Author Topic: electron-phonon interaction in two probe system (Read 8656 times)

rebeda · « **on:** June 8, 2015, 10:50 »

Can we calculate electron-phonon interaction for two probe system ?

Umberto Martinez · « **Reply #1 on:** June 8, 2015, 15:21 »

It will be introduce in the next release ATK 2015, coming out soon (next few months).

A preview of this can be found here:
http://quantumwise.com/publications/tutorials/item/837-inelastic-transmission
http://quantumwise.com/publications/tutorials/item/877-inelastic-electron-spectroscopy-of-h-molecule-between-1d-au-chains

rebeda · « **Reply #2 on:** December 14, 2015, 11:58 »

while I was anlysing my result( *. nc file) on the labfloor for ElectronPhononCoupling calculation I got an error message that goes below. Will you please help me

"Exception message:
Traceback (most recent call last):
File ".\zipdir\NL\GUI\MainWindow\AnalysisBar\AnalysisBar.py", line 58, in widget
File "C:\Program Files (x86)\QuantumWise\VNL-ATK-2015.0\Lib\site-packages\AddOns\ElectronPhononCouplingPlugins\ElectronPhononCouplingPlugin.py", line 47, in createWidget
widget = ElectronPhononCouplingWidget(item, self.labFloor())
File "C:\Program Files (x86)\QuantumWise\VNL-ATK-2015.0\lib\site-packages\AddOns\ElectronPhononCouplingPlugins\ElectronPhononCouplingWidget.py", line 106, in __init__
self.update()
File "C:\Program Files (x86)\QuantumWise\VNL-ATK-2015.0\lib\site-packages\AddOns\ElectronPhononCouplingPlugins\ElectronPhononCouplingWidget.py", line 117, in update
self._plotter_widget.plotData(model)
File "C:\Program Files (x86)\QuantumWise\VNL-ATK-2015.0\lib\site-packages\AddOns\ElectronPhononCouplingPlugins\ElectronPhononCouplingWidget.py", line 395, in plotData
x_dir = 'xyz'[periodic_directions[0]]
IndexError: list index out of range"

Regards
Rebeda

Umberto Martinez · « **Reply #3 on:** December 14, 2015, 13:27 »

can you please provide input/output files?

Also note that 2015.1 has been released: http://quantumwise.com/products/download

rebeda · « **Reply #4 on:** December 15, 2015, 05:45 »

Python file for relaxation for gold nanowire ---

"# -------------------------------------------------------------
# Bulk configuration
# -------------------------------------------------------------

# Set up lattice
vector_a = [22.0, 0.0, 0.0]*Angstrom
vector_b = [ 0.0, 22.0, 0.0]*Angstrom
vector_c = [ 0.0, 0.0, 4.741513]*Angstrom
lattice = UnitCell(vector_a, vector_b, vector_c)

elements = 14*[Gold]

# Define coordinates
cartesian_coordinates = [[ 6.754023, 4.219484, 1.185378],
[ 5.375828, 1.823166, 1.185378],

------

[ 4.097240, 4.219487, 3.556135]]*Angstrom

# Set up configuration
bulk_configuration = BulkConfiguration(
bravais_lattice=lattice,
elements=elements,
cartesian_coordinates=cartesian_coordinates
)

###############################################################
# Calculator
###############################################################
#----------------------------------------
# Numerical Accuracy Settings
#----------------------------------------
numerical_accuracy_parameters = NumericalAccuracyParameters(
k_point_sampling=(1, 1, 800),
)
#----------------------------------------
# Basis Set
#----------------------------------------
basis_set = [
GGABasis.Gold_DoubleZetaPolarized,
]

#----------------------------------------
# Exchange-Correlation
#----------------------------------------
exchange_correlation = GGA.RPBE

#----------------------------------------
# Electrode Calculators
#----------------------------------------
calculator = LCAOCalculator(
basis_set=basis_set,
exchange_correlation=exchange_correlation,
numerical_accuracy_parameters=numerical_accuracy_parameters,
)

bulk_configuration.setCalculator(calculator)
bulk_configuration.update()
nlsave('60nw_bulk.nc', bulk_configuration)
nlprint(bulk_configuration)"

python file for electron-phonon-coupling calculation for the same system--

"bulk_configuration = nlread('60nw_bulk.nc', object_id='gID000')[0]

