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/)
