Re: [SIESTA-L] error from Transiesta calculating I-V characterisitc

[maryam jamaati]

Dear Dr. Papior,

I appreciate your attention to this matter.

Sincerely yours,
Maryam Jamaati

On Tue, Nov 20, 2018 at 12:31 AM Nick Papior  wrote:

> These are not errors, you can "safely" ignore them. In the next 4.1-b5/4.1
> release the manual will contain details of what they mean.
>
> Secondly, if the calculation hasn't finished then wait until it has. Then
> TSHS should be created.
>
> Den søn. 18. nov. 2018 kl. 22.01 skrev maryam jamaati <
> m.sjama...@gmail.com>:
>
>> Dear Siesta users,
>>
>> We are calculating the I-V characteristic of a hybrid structure. For zero
>> bias voltage Transiesta converges very fast. But for other bias voltages it
>> didn't
>> converge. We changed scf parameters and it converged. We increased number
>> of contour points. Now. scf converges but the code is still running and the
>> below error message appears. Also no TSHS file is created.
>>
>> I would be pleased if one could help us to solve the problem.
>>
>>
>> SCF cycle converged after 898 iterations
>> ts-err-D: ij( 1273,  1273), M = 0.83772   , ew = 0.29574   , em =
>> 0.32983   . avg_m = 0.34189E-04
>> ts-err-E: ij( 1138,  1138), M = -1.2121   , ew = 0.10506E-1, em =
>> 0.12548E-1. avg_m = 0.18626E-05
>> transiesta: constant dEf = -0.1747E-02 eV
>> ts-err-D: ij( 1273,  1273), M = 0.80236   , ew = 0.34517   , em =
>> 0.35972   . avg_m = 0.18146E-04
>> ts-err-E: ij( 1273,  1273), M = -1.1882   , ew = 0.12167E-1, em =
>> 0.12680E-1. avg_m = 0.56860E-06
>>
>>
>> Best regards,
>> Maryam Jamaati
>>
>
>
> --
> Kind regards Nick
>

[SIESTA-L] error from Transiesta calculating I-V characterisitc

[maryam jamaati]

Dear Siesta users,

We are calculating the I-V characteristic of a hybrid structure. For zero
bias voltage Transiesta converges very fast. But for other bias voltages it
didn't
converge. We changed scf parameters and it converged. We increased number
of contour points. Now. scf converges but the code is still running and the
below error message appears. Also no TSHS file is created.

I would be pleased if one could help us to solve the problem.


SCF cycle converged after 898 iterations
ts-err-D: ij( 1273,  1273), M = 0.83772   , ew = 0.29574   , em = 0.32983
. avg_m = 0.34189E-04
ts-err-E: ij( 1138,  1138), M = -1.2121   , ew = 0.10506E-1, em =
0.12548E-1. avg_m = 0.18626E-05
transiesta: constant dEf = -0.1747E-02 eV
ts-err-D: ij( 1273,  1273), M = 0.80236   , ew = 0.34517   , em = 0.35972
. avg_m = 0.18146E-04
ts-err-E: ij( 1273,  1273), M = -1.1882   , ew = 0.12167E-1, em =
0.12680E-1. avg_m = 0.56860E-06


Best regards,
Maryam Jamaati

Re: [SIESTA-L] problem transiesta convergence for non-zero bias voltages

[maryam jamaati]

Dear Leo,
Thank you for your attention to this matter.
We had lowered DM before asking question.
We took your suggestion and copied DM and TSDE file from zero voltage. and
also lowered the bias step. But the system is not still converging.
Is the version of used package is important? what version do you suggest?

