Den man. 18. maj 2020 kl. 22.00 skrev El-abed Haidar < ehai2...@uni.sydney.edu.au>:
> 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 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 <nickpap...@gmail.com> > *Sent: *Monday, 18 May 2020 6:01 AM > *To: *siesta-l <siesta-l@uam.es> > *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 < > 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 > <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 <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/ > <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/) > -- 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/)
