>
>>> Thank you for your help.
>>> I have installed sisl package. It was installed completely and correctly
>>> as you can see in the below:
>>>
>>>
>>> " Installed /usr/local/lib/python2.7/dist-packages/sisl-0.8.3-py2.7-linu
>>> x-i686.egg
>>> Processing dependencies for sisl==0.8.3
>>> Searching for netCDF4==1.2.7
>>> Best match: netCDF4 1.2.7
>>> Adding netCDF4 1.2.7 to easy-install.pth file
>>> Installing ncinfo script to /usr/local/bin
>>> Installing nc4tonc3 script to /usr/local/bin
>>> Installing nc3tonc4 script to /usr/local/bin
>>>
>>> Using /usr/local/lib/python2.7/dist-packages
>>> Searching for scipy==0.19.0
>>> Best match: scipy 0.19.0
>>> Adding scipy 0.19.0 to easy-install.pth file
>>>
>>> Using /usr/local/lib/python2.7/dist-packages
>>> Searching for numpy==1.12.1
>>> Best match: numpy 1.12.1
>>> Adding numpy 1.12.1 to easy-install.pth file
>>>
>>> Using /usr/local/lib/python2.7/dist-packages
>>> Searching for setuptools==3.3
>>> Best match: setuptools 3.3
>>> Adding setuptools 3.3 to easy-install.pth file
>>> Installing easy_install script to /usr/local/bin
>>> Installing easy_install-2.7 script to /usr/local/bin
>>>
>>> Using /usr/lib/python2.7/dist-packages
>>> Searching for six==1.10.0
>>> Best match: six 1.10.0
>>> Adding six 1.10.0 to easy-install.pth file
>>>
>>> Using /home/sf/.local/lib/python2.7/site-packages
>>> Finished processing dependencies for sisl==0.8.3"
>>>
>>> *But unfortunately*, when I run the code the *below error *appears:
>>>
>>> /usr/lib/python2.7/dist-packages/pkg_resources.py:1031: UserWarning:
>>> /home/sf/.python-eggs is writable by group/others and vulnerable to attack
>>> when used with get_resource_filename. Consider a more secure location (set
>>> with .set_extraction_path or the PYTHON_EGG_CACHE environment variable).
>>> warnings.warn(msg, UserWarning)
>>> Traceback (most recent call last):
>>> File "convert-tshs-nc.py", line 5, in 
>>> H = sisl.get_sile(sys.argv[1]).read_es()
>>> File "build/bdist.linux-i686/egg/sisl/io/siesta/binaries.py", line 89,
>>> in read_es
>>> File "build/bdist.linux-i686/egg/sisl/io/siesta/binaries.py", line 50,
>>> in read_geom
>>> File "build/bdist.linux-i686/egg/sisl/io/siesta/binaries.py", line 35,
>>> in read_sc
>>> ValueError: failed to create intent(cache|hide)|optional array— must
>>> have defined dimensions but got (3,0,)
>>>
>>> Best Regards,
>>>
>>> Maryam Jamaati
>>>
>>>
>>> On Wed, May 24, 2017 at 11:21 AM, Nick Papior 
>>> wrote:
>>>
 I haven't tried the fortran extensions through pip.

 Could you please try and install sisl the manual way?
 Download the tar-ball and issue:

 python setup.py install


 2017-05-23 10:09 GMT+02:00 maryam jamaati :

> Dear Nick,
>
> thanks for your attention.
> I installed sisl via pip command. And it was successfully installed
> without any errors.
> Also i installed pre-requisite before installing sisl such as :
> setuptools, numpy (>=1.9), scipy, netcdf4-python.
>
> ‌Best Regards,
>
> On Mon, May 22, 2017 at 5:44 PM, Nick Papior 
> wrote:
>
>> Could you tell us how you have installed sisl?
>>
>> Also, I think I made a mistake in the script, it should be:
>>
>> >>> script begin <<<
>> #!/usr/bin/env python
>> import sys
>> import sisl
>> # Read the electronic structure from the file
>> H = sisl.get_sile(sys.argv[1]).read_es()
>> H.write('output.nc')
>> >>> script end <<<
>>
>> 2017-05-21 7:26 GMT+02:00 maryam jamaati :
>>
>>> Dear siesta users,
>>>
>>> In order to convert from TSHS to nc we used this small script from (
>>> https://answers.launchpad.net/siesta/+question/435947):
>>>
>>> #!/usr/bin/env python
>>> import sys
>>> import sisl
>>> # Read 

