Dear Anders,
Thanks for your reply.
I will read it carefully, and try to understand the process of calculation IETS in ATK.
With best regards,
Guangping
Dear Anders,
I have followed the tutorial, but still have some questions on the calculation of IETS in ATK.
(1) In the tutorial, it metioned that "The dynamical matrix can be calculated in parallel over the atomic displacements in each direction. Consequently this calculation can be performed efficiently using six cores." So, to speed up the calculation, the cores used must be six or multiple of six, in that each core has a very similar computational load, right?
(2) Concerning the setting of q-points in vibration calculation, if I just inlcude the molecule in a molecular junction in the "Dynamical Matrix" calcualtion, can I safely set a 1x1 q-point sampling since the molecular is supposed not to interact wtih its image in repetition unit cells ?
(3) What is the effect of "repetitions=(x, x, x)" in "DynamicalMatrix" and "HamiltonianDerivatives" class? As the reason stated in (2), can I safely set repetitions=(1, 1, 1)? I found, it is ok for DynamicalMatrix, but not for HamiltonianDerivatives. I get errors like
Traceback (most recent call last):
File "/tmp/1366.node00/CH3-C7-Au-IETS.py", line 463, in <module>
Traceback (most recent call last):
File "/tmp/1366.node00/CH3-C7-Au-IETS.py", line 463, in <module>
Traceback (most recent call last):
File "/tmp/1366.node00/CH3-C7-Au-IETS.py", line 463, in <module>
Traceback (most recent call last):
File "/tmp/1366.node00/CH3-C7-Au-IETS.py", line 463, in <module>
use_equivalent_bulk=True,
use_equivalent_bulk=True,
File "./zipdir/NL/Analysis/HamiltonianDerivatives.py", line 132, in __init__
File "./zipdir/NL/Analysis/HamiltonianDerivatives.py", line 132, in __init__
use_equivalent_bulk=True,
File "./zipdir/NL/Analysis/HamiltonianDerivatives.py", line 132, in __init__
Traceback (most recent call last):
use_equivalent_bulk=True,
File "./zipdir/NL/Analysis/HamiltonianDerivatives.py", line 132, in __init__
Traceback (most recent call last):
File "/tmp/1366.node00/CH3-C7-Au-IETS.py", line 463, in <module>
File "/tmp/1366.node00/CH3-C7-Au-IETS.py", line 463, in <module>
Traceback (most recent call last):
File "/tmp/1366.node00/CH3-C7-Au-IETS.py", line 463, in <module>
use_equivalent_bulk=True,
File "./zipdir/NL/Analysis/HamiltonianDerivatives.py", line 132, in __init__
use_equivalent_bulk=True,
File "./zipdir/NL/Analysis/HamiltonianDerivatives.py", line 132, in __init__
Traceback (most recent call last):
File "/tmp/1366.node00/CH3-C7-Au-IETS.py", line 463, in <module>
use_equivalent_bulk=True,
File "./zipdir/NL/Analysis/HamiltonianDerivatives.py", line 132, in __init__
use_equivalent_bulk=True,
File "./zipdir/NL/Analysis/HamiltonianDerivatives.py", line 132, in __init__
Traceback (most recent call last):
File "/tmp/1366.node00/CH3-C7-Au-IETS.py", line 463, in <module>
Traceback (most recent call last):
File "/tmp/1366.node00/CH3-C7-Au-IETS.py", line 463, in <module>
Traceback (most recent call last):
File "/tmp/1366.node00/CH3-C7-Au-IETS.py", line 463, in <module>
use_equivalent_bulk=True,
Traceback (most recent call last):
File "/tmp/1366.node00/CH3-C7-Au-IETS.py", line 463, in <module>
File "./zipdir/NL/Analysis/HamiltonianDerivatives.py", line 132, in __init__
use_equivalent_bulk=True,
File "./zipdir/NL/Analysis/HamiltonianDerivatives.py", line 132, in __init__
use_equivalent_bulk=True,
File "./zipdir/NL/Analysis/HamiltonianDerivatives.py", line 132, in __init__
use_equivalent_bulk=True,
File "./zipdir/NL/Analysis/HamiltonianDerivatives.py", line 132, in __init__
File "./zipdir/NL/Analysis/HamiltonianDerivatives.py", line 978, in setAndCheckAtomsDisplacedWithinSuperCell
File "./zipdir/NL/Analysis/HamiltonianDerivatives.py", line 978, in setAndCheckAtomsDisplacedWithinSuperCell
File "./zipdir/NL/Analysis/HamiltonianDerivatives.py", line 978, in setAndCheckAtomsDisplacedWithinSuperCell
File "./zipdir/NL/Analysis/HamiltonianDerivatives.py", line 978, in setAndCheckAtomsDisplacedWithinSuperCell
File "./zipdir/NL/Analysis/HamiltonianDerivatives.py", line 978, in setAndCheckAtomsDisplacedWithinSuperCell
File "./zipdir/NL/Analysis/HamiltonianDerivatives.py", line 978, in setAndCheckAtomsDisplacedWithinSuperCell
NL.ComputerScienceUtilities.Exceptions.NLValueError: File "./zipdir/NL/Analysis/HamiltonianDerivatives.py", line 978, in setAndCheckAtomsDisplacedWithinSuperCell
NL.ComputerScienceUtilities.Exceptions.NLValueError: Atoms are being displaced out of the unit cell in directions where the cell repetition is less that 3. Please increase the unit cell repetition in the direction(s): A.