Best regards,
Maryam Jamaati

On Sun, Nov 11, 2018 at 12:32 AM Leonardo Fonseca 
wrote:

> Hello,
>
> First of all, I wonder why you are using so many k-points along z given
> the size of this system in this direction. Regarding your question, I have
> two suggestions:
>
> 1) lower your DM.mixing
> 2) lower your bias step. Right now you should be taking your converged DM
> or TSDE obtained at zero bias and using it as input for 0.2 eV calculation.
> Maybe 0.2 is too large as step. Try 0.1 or even less
>
> Good luck! Leo
>
> Em sex, 9 de nov de 2018 às 19:00, maryam jamaati 
> escreveu:
>
>> Dear Siesta users,
>>
>> We are trying to calculate the I-V characteristic of a hybrid structure.
>> For zero bias voltage Transiesta converges very fast. But for other bias
>> voltages it doesn't
>> converge even after 1000 step. The fdf file is attached.
>> I would be pleased if one could help us to solve the problem.
>>
>> Best regards,
>> Maryam Jamaati
>>
>

Re: [SIESTA-L] problem transiesta convergence for non-zero bias voltages

[maryam jamaati]

Dear El_abed,
Thanks a lot for your attention.
We have coped MD and TSDE file from obtained zero voltage, but it doesn't
solve the problem and still it doesn't converge.
Best regards
Maryam Jamaati

On Sun, Nov 11, 2018 at 12:31 AM El-abed Haidar 
wrote:

> Hello Maryam,
>
> In addition to copying the left and right TSHS files, you have to copy the
> DM or TSDE file from the obtained zero voltage.
>
> Also based on what I have read from the siesta mail, you might have to
> change some of the contour parameters.
>
> Hope that can help you out.
>
> El-Abed
>
>  El-abed Haidar | Doctor of Philosophy (Science)
>  Condensed Matter Theory (CMT) Group
>  | School of Physics
>  THE UNIVERSITY OF SYDNEY  | NSW | 2006
>
> ------
> *From:* siesta-l-requ...@uam.es  on behalf of
> maryam jamaati 
> *Sent:* Friday, 9 November 2018 5:08:24 PM
> *To:* siesta-l@uam.es
> *Subject:* [SIESTA-L] problem transiesta convergence for non-zero bias
> voltages
>
> Dear Siesta users,
>
> We are trying to calculate the I-V characteristic of a hybrid structure.
> For zero bias voltage Transiesta converges very fast. But for other bias
> voltages it doesn't
> converge even after 1000 step. The fdf file is attached.
> I would be pleased if one could help us to solve the problem.
>
> Best regards,
> Maryam Jamaati
>

Re: [SIESTA-L] problem transiesta convergence for non-zero bias voltages

[maryam jamaati]

Dear Esmaeil,

Thank you for your kind helps.
We have done this before but it didn't work and the problem was still
outstanding.
Best wishes,
Maryam Jamaati

On Sun, Nov 11, 2018 at 12:32 AM Esmaeil Farajpour Bonab <
e.farajpou...@gmail.com> wrote:

> Dear Maryam,
>
> Please consider to what it is recommended to do during different finite
> bias calculations: manual page 125.
> You could increase the MaxSCFIterations first, if it does not work during
> for example 5000 iteration, you can change either the value of
> DM.MixingWeight or DM.NumberPulay.
> I hope it helps you to solve the problem.
>
> Regards,
> Esmaeil.
>
> On Fri, Nov 9, 2018 at 10:00 PM maryam jamaati 
> wrote:
>
>> Dear Siesta users,
>>
>> We are trying to calculate the I-V characteristic of a hybrid structure.
>> For zero bias voltage Transiesta converges very fast. But for other bias
>> voltages it doesn't
>> converge even after 1000 step. The fdf file is attached.
>> I would be pleased if one could help us to solve the problem.
>>
>> Best regards,
>> Maryam Jamaati
>>
>

[SIESTA-L] problem transiesta convergence for non-zero bias voltages

[maryam jamaati]

Dear Siesta users,

We are trying to calculate the I-V characteristic of a hybrid structure.
For zero bias voltage Transiesta converges very fast. But for other bias
voltages it doesn't
converge even after 1000 step. The fdf file is attached.
I would be pleased if one could help us to solve the problem.