Re: [SIESTA-L] problem writting Transiesta TSHS file as NetCDF format

[maryam jamaati]

Dear Nick,

I have installed sisl manually by "$> python setup.py install" as you said.
But the mentioned error appeared again in the terminal. I attach the
installation log file.

Best Regards,





On Sun, May 28, 2017 at 12:41 AM, Nick Papior  wrote:

> It seems like you are installing using pip?
>
> As I mentioned in the previous mail, you should download the tarball and
> install sisl manually by using this command:
>
> $> python setup.py install
>
> If this is indeed what you did, could you please attach the entire
> installation log.
>
> 2017-05-27 7:54 GMT+02:00 maryam jamaati :
>
>> Dear Nick,
>>
>> Thank you for your help.
>> I have installed sisl package. It was installed completely and correctly
>> as you can see in the below:
>>
>>
>> " Installed /usr/local/lib/python2.7/dist-packages/sisl-0.8.3-py2.7-linu
>> x-i686.egg
>> Processing dependencies for sisl==0.8.3
>> Searching for netCDF4==1.2.7
>> Best match: netCDF4 1.2.7
>> Adding netCDF4 1.2.7 to easy-install.pth file
>> Installing ncinfo script to /usr/local/bin
>> Installing nc4tonc3 script to /usr/local/bin
>> Installing nc3tonc4 script to /usr/local/bin
>>
>> Using /usr/local/lib/python2.7/dist-packages
>> Searching for scipy==0.19.0
>> Best match: scipy 0.19.0
>> Adding scipy 0.19.0 to easy-install.pth file
>>
>> Using /usr/local/lib/python2.7/dist-packages
>> Searching for numpy==1.12.1
>> Best match: numpy 1.12.1
>> Adding numpy 1.12.1 to easy-install.pth file
>>
>> Using /usr/local/lib/python2.7/dist-packages
>> Searching for setuptools==3.3
>> Best match: setuptools 3.3
>> Adding setuptools 3.3 to easy-install.pth file
>> Installing easy_install script to /usr/local/bin
>> Installing easy_install-2.7 script to /usr/local/bin
>>
>> Using /usr/lib/python2.7/dist-packages
>> Searching for six==1.10.0
>> Best match: six 1.10.0
>> Adding six 1.10.0 to easy-install.pth file
>>
>> Using /home/sf/.local/lib/python2.7/site-packages
>> Finished processing dependencies for sisl==0.8.3"
>>
>> *But unfortunately*, when I run the code the *below error *appears:
>>
>> /usr/lib/python2.7/dist-packages/pkg_resources.py:1031: UserWarning:
>> /home/sf/.python-eggs is writable by group/others and vulnerable to attack
>> when used with get_resource_filename. Consider a more secure location (set
>> with .set_extraction_path or the PYTHON_EGG_CACHE environment variable).
>> warnings.warn(msg, UserWarning)
>> Traceback (most recent call last):
>> File "convert-tshs-nc.py", line 5, in 
>> H = sisl.get_sile(sys.argv[1]).read_es()
>> File "build/bdist.linux-i686/egg/sisl/io/siesta/binaries.py", line 89,
>> in read_es
>> File "build/bdist.linux-i686/egg/sisl/io/siesta/binaries.py", line 50,
>> in read_geom
>> File "build/bdist.linux-i686/egg/sisl/io/siesta/binaries.py", line 35,
>> in read_sc
>> ValueError: failed to create intent(cache|hide)|optional array— must have
>> defined dimensions but got (3,0,)
>>
>> Best Regards,
>>
>> Maryam Jamaati
>>
>>
>> On Wed, May 24, 2017 at 11:21 AM, Nick Papior 
>> wrote:
>>
>>> I haven't tried the fortran extensions through pip.
>>>
>>> Could you please try and install sisl the manual way?
>>> Download the tar-ball and issue:
>>>
>>> python setup.py install
>>>
>>>
>>> 2017-05-23 10:09 GMT+02:00 maryam jamaati :
>>>
 Dear Nick,