# -------------------------------------------------------------
# Calculator
# -------------------------------------------------------------

# -------------------------------------------------------------
# Hamiltonian derivatives
# -------------------------------------------------------------
hamiltonian_derivatives = HamiltonianDerivatives(
bulk_configuration,
repetitions=(1, 1, 1),
)

nlsave('60nw_bulk.nc', hamiltonian_derivatives)

# -------------------------------------------------------------
# Dynamical matrix
# -------------------------------------------------------------
dynamical_matrix = DynamicalMatrix(
bulk_configuration,
repetitions=(1, 1, 1),
atomic_displacement=0.01*Ang,
max_interaction_range=10*Angstrom,
)

nlsave('60nw_bulk.nc', dynamical_matrix)

# -------------------------------------------------------------
# Electron-phonon coupling
# -------------------------------------------------------------
electron_phonon_coupling = ElectronPhononCoupling(
configuration=bulk_configuration,
hamiltonian_derivatives=hamiltonian_derivatives,
dynamical_matrix=dynamical_matrix,
kpoints_fractional=[[0.0, 0.0, 0.0], [0.0, 0.0, 1.0]],
qpoints_fractional=[[0.0, 0.0, 0.0], [0.0, 0.0, 1.0]],
)

nlsave('60nw_bulk.nc', electron_phonon_coupling)

# -------------------------------------------------------------
# Deformation potential
# -------------------------------------------------------------
deformation_potential = DeformationPotential(
bulk_configuration,
hamiltonian_derivatives,
dynamical_matrix,
kpoint_fractional=[0.0, 0.0, 0.5],
q_path=[[0.0, 0.0, 0.0], [0.0, 0.0, 0.2], [0.0, 0.0, 0.3], \
[0.0, 0.0, 0.4], [0.0, 0.0, 0.45], [0.0, 0.0, 0.5]],
)

nlsave('60nw_bulk.nc', deformation_potential)

# -------------------------------------------------------------
# Mobility
# -------------------------------------------------------------
mobility = Mobility(
configuration=bulk_configuration,
electron_phonon_coupling=electron_phonon_coupling,
)

nlsave('60nw_bulk.nc', mobility)"

Jess Wellendorff · « **Reply #5 on:** December 21, 2015, 12:09 »

I ran your script as you have cited it above, and found no errors with ATK 2015.1

rebeda · « **Reply #6 on:** February 11, 2016, 06:21 »

Dear Sir,
While working on a two-probe system (spin-polarizd) with QuantumWise, I am struggling with the convergence
issue for the device, while the electrodes as well as the equivalent bulk behave as it should [see below].
Could you please help me out in resolving it? The problem mainly lies in converging dH, though there is no
such issue for dE. The k-points are chosen as "k_point_sampling=(3, 3, 100)", the contour parametrs are
chosen such that "circle_points=60", the iteration control parameters are chosen with "damping_factor=0.1".