Best regards,
Maryam Jamaati


TBTransv0.fdf
Description: Binary data

[SIESTA-L] problem transiesta convergence for non-zero bias voltages

[maryam jamaati]

Dear Siesta users,

We are trying to calculate the I-V characteristic of a hybrid structure.
For zero bias voltage Transiesta converges very fast. But for other bias
voltages it doesn't
converge even after 1000 step. The fdf file is attached.
I would be pleased if one could help us to solve the problem.

Best regards,
Maryam Jamaati


TBTransv0.fdf
Description: Binary data

[SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

[maryam jamaati]

Dear siesta users,

When we run the command sdata trans.TBT.nc—atom 181-197 —dos —out dos.dat
in vrsion 4.1.b3 of tbttrans, we recieve below error:

Traceback (most recent call last):
File "/home/sf/.local/bin/sdata", line 11, in 
sys.exit(sdata())
File "/home/sf/.local/lib/python2.7/site-packages/sisl/utils/sdata.py",
line 123, in sdata
p.parse_args(argv, namespace=ns)
File "/usr/lib/python2.7/argparse.py", line 1690, in parse_args
args, argv = self.parse_known_args(args, namespace)
File "/usr/lib/python2.7/argparse.py", line 1722, in parse_known_args
namespace, args = self._parse_known_args(args, namespace)
File "/usr/lib/python2.7/argparse.py", line 1928, in _parse_known_args
start_index = consume_optional(start_index)
File "/usr/lib/python2.7/argparse.py", line 1868, in consume_optional
take_action(action, args, option_string)
File "/usr/lib/python2.7/argparse.py", line 1796, in take_action
action(self, namespace, argument_values, option_string)
File "/home/sf/.local/lib/python2.7/site-packages/sisl/utils/cmd.py", line
217, in run
A(*Aargs, **Akwargs)
File "/home/sf/.local/lib/python2.7/site-packages/sisl/utils/cmd.py", line
184, in collect
return func(self, *args, **kwargs)
File "/home/sf/.local/lib/python2.7/site-packages/sisl/io/tbtrans/tbt.py",
line 1578, in assign_E
return func(self, *args, **kwargs)
File "/home/sf/.local/lib/python2.7/site-packages/sisl/io/tbtrans/tbt.py",
line 1810, in *call*
data = ns._tbt.DOS(kavg=ns._krng, orbital=ns._Orng, norm=ns._norm)
File "/home/sf/.local/lib/python2.7/site-packages/sisl/io/tbtrans/tbt.py",
line 723, in DOS
return self._DOS(self._value_E('DOS', kavg=kavg, E=E),
File "/home/sf/.local/lib/python2.7/site-packages/sisl/io/tbtrans/tbt.py",
line 149, in _value_E
return self._value_avg(name, tree, kavg)
File "/home/sf/.local/lib/python2.7/site-packages/sisl/io/tbtrans/tbt.py",
line 112, in _value_avg
v = self._variable(name, tree=tree)
File "/home/sf/.local/lib/python2.7/site-packages/sisl/io/sile.py", line
753, in _variable
return self._variables(self, name, tree=tree)
File "/home/sf/.local/lib/python2.7/site-packages/sisl/io/sile.py", line
766, in _variables
return n.variables[name]
KeyError: 'DOS'

We would be pleased if one could help us to solve the problem.

Sincerely yours,
maryam jamaati

Re: [SIESTA-L] wsf.band.max problem

[maryam jamaati]

Dear Afsal,
 Many thanks for your attention and kind helps.
 We solved our problem. But we don't know how we can determine wsf.band.max
value for e.g. hybrid graphene/hBN systems.
How this value is related to the system component.