 thanks for your attention.
 I installed sisl via pip command. And it was successfully installed
 without any errors.
 Also i installed pre-requisite before installing sisl such as :
 setuptools, numpy (>=1.9), scipy, netcdf4-python.

 ‌Best Regards,

 On Mon, May 22, 2017 at 5:44 PM, Nick Papior 
 wrote:

> Could you tell us how you have installed sisl?
>
> Also, I think I made a mistake in the script, it should be:
>
> >>> script begin <<<
> #!/usr/bin/env python
> import sys
> import sisl
> # Read the electronic structure from the file
> H = sisl.get_sile(sys.argv[1]).read_es()
> H.write('output.nc')
> >>> script end <<<
>
> 2017-05-21 7:26 GMT+02:00 maryam jamaati :
>
>> Dear siesta users,
>>
>> In order to convert from TSHS to nc we used this small script from (
>> https://answers.launchpad.net/siesta/+question/435947):
>>
>> #!/usr/bin/env python
>> import sys
>> import sisl
>> # Read the electronic structure from the file
>> H = get_sile(sys.argv[1]).read_es()
>> H.write('output.nc')
>> »> script end «<
>>
>> and then call it by:
>> python convert.py siesta.TSHS
>>
>>
>>
>> But after running the code, the below error appears:
>> ValueError: failed to create intent(cache|hide)|optional array— must
>> have defined dimensions but got (3,0,)
>>
>> I would be pleased if anyone could help me to solve this problem.
>>
>> Best Regards,
>>
>>
>

Re: [SIESTA-L] problem writting Transiesta TSHS file as NetCDF format

[Nick Papior]

It seems like you are installing using pip?

As I mentioned in the previous mail, you should download the tarball and
install sisl manually by using this command:

$> python setup.py install

If this is indeed what you did, could you please attach the entire
installation log.

2017-05-27 7:54 GMT+02:00 maryam jamaati :