NL.ComputerScienceUtilities.Exceptions.NLValueError: Atoms are being displaced out of the unit cell in directions where the cell repetition is less that 3. Please increase the unit cell repetition in the direction(s): A.
Atoms are being displaced out of the unit cell in directions where the cell repetition is less that 3. Please increase the unit cell repetition in the direction(s): A.
NL.ComputerScienceUtilities.Exceptions.NLValueError: Atoms are being displaced out of the unit cell in directions where the cell repetition is less that 3. Please increase the unit cell repetition in the direction(s): A.
File "./zipdir/NL/Analysis/HamiltonianDerivatives.py", line 978, in setAndCheckAtomsDisplacedWithinSuperCell
File "./zipdir/NL/Analysis/HamiltonianDerivatives.py", line 978, in setAndCheckAtomsDisplacedWithinSuperCell
NL.ComputerScienceUtilities.Exceptions.NLValueError: Atoms are being displaced out of the unit cell in directions where the cell repetition is less that 3. Please increase the unit cell repetition in the direction(s): A.
NL.ComputerScienceUtilities.Exceptions.NLValueError: Atoms are being displaced out of the unit cell in directions where the cell repetition is less that 3. Please increase the unit cell repetition in the direction(s): A.
File "./zipdir/NL/Analysis/HamiltonianDerivatives.py", line 978, in setAndCheckAtomsDisplacedWithinSuperCell
File "./zipdir/NL/Analysis/HamiltonianDerivatives.py", line 978, in setAndCheckAtomsDisplacedWithinSuperCell
NL.ComputerScienceUtilities.Exceptions.NLValueError: Atoms are being displaced out of the unit cell in directions where the cell repetition is less that 3. Please increase the unit cell repetition in the direction(s): A.
NL.ComputerScienceUtilities.Exceptions.NLValueError: Atoms are being displaced out of the unit cell in directions where the cell repetition is less that 3. Please increase the unit cell repetition in the direction(s): A.
NL.ComputerScienceUtilities.Exceptions.NLValueError: Atoms are being displaced out of the unit cell in directions where the cell repetition is less that 3. Please increase the unit cell repetition in the direction(s): A.
File "./zipdir/NL/Analysis/HamiltonianDerivatives.py", line 978, in setAndCheckAtomsDisplacedWithinSuperCell
NL.ComputerScienceUtilities.Exceptions.NLValueError: Atoms are being displaced out of the unit cell in directions where the cell repetition is less that 3. Please increase the unit cell repetition in the direction(s): A.
NL.ComputerScienceUtilities.ExceptionsNL.ComputerScienceUtilities.Exceptions.NLValueError: Atoms are being displaced out of the unit cell in directions where the cell repetition is less that 3. Please increase the unit cell repetition in the direction(s): A.
.NLValueError: Atoms are being displaced out of the unit cell in directions where the cell repetition is less that 3. Please increase the unit cell repetition in the direction(s): A.
(4) How to continue an IETS calculation in ATK?
For example, in the .py file the main calculation are lined as the following as instructed in the tutorial Au-H2-Au.
...
device_configuration.update()
...
dynamical_matrix = DynamicalMatrix(...)
...
vibrational_mode = VibrationalMode(...)
...
hamiltonian_derivatives = HamiltonianDerivatives(...)
...
inelastic_transmission_spectrum = InelasticTransmissionSpectrum(...)
Like the case in (3), how can one continue the job?
Can you give me some help on this?
Thanks so much.