Believe it or not, it did speed things up 😊 As for TBT.DOS.Gf its for both DOS and PDOS? So as a summary of all this:
1. Use TBT.DOS.Gf in fdf 2. To extract pdos we use sisl own command sdata Thank you Nick! 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: Wednesday, 20 May 2020 6:00 AM To: siesta-l<mailto:[email protected]> Subject: Re: [SIESTA-L] Transietsa/sisl problem Den man. 18. maj 2020 kl. 22.00 skrev El-abed Haidar <[email protected]<mailto:[email protected]>>: 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? It depends on what you want. TBT.DOS.A will give you the spectral DOS (originating from an electrode) TBT.DOS.Gf<https://protect-au.mimecast.com/s/A_CWCq71mwfG1L35UEMBUI?domain=tbt.dos.gf> will give you the full DOS. Generally you don't need TBT.DOS.A.All since there is a relation between DOS(Gf) and SUM_elec(DOS(A_elec)) (see manual). You should definitely play around with these options to get a feel for the performance implications of doing 1, 2 or all 3 options. Both Gf and A DOS can be divided into orbitals/atoms using sdata. Also, you don't need TBT.CDF.MPI regardless of whether you are doing a serial or parallel calculation. It only affects performance, so try it out and see if it is faster for your HPC system, if so, prefer to use it. :) 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/zOM_Cnx1jniQXl2of9eHDT?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/zOM_Cnx1jniQXl2of9eHDT?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/-QlaCoV1kpfJDlRzuz-97Z?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/gL19Cp81lrtP9QW8UYB04m?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/gL19Cp81lrtP9QW8UYB04m?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/gL19Cp81lrtP9QW8UYB04m?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/<https://protect-au.mimecast.com/s/gL19Cp81lrtP9QW8UYB04m?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/)
