Hi, Den ons. 20. maj 2020 kl. 22.04 skrev shirin zandi < shirinzandi1...@gmail.com>:
> Dear Nick, > The sgeom works and it produces: > info:0: SislInfo: Scaling vector by: 2.7056029424251387 > > What was wrong with the sdata command? and also how I can scaling all the > bond current vectors by specific values (multiple by 3, 4, and ..) > It is an _internal_ thing. Basically if you specify the xsf file as output you will _only_ get the correct output options if runned by the sgeom command. if you do sgeom siesta.TBT.nc --out test.xsf --help you can see the options to manually specify the scaling factor. > > > And one more question! is there any graphical package that I can use to > visualize the bond current vectors inserted xcrysden? > I don't get what you mean? You can use xcrysden? > > Thanks. > Sincerely, > SH. > > On Wed, May 20, 2020 at 12:33 AM Nick Papior <nickpap...@gmail.com> wrote: > >> Could you try with: >> sgeom instead of sdata? >> That forces the interpreter to recognize geometry output settings. >> >> Den man. 18. maj 2020 kl. 22.02 skrev shirin zandi < >> shirinzandi1...@gmail.com>: >> >>> Dear Nick, >>> >>> Many thanks. >>> >>> I did the data por.TBT.nc <http://por.tbt.nc/> --info command and >>> this is what code produces: >>> >>> Device information: >>> - number of kpoints: 1 <- [ A = 1 , B = 1 , C = 1 ] (time-reversal >>> unknown) >>> - energy range: >>> -4.99950 -- 4.99950 eV [1.000 meV] >>> - imaginary part (eta): 0.0000 meV >>> - atoms with DOS (fortran indices): >>> 1-149, 155-160, 166-168, 179-181 >>> - number of BTD blocks: 3 >>> + DOS Green function: true >>> - Density matrix Green function: false [TBT.DM.Gf] >>> - COOP Green function: false [TBT.COOP.Gf >>> ] >>> - COHP Green function: false [TBT.COHP.Gf >>> ] >>> >>> Electrode: elec_1 >>> - number of BTD blocks: 2 >>> - Bloch: [1, 1, 1] >>> - chemical potential: 0.0000 eV >>> - electron temperature: 300.00 K >>> - imaginary part (eta): 0.0100 meV >>> + DOS bulk: true >>> + DOS spectral: true >>> + orbital-current: true >>> - Density matrix spectral: false [TBT.DM.A] >>> - COOP spectral: false [TBT.COOP.A] >>> - COHP spectral: false [TBT.COHP.A] >>> + transmission bulk: true >>> - transmission out: false [TBT.T.Out] >>> - transmission out correction: false [TBT.T.Out] >>> - transmission out correction (eigen): false [TBT.T.Out, >>> TBT.T.Eig] >>> + transmission -> elec_2: true >>> - transmission (eigen) -> elec_2: false [TBT.T.Eig] >>> + transmission -> elec_3: true >>> - transmission (eigen) -> elec_3: false [TBT.T.Eig] >>> + transmission -> elec_4: true >>> - transmission (eigen) -> elec_4: false [TBT.T.Eig] >>> >>> Electrode: elec_2 >>> - number of BTD blocks: 2 >>> - Bloch: [1, 1, 1] >>> - chemical potential: 0.0000 eV >>> - electron temperature: 300.00 K >>> - imaginary part (eta): 0.0100 meV >>> + DOS bulk: true >>> + DOS spectral: true >>> + orbital-current: true >>> - Density matrix spectral: false [TBT.DM.A] >>> - COOP spectral: false [TBT.COOP.A] >>> - COHP spectral: false [TBT.COHP.A] >>> + transmission bulk: true >>> - transmission out: false [TBT.T.Out] >>> - transmission out correction: false [TBT.T.Out] >>> - transmission out correction (eigen): false [TBT.T.Out, >>> TBT.T.Eig] >>> - transmission -> elec_1: false >>> - transmission (eigen) -> elec_1: false [TBT.T.Eig] >>> + transmission -> elec_3: true >>> - transmission (eigen) -> elec_3: false [TBT.T.Eig] >>> + transmission -> elec_4: true >>> - transmission (eigen) -> elec_4: false [TBT.T.Eig] >>> >>> Electrode: elec_3 >>> - number of BTD blocks: 2 >>> - Bloch: [1, 1, 1] >>> - chemical potential: 0.0000 eV >>> - electron temperature: 300.00 K >>> - imaginary part (eta): 0.0100 meV >>> + DOS bulk: true >>> + DOS spectral: true >>> + orbital-current: true >>> - Density matrix spectral: false [TBT.DM.A] >>> - COOP spectral: false [TBT.COOP.A] >>> - COHP spectral: false [TBT.COHP.A] >>> + transmission bulk: true >>> - transmission out: false [TBT.T.Out] >>> - transmission out correction: false [TBT.T.Out] >>> - transmission out correction (eigen): false [TBT.T.Out, >>> TBT.T.Eig] >>> - transmission -> elec_1: false >>> - transmission (eigen) -> elec_1: false [TBT.T.Eig] >>> - transmission -> elec_2: false >>> - transmission (eigen) -> elec_2: false [TBT.T.Eig] >>> + transmission -> elec_4: true >>> - transmission (eigen) -> elec_4: false [TBT.T.Eig] >>> >>> Electrode: elec_4 >>> - number of BTD blocks: 2 >>> - Bloch: [1, 1, 1] >>> - chemical potential: 0.0000 eV >>> - electron temperature: 300.00 K >>> - imaginary part (eta): 0.0100 meV >>> + DOS bulk: true >>> - DOS spectral: false [TBT.DOS.A] >>> - orbital-current: false >>> [TBT.Current.Orb] >>> - Density matrix spectral: false [TBT.DM.A] >>> - COOP spectral: false [TBT.COOP.A] >>> - COHP spectral: false [TBT.COHP.A] >>> + transmission bulk: true >>> - transmission out: false [TBT.T.Out] >>> - transmission out correction: false [TBT.T.Out] >>> - transmission out correction (eigen): false [TBT.T.Out, >>> TBT.T.Eig] >>> - transmission -> elec_1: false >>> - transmission (eigen) -> elec_1: false [TBT.T.Eig] >>> - transmission -> elec_2: false >>> - transmission (eigen) -> elec_2: false [TBT.T.Eig] >>> - transmission -> elec_3: false >>> - transmission (eigen) -> elec_3: false [TBT.T.Eig] >>> >>> >>> >>> >>> Wishes, >>> >>> SH. >>> >>> >>> On Mon, May 18, 2020 at 12:31 AM Nick Papior <nickpap...@gmail.com> >>> wrote: >>> >>>> Hi, >>>> >>>> Simply do: >>>> >>>> sdata por.TBT.nc --help >>>> and you'll see what commands are available. >>>> >>>> Please give back this command: >>>> sdata por.TBT.nc --info >>>> >>>> >>>> >>>> Den lør. 16. maj 2020 kl. 22.02 skrev shirin zandi < >>>> shirinzandi1...@gmail.com>: >>>> >>>>> Dear Nick, >>>>> >>>>> Thank you so much for your reply. After that I've got the following >>>>> error : >>>>> >>>>> No data has been collected in the arguments, nothing will be written, >>>>> have you forgotten arguments? >>>>> >>>>> >>>>> The command I have run is this : sdata por.TBT.nc >>>>> <http://por.tbt.nc/> --vector vector_current elec_1 0.1 --out A1.xsf >>>>> >>>>> I know, the electrode name and energy range should be written in bond >>>>> currents command line, is it need something else? And generally from >>>>> where I can find a complete list of commands and their requirements which >>>>> can be done with sisl. I am really new in using sisl!!! >>>>> >>>>> >>>>> >>>>> Regards, >>>>> SH. >>>>> >>>>> On Sat, May 16, 2020 at 12:30 AM Nick Papior <nickpap...@gmail.com> >>>>> wrote: >>>>> >>>>>> Hi, >>>>>> >>>>>> You probably haven't calculated bond currents. Please check your >>>>>> tbtrans input options. >>>>>> >>>>>> / Nick >>>>>> >>>>>> On Thu, 14 May 2020, 22:13 shirin zandi, <shirinzandi1...@gmail.com> >>>>>> wrote: >>>>>> >>>>>>> Dear Transiesta/sisl user >>>>>>> >>>>>>> I am trying to use sisl code to analyze the Transiesta obtained >>>>>>> data, But when I use this code the below error has appeared: >>>>>>> >>>>>>> >>>>>>> Traceback (most recent call last): >>>>>>> File "/share/apps/anaconda3/bin/sdata", line 11, in <module> >>>>>>> load_entry_point('sisl==0.9.5', 'console_scripts', 'sdata')() >>>>>>> File >>>>>>> "/share/apps/anaconda3/lib/python3.7/site-packages/sisl/utils/sdata.py", >>>>>>> line 122, in sdata >>>>>>> p.parse_args(argv, namespace=ns) >>>>>>> File "/share/apps/anaconda3/lib/python3.7/argparse.py", line 1749, >>>>>>> in parse_args >>>>>>> args, argv = self.parse_known_args(args, namespace) >>>>>>> File "/share/apps/anaconda3/lib/python3.7/argparse.py", line 1781, >>>>>>> in parse_known_args >>>>>>> namespace, args = self._parse_known_args(args, namespace) >>>>>>> File "/share/apps/anaconda3/lib/python3.7/argparse.py", line 1987, >>>>>>> in _parse_known_args >>>>>>> start_index = consume_optional(start_index) >>>>>>> File "/share/apps/anaconda3/lib/python3.7/argparse.py", line 1927, >>>>>>> in consume_optional >>>>>>> take_action(action, args, option_string) >>>>>>> File "/share/apps/anaconda3/lib/python3.7/argparse.py", line 1855, >>>>>>> in take_action >>>>>>> action(self, namespace, argument_values, option_string) >>>>>>> File >>>>>>> "/share/apps/anaconda3/lib/python3.7/site-packages/sisl/io/xsf.py", line >>>>>>> 339, in __call__ >>>>>>> vector = input_sile.read_data(*values, **d) >>>>>>> File >>>>>>> "/share/apps/anaconda3/lib/python3.7/site-packages/sisl/io/tbtrans/tbt.py", >>>>>>> line 1930, in read_data >>>>>>> val.append(self.vector_current(*args)) >>>>>>> File >>>>>>> "/share/apps/anaconda3/lib/python3.7/site-packages/sisl/io/tbtrans/tbt.py", >>>>>>> line 1377, in vector_current >>>>>>> Jab = self.bond_current(elec, E, kavg, only=only) >>>>>>> File >>>>>>> "/share/apps/anaconda3/lib/python3.7/site-packages/sisl/io/tbtrans/tbt.py", >>>>>>> line 1187, in bond_current >>>>>>> Jij = self.orbital_current(elec, E, kavg, isc, only=only) >>>>>>> File >>>>>>> "/share/apps/anaconda3/lib/python3.7/site-packages/sisl/io/tbtrans/tbt.py", >>>>>>> line 1063, in orbital_current >>>>>>> J = self._sparse_data('J', elec, E, kavg, isc) >>>>>>> File >>>>>>> "/share/apps/anaconda3/lib/python3.7/site-packages/sisl/io/tbtrans/tbt.py", >>>>>>> line 865, in _sparse_data >>>>>>> rptr = np.insert(_a.cumsumi(self._value('n_col')), 0, 0) >>>>>>> File >>>>>>> "/share/apps/anaconda3/lib/python3.7/site-packages/sisl/io/sile.py", >>>>>>> line >>>>>>> 757, in _value >>>>>>> return self._variable(name, tree)[:] >>>>>>> File >>>>>>> "/share/apps/anaconda3/lib/python3.7/site-packages/sisl/io/sile.py", >>>>>>> line >>>>>>> 750, in _variable >>>>>>> return self._variables(self, name, tree=tree) >>>>>>> File >>>>>>> "/share/apps/anaconda3/lib/python3.7/site-packages/sisl/io/sile.py", >>>>>>> line >>>>>>> 763, in _variables >>>>>>> return n.variables[name] >>>>>>> KeyError: 'n_col' >>>>>>> >>>>>>> Could you please help me to solve this issue? >>>>>>> >>>>>>> >>>>>>> Many thanks, >>>>>>> SH. >>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> SIESTA is supported by the Spanish Research Agency (AEI) and by the >>>>>>> European H2020 MaX Centre of Excellence (http://www.max-centre.eu/) >>>>>>> >>>>>> >>>>>> -- >>>>>> SIESTA is supported by the Spanish Research Agency (AEI) and by the >>>>>> European H2020 MaX Centre of Excellence (http://www.max-centre.eu/) >>>>>> >>>>> >>>>> -- >>>>> SIESTA is supported by the Spanish Research Agency (AEI) and by the >>>>> European H2020 MaX Centre of Excellence (http://www.max-centre.eu/) >>>>> >>>> >>>> >>>> -- >>>> Kind regards Nick >>>> >>>> -- >>>> SIESTA is supported by the Spanish Research Agency (AEI) and by the >>>> European H2020 MaX Centre of Excellence (http://www.max-centre.eu/) >>>> >>> >>> -- >>> SIESTA is supported by the Spanish Research Agency (AEI) and by the >>> European H2020 MaX Centre of Excellence (http://www.max-centre.eu/) >>> >> >> >> -- >> Kind regards Nick >> >> -- >> SIESTA is supported by the Spanish Research Agency (AEI) and by the >> European H2020 MaX Centre of Excellence (http://www.max-centre.eu/) >> > > -- > SIESTA is supported by the Spanish Research Agency (AEI) and by the > European H2020 MaX Centre of Excellence (http://www.max-centre.eu/) > -- Kind regards Nick
-- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
