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 <[email protected]>: > 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 <[email protected]> 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 <[email protected]>: >> >>> 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 <[email protected]> >>> 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 <[email protected]>: >>>> >>>>> 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 <[email protected]> >>>>> 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 <[email protected]>: >>>>>> >>>>>>> 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 >>>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> Kind regards Nick >>>>>> >>>>> >>>>> >>>> >>>> >>>> -- >>>> Kind regards Nick >>>> >>> >>> >> >> >> -- >> Kind regards Nick >> > > -- Kind regards Nick