> Dear Nick,
>
> Thank you for your help.
> I have installed sisl package. It was installed completely and correctly
> as you can see in the below:
>
>
> " Installed /usr/local/lib/python2.7/dist-packages/sisl-0.8.3-py2.7-
> linux-i686.egg
> Processing dependencies for sisl==0.8.3
> Searching for netCDF4==1.2.7
> Best match: netCDF4 1.2.7
> Adding netCDF4 1.2.7 to easy-install.pth file
> Installing ncinfo script to /usr/local/bin
> Installing nc4tonc3 script to /usr/local/bin
> Installing nc3tonc4 script to /usr/local/bin
>
> Using /usr/local/lib/python2.7/dist-packages
> Searching for scipy==0.19.0
> Best match: scipy 0.19.0
> Adding scipy 0.19.0 to easy-install.pth file
>
> Using /usr/local/lib/python2.7/dist-packages
> Searching for numpy==1.12.1
> Best match: numpy 1.12.1
> Adding numpy 1.12.1 to easy-install.pth file
>
> Using /usr/local/lib/python2.7/dist-packages
> Searching for setuptools==3.3
> Best match: setuptools 3.3
> Adding setuptools 3.3 to easy-install.pth file
> Installing easy_install script to /usr/local/bin
> Installing easy_install-2.7 script to /usr/local/bin
>
> Using /usr/lib/python2.7/dist-packages
> Searching for six==1.10.0
> Best match: six 1.10.0
> Adding six 1.10.0 to easy-install.pth file
>
> Using /home/sf/.local/lib/python2.7/site-packages
> Finished processing dependencies for sisl==0.8.3"
>
> *But unfortunately*, when I run the code the *below error *appears:
>
> /usr/lib/python2.7/dist-packages/pkg_resources.py:1031: UserWarning:
> /home/sf/.python-eggs is writable by group/others and vulnerable to attack
> when used with get_resource_filename. Consider a more secure location (set
> with .set_extraction_path or the PYTHON_EGG_CACHE environment variable).
> warnings.warn(msg, UserWarning)
> Traceback (most recent call last):
> File "convert-tshs-nc.py", line 5, in 
> H = sisl.get_sile(sys.argv[1]).read_es()
> File "build/bdist.linux-i686/egg/sisl/io/siesta/binaries.py", line 89, in
> read_es
> File "build/bdist.linux-i686/egg/sisl/io/siesta/binaries.py", line 50, in
> read_geom
> File "build/bdist.linux-i686/egg/sisl/io/siesta/binaries.py", line 35, in
> read_sc
> ValueError: failed to create intent(cache|hide)|optional array— must have
> defined dimensions but got (3,0,)
>
> Best Regards,
>
> Maryam Jamaati
>
>
> On Wed, May 24, 2017 at 11:21 AM, Nick Papior 
> wrote:
>
>> I haven't tried the fortran extensions through pip.
>>
>> Could you please try and install sisl the manual way?
>> Download the tar-ball and issue:
>>
>> python setup.py install
>>
>>
>> 2017-05-23 10:09 GMT+02:00 maryam jamaati :
>>
>>> Dear Nick,
>>>
>>> thanks for your attention.
>>> I installed sisl via pip command. And it was successfully installed
>>> without any errors.
>>> Also i installed pre-requisite before installing sisl such as :
>>> setuptools, numpy (>=1.9), scipy, netcdf4-python.
>>>
>>> ‌Best Regards,
>>>
>>> On Mon, May 22, 2017 at 5:44 PM, Nick Papior 
>>> wrote:
>>>
 Could you tell us how you have installed sisl?

 Also, I think I made a mistake in the script, it should be:

 >>> script begin <<<
 #!/usr/bin/env python
 import sys
 import sisl
 # Read the electronic structure from the file
 H = sisl.get_sile(sys.argv[1]).read_es()
 H.write('output.nc')
 >>> script end <<<

 2017-05-21 7:26 GMT+02:00 maryam jamaati :

> Dear siesta users,
>
> In order to convert from TSHS to nc we used this small script from (
> https://answers.launchpad.net/siesta/+question/435947):
>
> #!/usr/bin/env python
> import sys
> import sisl
> # Read the electronic structure from the file
> H = get_sile(sys.argv[1]).read_es()
> H.write('output.nc')
> »> script end «<
>
> and then call it by:
> python convert.py siesta.TSHS
>
>
>
> But after running the code, the below error appears:
> ValueError: failed to create intent(cache|hide)|optional array— must
> have defined dimensions but got (3,0,)
>
> I would be pleased if anyone could help me to solve this problem.
>
> Best Regards,
>
>


 --
 Kind regards Nick

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


-- 
Kind regards Nick

Re: [SIESTA-L] problem writting Transiesta TSHS file as NetCDF format

[maryam jamaati]

Dear Nick,

Thank you for your help.
I have installed sisl package. It was installed completely and correctly as
you can see in the below:


" Installed
/usr/local/lib/python2.7/dist-packages/sisl-0.8.3-py2.7-linux-i686.egg
Processing dependencies for sisl==0.8.3
Searching for netCDF4==1.2.7
Best match: netCDF4 1.2.7
Adding netCDF4 1.2.7 to easy-install.pth file
Installing ncinfo script to /usr/local/bin
Installing nc4tonc3 script to /usr/local/bin
Installing nc3tonc4 script to /usr/local/bin

Using /usr/local/lib/python2.7/dist-packages
Searching for scipy==0.19.0
Best match: scipy 0.19.0
Adding scipy 0.19.0 to easy-install.pth file

