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/)