Best Regards,
Maryam Jamaati

On Tue, Feb 6, 2018 at 1:53 AM, KAREEKUNNAN Afsal  wrote:

> Dear Maryam Jamaati,
>
> Could you please elaborate your problem. What did you mean by "for
> different physical systems".
>
> Thanks & Regards
> Afsal
>
> ------
> *From: *"maryam jamaati" 
> *To: *siesta-l@uam.es
> *Sent: *Monday, February 5, 2018 2:20:30 PM
> *Subject: *Re: [SIESTA-L] wsf.band.max problem
>
> Dear Afsal,
>
> Thanks a lot for your kind helps. We read the mentioned tutorial. But our
> problem doesn't solve.
> We want to know how one can specify WFS.Band.Max for different physical
> systems.
>
> Best regards,
> Maryam Jamaati
>
> On Fri, Feb 2, 2018 at 2:13 AM, KAREEKUNNAN Afsal 
> wrote:
>
>> Dear Maryam Jamaati,
>>
>> It is specified by putting the number of highest band you need to
>> calculate fatbands. An example is given below.
>>
>> WFS.Write.For.Bands.true.
>> WFS.Band.Min 1
>> WFS.Band.Max 10
>>
>> This gives the information for bands from 1 to 10. Note that WFS.Band.Min
>> represent the band with lowest energy.
>>
>> You may also refer to this tutorial by Prof. Javier Junquera on fatbands.
>>
>> http://personales.unican.es/junqueraj/JavierJunquera_files/Metodos/
>> Structuralproperties/Fatbands-SrTiO3/Exercise-Fatbands-SrTiO3.pdf
>>
>> For more tutorials, refer to his page
>>
>> http://personales.unican.es/junqueraj/JavierJunquera_
>> files/Metodos/Hands-on-session.html
>>
>> Thanks & Regards
>> Afsal
>>
>> --
>> *From: *"maryam jamaati" 
>> *To: *siesta-l@uam.es
>> *Sent: *Friday, February 2, 2018 1:48:49 AM
>> *Subject: *[SIESTA-L] wsf.band.max problem
>>
>> Dear siesta users,
>> How we can specify number of wfs.band.max for calculation of fatband?
>>
>> sincerely yours,
>>
>> maryam jamaati
>>
>>
>

Re: [SIESTA-L] wsf.band.max problem

[maryam jamaati]

Dear Afsal,

Thanks a lot for your kind helps. We read the mentioned tutorial. But our
problem doesn't solve.
We want to know how one can specify WFS.Band.Max for different physical
systems.

Best regards,
Maryam Jamaati

On Fri, Feb 2, 2018 at 2:13 AM, KAREEKUNNAN Afsal  wrote:

> Dear Maryam Jamaati,
>
> It is specified by putting the number of highest band you need to
> calculate fatbands. An example is given below.
>
> WFS.Write.For.Bands.true.
> WFS.Band.Min 1
> WFS.Band.Max 10
>
> This gives the information for bands from 1 to 10. Note that WFS.Band.Min
> represent the band with lowest energy.
>
> You may also refer to this tutorial by Prof. Javier Junquera on fatbands.
>
> http://personales.unican.es/junqueraj/JavierJunquera_files/Metodos/
> Structuralproperties/Fatbands-SrTiO3/Exercise-Fatbands-SrTiO3.pdf
>
> For more tutorials, refer to his page
>
> http://personales.unican.es/junqueraj/JavierJunquera_
> files/Metodos/Hands-on-session.html
>
> Thanks & Regards
> Afsal
>
> --
> *From: *"maryam jamaati" 
> *To: *siesta-l@uam.es
> *Sent: *Friday, February 2, 2018 1:48:49 AM
> *Subject: *[SIESTA-L] wsf.band.max problem
>
> Dear siesta users,
> How we can specify number of wfs.band.max for calculation of fatband?
>
> sincerely yours,
>
> maryam jamaati
>
>

[SIESTA-L] wsf.band.max problem

[maryam jamaati]

Dear siesta users,

How we can specify number of wfs.band.max for calculation of fatband?

sincerely yours,

maryam jamaati

Re: [SIESTA-L] Error using eigemchannels from inelastica

[maryam jamaati]

Dear Nick,

Thanks for your kind help.

yours sincerely,

maryam jamaati

On Tue, Jan 23, 2018 at 11:13 AM, Nick Papior  wrote:

> Hi,
>
> 1) Use the latest version of Inelastica, https://sourceforge.net/projects/
> inelastica/files/inelastica-code-446.zip/download
> 2) Using the latest version you don't need to use the tshs2tshs utility as
> inelastica will read the 4.1 TSHS without problems.
>
> 2018-01-22 6:59 GMT+01:00 maryam jamaati :
>
>> Dear Siesta users,
>> We use eigenchannels from inelastica to get local current and MPSH from
>> transiesta output file "*. TSHS". But when running inelastica the below
>> error appears:
>>
>> sudo EigenChannels -F 181 -L 195 -w XSF -f olymchap.fdf -u —nobulk
>> ../eigenchannel/
>> [sudo] password for sf:
>> SVN $Id: EigenChannels.py <http://eigenchannels.py/> 346 2015-04-22
>> 11:11:02Z magnuspaulsson $
>> SVN $Id: NEGF.py <http://negf.py/> 337 2015-03-01 10:23:41Z zerothi $
>> SVN $Id: SiestaIO.py <http://siestaio.py/> 337 2015-03-01 10:23:41Z
>> zerothi $
>> SVN $Id: MakeGeom.py <http://makegeom.py/> 318 2014-08-07 09:00:10Z
>> tfrederiksen $
>> SVN $Id: VaspIO.py <http://vaspio.py/> 318 2014-08-07 09:00:10Z
>> tfrederiksen $
>> SVN $Id: PhysicalConstants.py <http://physicalconstants.py/> 318
>> 2014-08-07 09:00:10Z tfrederiksen $
>> SVN $Id: ValueCheck.py <http://valuecheck.py/> 332 2014-12-16 13:37:53Z
>> zerothi $
>> SVN $Id: MiscMath.py <http://miscmath.py/> 346 2015-04-22 11:11:02Z
>> magnuspaulsson $
>> SVN $Id: CommonFunctions.py <http://commonfunctions.py/> 318 2014-08-07
>> 09:00:10Z tfrederiksen $
>> EigenChannels: Reading keywords from olymchap.fdf
>>
>> STOP Unsupported TSHS version file
>>
>> we use siesta version 4.1-b3
>> We have also changed the TSHS file version with the "tshs1tshs" utillity
>> to older version, but the error is not altered.
>> We would be pleased if siesta users could help us to solve the poblem.
>>
>> sincerely yours,
>>
>
>
>
> --
> Kind regards Nick
>

[SIESTA-L] Error using eigemchannels from inelastica

[maryam jamaati]

Dear Siesta users,
We use eigenchannels from inelastica to get local current and MPSH from
transiesta output file "*. TSHS". But when running inelastica the below
error appears:

sudo EigenChannels -F 181 -L 195 -w XSF -f olymchap.fdf -u —nobulk
../eigenchannel/
[sudo] password for sf:
SVN $Id: EigenChannels.py  346 2015-04-22
11:11:02Z magnuspaulsson $
SVN $Id: NEGF.py  337 2015-03-01 10:23:41Z zerothi $
SVN $Id: SiestaIO.py  337 2015-03-01 10:23:41Z zerothi
$
SVN $Id: MakeGeom.py  318 2014-08-07 09:00:10Z
tfrederiksen $
SVN $Id: VaspIO.py  318 2014-08-07 09:00:10Z
tfrederiksen $
SVN $Id: PhysicalConstants.py  318 2014-08-07
09:00:10Z tfrederiksen $
SVN $Id: ValueCheck.py  332 2014-12-16 13:37:53Z
zerothi $
SVN $Id: MiscMath.py  346 2015-04-22 11:11:02Z
magnuspaulsson $
SVN $Id: CommonFunctions.py  318 2014-08-07
09:00:10Z tfrederiksen $
EigenChannels: Reading keywords from olymchap.fdf

STOP Unsupported TSHS version file

we use siesta version 4.1-b3
We have also changed the TSHS file version with the "tshs1tshs" utillity to
older version, but the error is not altered.
We would be pleased if siesta users could help us to solve the poblem.

sincerely yours,

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/

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
>>>> Value

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 <<&

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

[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
>

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

[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,

[SIESTA-L] problem with band structure of ZGNR

[maryam jamaati]

Dear Siesta users,

I want to calculate band structure of ZGNR. I calculate it for 1 unitcell
ZGNR. The result is correct for 1 unit cell.
But I have problem with calculation of band structure for a supercell
(containing 3 unit cells).
Relaxation of the system has been done before band structure calculation.
I attach my code and results.
Would you please help me to calculate band structure of supercell correctly.

