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 ..) And one more question! is there any graphical package that I can use to visualize the bond current vectors inserted xcrysden? Thanks. Sincerely, SH. On Wed, May 20, 2020 at 12:33 AM Nick Papior <[email protected]> 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 < > [email protected]>: > >> 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/) >> > > > -- > 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/)