Using /usr/local/lib/python2.7/dist-packages
Searching for numpy==1.12.1
Best match: numpy 1.12.1
Adding numpy 1.12.1 to easy-install.pth file

Using /usr/local/lib/python2.7/dist-packages
Searching for setuptools==3.3
Best match: setuptools 3.3
Adding setuptools 3.3 to easy-install.pth file
Installing easy_install script to /usr/local/bin
Installing easy_install-2.7 script to /usr/local/bin

Using /usr/lib/python2.7/dist-packages
Searching for six==1.10.0
Best match: six 1.10.0
Adding six 1.10.0 to easy-install.pth file

Using /home/sf/.local/lib/python2.7/site-packages
Finished processing dependencies for sisl==0.8.3"

*But unfortunately*, when I run the code the *below error *appears:

/usr/lib/python2.7/dist-packages/pkg_resources.py:1031: UserWarning:
/home/sf/.python-eggs is writable by group/others and vulnerable to attack
when used with get_resource_filename. Consider a more secure location (set
with .set_extraction_path or the PYTHON_EGG_CACHE environment variable).
warnings.warn(msg, UserWarning)
Traceback (most recent call last):
File "convert-tshs-nc.py", line 5, in 
H = sisl.get_sile(sys.argv[1]).read_es()
File "build/bdist.linux-i686/egg/sisl/io/siesta/binaries.py", line 89, in
read_es
File "build/bdist.linux-i686/egg/sisl/io/siesta/binaries.py", line 50, in
read_geom
File "build/bdist.linux-i686/egg/sisl/io/siesta/binaries.py", line 35, in
read_sc
ValueError: failed to create intent(cache|hide)|optional array— must have
defined dimensions but got (3,0,)

Best Regards,

Maryam Jamaati


On Wed, May 24, 2017 at 11:21 AM, Nick Papior  wrote:

> I haven't tried the fortran extensions through pip.
>
> Could you please try and install sisl the manual way?
> Download the tar-ball and issue:
>
> python setup.py install
>
>
> 2017-05-23 10:09 GMT+02:00 maryam jamaati :
>
>> Dear Nick,
>>
>> thanks for your attention.
>> I installed sisl via pip command. And it was successfully installed
>> without any errors.
>> Also i installed pre-requisite before installing sisl such as :
>> setuptools, numpy (>=1.9), scipy, netcdf4-python.
>>
>> ‌Best Regards,
>>
>> On Mon, May 22, 2017 at 5:44 PM, Nick Papior 
>> wrote:
>>
>>> Could you tell us how you have installed sisl?
>>>
>>> Also, I think I made a mistake in the script, it should be:
>>>
>>> >>> script begin <<<
>>> #!/usr/bin/env python
>>> import sys
>>> import sisl
>>> # Read the electronic structure from the file
>>> H = sisl.get_sile(sys.argv[1]).read_es()
>>> H.write('output.nc')
>>> >>> script end <<<
>>>
>>> 2017-05-21 7:26 GMT+02:00 maryam jamaati :
>>>
 Dear siesta users,

 In order to convert from TSHS to nc we used this small script from (
 https://answers.launchpad.net/siesta/+question/435947):

 #!/usr/bin/env python
 import sys
 import sisl
 # Read the electronic structure from the file
 H = get_sile(sys.argv[1]).read_es()
 H.write('output.nc')
 »> script end «<

 and then call it by:
 python convert.py siesta.TSHS



 But after running the code, the below error appears:
 ValueError: failed to create intent(cache|hide)|optional array— must
 have defined dimensions but got (3,0,)

 I would be pleased if anyone could help me to solve this problem.

 Best Regards,


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

Re: [SIESTA-L] problem writting Transiesta TSHS file as NetCDF format

[Nick Papior]

I haven't tried the fortran extensions through pip.

