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 <[email protected]> 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 < > [email protected]>: > >> 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 <[email protected]> >> 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, <[email protected]> >>> 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/)