Sincerely,

Maryam Jamaati

Re: [SIESTA-L] Band structure for doped ZGNR

[maryam jamaati]

Hi,

Yes I have a supercell instead of one unit cell of ZGNR.

BW,


On Sun, Jul 31, 2016 at 1:19 AM, Максим Арсентьев 
wrote:

> so you mean because of doping you have a supercell now? Anyway your system
> still have symmmetry - for choosing k - points use this paper. It is
>  general manner. I did not dealt with supercells but do not think your
> problem is critical.
>
> 2016-07-30 23:00 GMT+04:00 Riya Rogers :
>
>> Doped means is it replacement of carbon or other molecule in vicinity?
>>
>> On 30-Jul-2016 10:38 pm, "maryam jamaati"  wrote:
>>
>>> Dear siesta users,
>>>
>>> According to helpful advices of some friends (Nick, Kamaraj,..), I
>>> reduced geometry to unit cell for calculation of ZGNR band structure.
>>> Whether we have to use minimal unit cell for doped ZGNR or not?
>>>
>>> Kind regards,
>>>
>>> Maryam Jamaati
>>>
>>>
>
>
> --
> Best wishes,
> Maxim Arsent'ev, Ph.D. (Chemistry)
> Laboratory of research of nanostructures
> Institute of Silicate Chemistry of RAS
>

[SIESTA-L] Band structure for doped ZGNR

[maryam jamaati]

Dear siesta users,

According to helpful advices of some friends (Nick, Kamaraj,..), I reduced
geometry to unit cell for calculation of ZGNR band structure.
Whether we have to use minimal unit cell for doped ZGNR or not?

Kind regards,

Maryam Jamaati

Re: [SIESTA-L] Problem with Calculation of Band Structure

[maryam jamaati]

Dear Nick,

Tanks for your kind reply.

Best Wishes,

On Wed, Jul 20, 2016 at 10:20 AM, Nick Papior  wrote:

> A ZGNR is a 1-dimensional system. This means that the corresponding
> reciprocal cell is 1-dimensional.
>
> Hence you should only calculate the bandstructure along periodic lattice
> vectors. In this case the third cell vector. This is not reflected in your
> bandlines block.
>
> Also, if you want the bandstructure of a pristine ZGNR, you should reduce
> your geometry to the minimal unit cell/atoms. Otherwise you have
> band-foldings (which may, or may not, be desired).
>
> 2016-07-20 6:32 GMT+02:00 maryam jamaati :
>
>> Dear SIESTA users,
>>
>> I'm trying to calculate band structure of ZGNR. But the obtained result
>> seems wrong. I checked everything but I don't find the problem.
>> So, could anyone help me with this problem? Any comment will be
>> appreciated. Thanks.
>>
>> my fdf:
>>
>>
>> SystemLabel  ZGNR
>>
>> NumberOfAtoms84
>>
>> NumberOfSpecies  1
>> %block ChemicalSpeciesLabel
>> 16  C
>> %endblock ChemicalSpeciesLabel
>>
>> LatticeConstant 1.00 Ang
>>
>> %block LatticeVectors
>>49.1902400.000   0.000
>>0.00017.216584   0.000
>>0.0000.000   17.216584
>> %endblock LatticeVectors
>>
>> AtomicCoordinatesFormat Ang
>> %block AtomicCoordinatesAndAtomicSpecies
>> 1.424573 0.00 -0.190 1
>> 2.130544 0.00 -1.2306270 1
>> 3.556068 0.00 -1.2306060 1
>> 4.262992 0.00 -0.220 1
>> 5.687207 0.00 -0.210 1
>> 6.394538 0.00 -1.2306100 1
>> 7.818672 0.00 -1.2306130 1
>> 8.526009 0.00 -0.160 1
>> 9.950250 0.00 -0.230 1
>> 10.657196 0.00 -1.2305960 1
>> 12.083009 0.00 -1.2306350 1
>> 12.788179 0.00 -0.540 1
>> 1.424447 0.00 2.4595040 1
>> 2.130573 0.00 1.2288990 1
>> 3.556074 0.00 1.2288950 1
>> 4.262993 0.00 2.4594960 1
>> 5.687210 0.00 2.4594970 1
>> 6.394541 0.00 1.2289100 1
>> 7.818672 0.00 1.2289110 1
>> 8.526009 0.00 2.4594970 1
>> 9.950253 0.00 2.4595030 1
>> 10.657212 0.00 1.2289130 1
>> 12.083118 0.00 1.2289050 1
>> 12.788176 0.00 2.4595420 1
>> 1.424491 0.00 4.9189870 1
>> 2.130618 0.00 3.6884220 1
>> 3.556085 0.00 3.6884230 1
>> 4.262994 0.00 4.9190080 1
>> 5.687208 0.00 4.9190080 1
>> 6.394541 0.00 3.6884210 1
>> 7.818670 0.00 3.6884240 1
>> 8.526006 0.00 4.919 1
>> 9.950232 0.00 4.9190150 1
>> 10.657200 0.00 3.6884120 1
>> 12.083023 0.00 3.6884340 1
>> 12.788375 0.00 4.9190900 1
>> 1.424593 0.00 7.3785450 1
>> 2.130528 0.00 6.1479280 1
>> 3.556070 0.00 6.1479440 1
>> 4.262987 0.00 7.3785220 1
>> 5.687208 0.00 7.3785200 1
>> 6.394542 0.00 6.1479280 1
>> 7.818671 0.00 6.1479310 1
>> 8.526002 0.00 7.3785130 1
>> 9.950230 0.00 7.3785240 1
>> 10.657157 0.00 6.1478930 1
>> 12.082766 0.00 6.1479730 1
>> 12.788722 0.00 7.3785650 1
>> 1.424597 0.00 9.8380290 1
>> 2.130523 0.00 8.6074510 1
>> 3.556065 0.00 8.6074470 1
>> 4.262982 0.00 9.8380360 1
>> 5.687207 0.00 9.8380350 1
>> 6.394536 0.00 8.6074450 1
>> 7.818675 0.00 8.6074460 1
>> 8.526000 0.00 9.8380320 1
>> 9.950221 0.00 9.8380360 1
>> 10.657120 0.00 8.6074320 1
>> 12.082572 0.00 8.6074650 1
>> 12.788849 0.00 9.8380450 1
>> 1.424567 0.00 12.2975670 1
>> 2.130516 0.00 11.0669660 1
>> 3.556065 0.00 11.0669560 1
>> 4.262983 0.00 12.2975440 1
>> 5.687204 0.00 12.2975430 1
>> 6.394539 0.00 11.0669610 1
>> 7.818672 0.00 11.0669590 1
>> 8.526001 0.00 12.2975490 1
>> 9.950227 0.00 12.2975360 1
>> 10.657112 0.00 11.0669600 1
>> 12.082526 0.00 11.0669460 1
>> 12.788823 0.00 12.2975090 1
>> 1.424530 0.00 14.7570410 1
>> 2.130569 0.00 13.5264530 1
>> 3.556073 0.00 13.5264630 1
>> 4.262983 0.00 14.7570470 1
>> 5.687206 0.00 14.7570490 1
>> 6.394537 0.00 13.5264650 1
>> 7.818669 0.00 13.5264620 1
>> 8.526003 0.00 14.7570560 1
>> 9.950232 0.00 14.7570400 1
>> 10.657143 0.00 13.5265080 1
>> 12.082699 0.00 13.5264050 1
>> 12.788415 0.00 14.7569600 1
>> %endblock AtomicCoordinatesAndAtomicSpec