Could you please try and install sisl the manual way?
Download the tar-ball and issue:

python setup.py install


2017-05-23 10:09 GMT+02:00 maryam jamaati :

> Dear Nick,
>
> thanks for your attention.
> I installed sisl via pip command. And it was successfully installed
> without any errors.
> Also i installed pre-requisite before installing sisl such as :
> setuptools, numpy (>=1.9), scipy, netcdf4-python.
>
> ‌Best Regards,
>
> On Mon, May 22, 2017 at 5:44 PM, Nick Papior  wrote:
>
>> Could you tell us how you have installed sisl?
>>
>> Also, I think I made a mistake in the script, it should be:
>>
>> >>> script begin <<<
>> #!/usr/bin/env python
>> import sys
>> import sisl
>> # Read the electronic structure from the file
>> H = sisl.get_sile(sys.argv[1]).read_es()
>> H.write('output.nc')
>> >>> script end <<<
>>
>> 2017-05-21 7:26 GMT+02:00 maryam jamaati :
>>
>>> Dear siesta users,
>>>
>>> In order to convert from TSHS to nc we used this small script from (
>>> https://answers.launchpad.net/siesta/+question/435947):
>>>
>>> #!/usr/bin/env python
>>> import sys
>>> import sisl
>>> # Read the electronic structure from the file
>>> H = get_sile(sys.argv[1]).read_es()
>>> H.write('output.nc')
>>> »> script end «<
>>>
>>> and then call it by:
>>> python convert.py siesta.TSHS
>>>
>>>
>>>
>>> But after running the code, the below error appears:
>>> ValueError: failed to create intent(cache|hide)|optional array— must
>>> have defined dimensions but got (3,0,)
>>>
>>> I would be pleased if anyone could help me to solve this problem.
>>>
>>> Best Regards,
>>>
>>>
>>
>>
>> --
>> Kind regards Nick
>>
>
>


-- 
Kind regards Nick

Re: [SIESTA-L] problem writting Transiesta TSHS file as NetCDF format

[maryam jamaati]

Dear Nick,

thanks for your attention.
I installed sisl via pip command. And it was successfully installed without
any errors.
Also i installed pre-requisite before installing sisl such as : setuptools,
numpy (>=1.9), scipy, netcdf4-python.

‌Best Regards,

On Mon, May 22, 2017 at 5:44 PM, Nick Papior  wrote:

> Could you tell us how you have installed sisl?
>
> Also, I think I made a mistake in the script, it should be:
>
> >>> script begin <<<
> #!/usr/bin/env python
> import sys
> import sisl
> # Read the electronic structure from the file
> H = sisl.get_sile(sys.argv[1]).read_es()
> H.write('output.nc')
> >>> script end <<<
>
> 2017-05-21 7:26 GMT+02:00 maryam jamaati :
>
>> Dear siesta users,
>>
>> In order to convert from TSHS to nc we used this small script from (
>> https://answers.launchpad.net/siesta/+question/435947):
>>
>> #!/usr/bin/env python
>> import sys
>> import sisl
>> # Read the electronic structure from the file
>> H = get_sile(sys.argv[1]).read_es()
>> H.write('output.nc')
>> »> script end «<
>>
>> and then call it by:
>> python convert.py siesta.TSHS
>>
>>
>>
>> But after running the code, the below error appears:
>> ValueError: failed to create intent(cache|hide)|optional array— must have
>> defined dimensions but got (3,0,)
>>
>> I would be pleased if anyone could help me to solve this problem.
>>
>> Best Regards,
>>
>>
>
>
> --
> Kind regards Nick
>

Re: [SIESTA-L] problem writting Transiesta TSHS file as NetCDF format

[Nick Papior]

Could you tell us how you have installed sisl?

