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 <[email protected]> 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 <[email protected]>: > >> 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 <[email protected]> >> 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 <[email protected]>: >>> >>>> 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 >
