A follow up question if I may: TO make sure we can use ssil should the fdf file contain TBT.DOS.A.All true and TBT.CDF.MPI true (for parallel job) ? Would those be enough? Any other blocks or command purely for PDOS we should be aware of? Thank you and looking forward to your reply. EL-Abed
El-abed Haidar | Doctor of Philosophy (Science) Condensed Matter Theory (CMT) Group | School of Physics THE UNIVERSITY OF SYDNEY | NSW | 2006 From: Nick Papior<mailto:[email protected]> Sent: Monday, 18 May 2020 6:01 AM To: siesta-l<mailto:[email protected]> Subject: Re: [SIESTA-L] Transietsa/sisl problem Hi, Simply do: sdata por.TBT.nc<https://protect-au.mimecast.com/s/f3bhCr81nytxYwkmc46V3_?domain=por.tbt.nc> --help and you'll see what commands are available. Please give back this command: sdata por.TBT.nc<https://protect-au.mimecast.com/s/f3bhCr81nytxYwkmc46V3_?domain=por.tbt.nc> --info Den lør. 16. maj 2020 kl. 22.02 skrev shirin zandi <[email protected]<mailto:[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<https://protect-au.mimecast.com/s/zEjpCp81lrt5WQVwCPjfEY?domain=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]<mailto:[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]<mailto:[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/<https://protect-au.mimecast.com/s/0NBFCq71mwf93LE2iXXFa9?domain=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/<https://protect-au.mimecast.com/s/0NBFCq71mwf93LE2iXXFa9?domain=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/<https://protect-au.mimecast.com/s/0NBFCq71mwf93LE2iXXFa9?domain=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/)
