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There is an "nlinspect", but perhaps you just need to use
print total_energy.evaluate()
instead of nlprint(total_energy) to achieve what you want?
Dear Forum,
I am a little confused about how to properly use the nlread function.
I have done a major calculation on a quite big system (120 atoms) which took days on my computer, but I would like to redo the DOS and transmission.
I got this example of how to load the "device configuration" from the .nc file that was saved to along the wayCodedevice_configuration = nlread('file.nc', DeviceConfiguration)[-1]
I am not quite sure why the object type/name is DeviceConfiguration. Where can I see a list of suitable names usable for nlread?
I would expect it to be 'device_configuration' since that is how it got saved in the original script (the standard when doing the script out the the Script Generator), or otherwise 'Device Configuration' as shown in the the VNL window when clicking on my .nc file.
Otherwise, I can refer to the object handle eg. 'gID000', right?
Lastly I do not know what the [-1] means. I learned that nlread gets a list (array?) and so you need to specify the element that you want to use, but how can that be [-1] ? In the VNL window I have two objects, 'Device Configuration' and 'Density of States' (the one I wish to redo). I would expect that the device configuration would be
- and DOS would be [1]. Is this correct/wrong?
Thank you a lot!
Kaspar
There are two ways to do it.
First of all, note that the "scf" is not a separate thing from the configuration. When you have run the self-consistent loop, the scf is stored on the configuration itself. So, if you want to use the approach to read the scf from the NC file, you would do like normal,Code: pythonscf = nlread("energy.nc", BulkConfiguration)[-1]
...
bulk_configuration.setCalculator(calculator, initial_state=scf)
There is however a better way to do it in your case. Since you are looping in the same script, you can just remember the state for the next step, like so:Code: pythonvector_a = [10.0, 0.0, 0.0]*Angstrom
vector_b = [0.0, 10.0, 0.0]*Angstrom
vector_c = [0.0, 0.0, 10.0]*Angstrom
lattice = UnitCell(vector_a, vector_b, vector_c)
# Define elements
elements = [Hydrogen]*2
scf = None # NEW
for dis in (a1,a2,a3,a4): # ai is the distance
fractional_coordinates = [[ 0. , 0. , 0. ],
[ 0. , 0. , dis]]
bulk_configuration = BulkConfiguration(
bravais_lattice=lattice,
elements=elements,
fractional_coordinates=fractional_coordinates
)
calculator = LCAOCalculator()
bulk_configuration.setCalculator(calculator, initial_state=scf) # NEW
bulk_configuration.update()
scf = bulk_configuration # NEW
nlsave('energy.nc', bulk_configuration)
total_energy = TotalEnergy(bulk_configuration)
nlsave('energy.nc', total_energy)
nlprint(total_energy)
Only 3 lines were modified, indicated by "NEW" above.