Also, I think I made a mistake in the script, it should be:

>>> script begin <<<
#!/usr/bin/env python
import sys
import sisl
# Read the electronic structure from the file
H = sisl.get_sile(sys.argv[1]).read_es()
H.write('output.nc')
>>> script end <<<

2017-05-21 7:26 GMT+02:00 maryam jamaati :

> Dear siesta users,
>
> In order to convert from TSHS to nc we used this small script from (
> https://answers.launchpad.net/siesta/+question/435947):
>
> #!/usr/bin/env python
> import sys
> import sisl
> # Read the electronic structure from the file
> H = get_sile(sys.argv[1]).read_es()
> H.write('output.nc')
> »> script end «<
>
> and then call it by:
> python convert.py siesta.TSHS
>
>
>
> But after running the code, the below error appears:
> ValueError: failed to create intent(cache|hide)|optional array— must have
> defined dimensions but got (3,0,)
>
> I would be pleased if anyone could help me to solve this problem.
>
> Best Regards,
>
>


-- 
Kind regards Nick

Re: [SIESTA-L] Problem with transiesta convergence

[Sebastian Caicedo D.]

I forgot to attach the Input file I'm using for the calculation.


On 12/10/2013 03:52 PM, Sebastian Caicedo D. wrote:

Dear transiesta users,

I'm having trouble with the convergence of the transiesta SCF. I was 
able to make the calculation converge at 0V polarization, but when I 
start increasing the voltage, it doesn't.


Formerly I performed a calculation with a very high DM.Tolerance 
parameter (0.001) and it worked for all voltages, but the results are 
not what I should expect from my system (I'm working on a triple 
barrier heterostructure, so I would expect to obtain some resonances, 
which I don't).


I looked into the mailing list and tried the solutions described there 
(like including more electrode layers in the scattering region input, 
and reducing the DM.MixingWeight parameter), but so far, I haven't 
been able to get convergence.


I'm using DZP basis set and GGA functional.

If anyone has faced a similar issue, I would really appreciate any help

Thanks in  advance

Sebastian Caicedo D.


SystemNamescat
SystemLabel   scat

%block kgrid_Monkhorst_Pack
  1   0   00.0
  0   1   00.0
  0   0   20.0
%endblock kgrid_Monkhorst_Pack

xc.functional   GGA
xc.authors  PBE

MeshCutoff  300 Ry
OccupationFunction  FD
ElectronicTemperature   300 K

SpinPolarized   F
FixSpin F

MaxSCFIterations300
DM.NumberBroyden3
DM.MixingWeight 0.002
#DM.OccupancyTolerance   0.10E-11
DM.NumberKick   100
DM.KickMixingWeight 0.002
DM.Tolerance0.1e-3
DM.UseSaveDMT

UseSaveData T
#MD.UseSaveCGT

MD.NumCGsteps   0
MD.TypeOfRunCG
MD.VariableCell F
MD.MaxCGDispl   0.15  Ang
#MD.MaxForceTol  0.05 eV/Ang
#MD.MaxStressTol 0.0001 eV/Ang**3

Diag.ParallelOverK  F
PAO.EnergyShift 65 meV
#PAO.SplitTailNorm  T
#PAO.SoftDefaultT
PAO.BasisType   split
PAO.BasisSize   DZP
PAO.SplitNorm   0.15
#PAO.OldStylePolOrbsF

%block PAO.Basis
In   3
 n=4 2 1
 0.00
 1.00
 n=5 0 2
 0.00  0.00
 1.00  1.00
 n=5 1 2 P
 0.00  0.00
 1.00  1.00
%endblock PAO.Basis

WriteMullikenPop0
WriteBands  F
WriteKpointsF
WriteForces F
WriteDM T
WriteKbands F
WriteEigenvaluesT
SaveRho F
SaveElectrostaticPotential  F
SaveTotalPotential  F
WriteCoorXmol   F

NumberOfAtoms 176
NumberOfSpecies 3

%block ChemicalSpeciesLabel
1   49  In
2   33  As
3   15  P
%endblock ChemicalSpeciesLabel

LatticeConstant 1.0 Ang

%block LatticeVectors
6.0583  0.  0.
0.  6.0583  0.
0.  0.  132.1468
%endblock LatticeVectors

