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zerothi / sisl

Electronic structure Python package for post analysis and large scale tight-binding DFT/NEGF calculations
https://zerothi.github.io/sisl
Mozilla Public License 2.0
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sisl.io.tbtrans.tbtncSileTBtrans use #669

Closed lucasem1 closed 7 months ago

lucasem1 commented 7 months ago

Dear Developers

I am trying to calculate the atom_current by using the class tbtavncSileTBtrans . I have a database TBT.nc generated by Siesta+Tbtrans for a system under a bias of 1Volt.
When I run the code:

db='myfile.TBT.nc' tbt = sisl.io.tbtrans.tbtncSileTBtrans(db) Jb = tbt.atom_current(elec=0, elec_other=1, activity=True, kavg=True, isc=None, orbitals=None)

I get the error :

Traceback (most recent call last): File "/home/luca/Codes/Python/anaconda3/envs/sisl_env/lib/python3.9/site-packages/sisl/io/tbtrans/tbt.py", line 216, in _value_E v = self._variable(name, tree=tree) File "/home/luca/Codes/Python/anaconda3/envs/sisl_env/lib/python3.9/site-packages/sisl/io/sile.py", line 1287, in _variable return self._variables(self, name, tree=tree) File "/home/luca/Codes/Python/anaconda3/envs/sisl_env/lib/python3.9/site-packages/sisl/io/sile.py", line 1309, in _variables return g.variables[name] KeyError: 'J'

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/media/sf_Vubuntu_share/IPCF-2014/Noureddine/NEGF/17Mar2023-CBN/DATA/SISLANALYSIS/bc.py", line 11, in Jb = tbt.atom_current(elec=0, elec_other=1, activity=True, kavg=True, isc=None, orbitals=None) File "/home/luca/Codes/Python/anaconda3/envs/sisl_env/lib/python3.9/site-packages/sisl/io/tbtrans/tbt.py", line 2096, in atom_current Jij = self.orbital_current( File "/home/luca/Codes/Python/anaconda3/envs/sisl_env/lib/python3.9/site-packages/sisl/messages.py", line 106, in wrapped return func(*args, **kwargs) File "/home/luca/Codes/Python/anaconda3/envs/sisl_env/lib/python3.9/site-packages/sisl/io/tbtrans/tbt.py", line 1631, in orbital_current J = reduce(getdata, enumerate(integrator(self.E)), 0.0) File "/home/luca/Codes/Python/anaconda3/envs/sisl_env/lib/python3.9/site-packages/sisl/io/tbtrans/tbt.py", line 1608, in func_all D = self._sparse_data("J", elec, i, kavg=kavg) File "/home/luca/Codes/Python/anaconda3/envs/sisl_env/lib/python3.9/site-packages/sisl/io/tbtrans/tbt.py", line 1086, in _sparse_data return self._value_E(name, elec, kavg, E) File "/home/luca/Codes/Python/anaconda3/envs/sisl_env/lib/python3.9/site-packages/sisl/io/tbtrans/tbt.py", line 224, in _value_E raise KeyError( KeyError: "tbtncSileTBtrans could not retrieve key 'Left.J' due to missing flags in the input file."

Could you please help overcome this issue?

Best Regards. Luca

zerothi commented 7 months ago

The KeyError tells me that you haven't calculated the bond/orbital current, please see in the tbtrans manual for the appropriate flag and recalculate again.

lucasem1 commented 7 months ago

Thank you for your help. Best Regards. Luca

zerothi commented 7 months ago

Closed via #670