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 <[email protected]> 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 <[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 >