AtomicCoordinatesFormat NotScaledCartesianAng

%block AtomicCoordinatesAndAtomicSpecies
0.000.000.001   In  1
3.02915 3.02915 0.001   In  2
1.5145751.5145751.5145752   As  3
4.5437254.5437251.5145752   As  4
0.003.02915 3.02915 1   In  5
3.02915 0.003.02915 1   In  6
1.5145754.5437254.5437252   As  7
4.5437251.5145754.5437252   As  8
0.000.006.0583  1   In  9
3.02915 3.02915 6.0583  1   In  10
1.5145751.5145757.5728752   As  11
4.5437254.5437257.5728752   As  12
0.003.02915 9.08745 1   In  13
3.02915 0.009.08745 1   In  14
1.5145754.54372510.602025   2   As  15
4.5437251.51457510.602025   2   As  16
0.000.0012.1166 1   In  17
3.02915 3.02915 12.1166 1   In  18
1.5145751.51457513.631175   2   As  19
4.5437254.54372513.631175   2   As  20
0.003.02915 15.145751   In  21
3.02915 0.0015.145751   In  22
1.5145754.54372516.660325   2   As  23
4.5437251.51457516.660325   2   As  24
0.000.0018.1749 1   In  25
3.02915 3.02915

Re: [SIESTA-L] Problem with Transiesta Run: MINVEC: BASIS VECTORS ARE LINEARLY DEPENDENT

[Nick Papior Andersen]

Try and include the Monkhorst-Pack grid and manually set it to the gamma
point. Siesta has two ways of specifying the k-grid, either MP or via a
cutoff length (see http://dx.doi.org/10.1103/PhysRevB.45.13891).

Kind regards Nick


2013/9/28 Sebastian Caicedo D. sebastian.caic...@correounivalle.edu.co

 Dear and Respected SIESTA/TranSiesta users,

 I'm new to Siesta/TranSiesta and have just performed a couple of tutorials
 and examples quite successfully. Now I'm Trying to perform a calculation of
 my own: Bulk InAs, which I need as an electrode for a larger device I
 intend to work on. I'm performing convergence tests, and Started with just
 a Gamma-point calculation. I faced some problems with the basis set, I
 could solve using the Mailing list info.

 Nevertheless I'm facing another issue. When calculating the unitary cell
 of InAs with Transiesta, I get the following error message:

 MINVEC: BASIS VECTORS ARE LINEARLY DEPENDENT

 So I tried the same calculation using SIESTA (compiled without Transiesta
 support) and it worked out just fine.

 At the end of the output file I found these lines:

 TS kgrid determined first with 3D cell !!!
  Specifying only cutoff in Electrode AND Scattering calculations might
 lead to problems !!

 So I assume this has something to do with the k-grid of the calculation
 (remember I'm performing a Gamma-point only test).

 Is my assumption correct? Does anyone have any ideas of how to deal with
 this problem?

 I attach the input and output files I'm using, so you can check them out.

 Thanks in advance.

 Sebastián Caicedo Dávila
 Bionanoelectronics Research Group
 Universidad del Valle
 Cali-Colombia

Re: [SIESTA-L] Problem with transiesta test run

[Henrik Löfås]

Hello,

What you see is one of the fixes going from 3.0-b to 3.0-rc2, where the
example is calculated where the example is calculated with beta while you're
using rc2. See release notes.

* The transmission function is now multiplied by two in the
  case of non spin-polarized calculations. As a consequence, the
  computed current is multiplied too.

Best Regards
Henrik

2011/1/19 Juzar Thingna juza...@gmail.com

 Hello Everyone,

 I was trying out the Fast test run of transiesta as described in the
 manual. After getting the transmission I plot it against the standard curve
 i.e the file TS_TBT/scat.fast.AVTRANS. The results I obtain from the
 compilation on my computer are quite different (File attached). Please could
 someone explain of why this error occurs and how it can be rectified?

 P.S. there is no error in the transiesta compilation.

 Regards,

 Juzar Thingna
 Department of Physics,
 Center for Computation Science and Engineering,
 National University of Singapore.