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 <m.sjama...@gmail.com>:
> 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 <nickpap...@gmail.com> 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 <m.sjama...@gmail.com>:
>>
>>> 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 <nickpap...@gmail.com>
>>> 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 <m.sjama...@gmail.com>:
>>>>
>>>>> 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 <module>
>>>>> 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 <nickpap...@gmail.com>
>>>>> 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 <m.sjama...@gmail.com>:
>>>>>>
>>>>>>> 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 <nickpap...@gmail.com>
>>>>>>> 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 <m.sjama...@gmail.com>:
>>>>>>>>
>>>>>>>>> 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
>>>>
>>>
>>>
>>
>>
>> --
>> Kind regards Nick
>>
>
>
--
Kind regards Nick