-------------------
| Left Electrode Calculation [Started ------ ] |
Calculating Eigenvalues : ==================================================
| 24 E = -143.906 dE = 3.632179e-04 dH = 4.283244e-05 |
Calculating Eigenvalues : ==================================================
| 25 E = -143.906 dE = 3.514783e-05 dH = 1.171219e-05 |
| Left Electrode Calculation [Finished ----- ] |
--------------------
| Right Electrode Calculation [Started ----- ] |
--------------------
Calculating Eigenvalues : ==================================================
| 24 E = -143.906 dE = 3.680349e-04 dH = 3.973195e-05 |
Calculating Eigenvalues : ==================================================
| 25 E = -143.906 dE = 3.113314e-05 dH = 8.242738e-06 |
| Right Electrode Calculation [Finished ] |
--------------------
| Equivalent Bulk [Started ------ ] |
Calculating Eigenvalues : ==================================================
| 40 E = -604.546 dE = 1.674462e-02 dH = 7.109732e-03 |
Calculating Eigenvalues : ==================================================
| 41 E = -604.55 dE = 3.249493e-03 dH = 3.351605e-03 |
| Equivalent Bulk [Finished ----- ] |
--------------------
------
| 210 E = -631.902 dE = 6.540553e-05 dH = 1.848707e-03 |
| 211 E = -631.903 dE = 6.446038e-04 dH = 1.820017e-03 |
| 212 E = -631.907 dE = 3.662838e-03 dH = 1.753000e-03 |
| 213 E = -631.908 dE = 1.013363e-03 dH = 2.456666e-03 |
| 214 E = -631.906 dE = 1.372071e-03 dH = 2.714449e-03 |
| 215 E = -631.892 dE = 1.380006e-02 dH = 2.288700e-03 |
| 216 E = -631.893 dE = 6.937208e-04 dH = 5.274790e-03 |
| 217 E = -631.893 dE = 4.849841e-05 dH = 5.752056e-03 |
| 218 E = -631.894 dE = 1.074899e-03 dH = 5.493987e-03 |
| 219 E = -631.898 dE = 3.471558e-03 dH = 4.989637e-03 |
| 220 E = -631.9 dE = 2.690475e-03 dH = 3.936320e-03 |
| 221 E = -631.898 dE = 2.843382e-03 dH = 3.412088e-03 |
| 222 E = -631.897 dE = 1.992910e-04 dH = 4.081402e-03 |
| 223 E = -631.897 dE = 7.049964e-05 dH = 4.022176e-03 |
| 224 E = -631.898 dE = 6.790056e-04 dH = 3.998828e-03 |
| 225 E = -631.898 dE = 1.639834e-04 dH = 4.121747e-03 |
| 226 E = -631.897 dE = 6.953735e-04 dH = 4.528531e-03 |
| 227 E = -631.897 dE = 6.417012e-04 dH = 4.451000e-03 |
| 228 E = -631.897 dE = 2.927810e-04 dH = 3.333894e-03 |
| 229 E = -631.897 dE = 3.350161e-04 dH = 3.087998e-03 |
| 230 E = -631.896 dE = 1.572252e-03 dH = 3.273902e-03 |
| 231 E = -631.893 dE = 2.436914e-03 dH = 3.563415e-03 |
| 232 E = -631.894 dE = 6.613918e-04 dH = 4.290060e-03 |
| 233 E = -631.898 dE = 3.723214e-03 dH = 4.320211e-03 |
| 234 E = -631.898 dE = 4.412318e-05 dH = 3.644584e-03 |
| 235 E = -631.897 dE = 4.934228e-04 dH = 2.729455e-03 |
| 236 E = -631.899 dE = 2.232635e-03 dH = 2.961352e-03 |
| 237 E = -631.901 dE = 1.345609e-03 dH = 2.987998e-03 |
| 238 E = -631.901 dE = 6.869148e-04 dH = 2.617813e-03 |
| 239 E = -631.9 dE = 1.389278e-03 dH = 2.480923e-03 |
| 240 E = -631.9 dE = 4.429134e-04 dH = 2.187557e-03 |
| 241 E = -631.9 dE = 6.041444e-04 dH = 2.788400e-03 |
| 242 E = -631.899 dE = 4.840091e-04 dH = 2.678021e-03 |
| 243 E = -631.899 dE = 1.118098e-04 dH = 2.643998e-03 |
| 244 E = -631.899 dE = 2.690704e-04 dH = 2.394330e-03 |
| 245 E = -631.9 dE = 6.676876e-04 dH = 2.401902e-03 |
| 246 E = -631.899 dE = 1.190354e-03 dH = 2.648432e-03 |
| 247 E = -631.898 dE = 1.446554e-04 dH = 2.502319e-03 |
| 248 E = -631.899 dE = 2.109255e-04 dH = 2.519078e-03 |
| 249 E = -631.899 dE = 8.053678e-04 dH = 2.355521e-03 |
-------------------
Awaiting your advice and useful inputs,

Regards,
Rebeda

Jess Wellendorff · « **Reply #7 on:** February 11, 2016, 08:10 »

Could you attach the script you use?

rebeda · « **Reply #8 on:** February 11, 2016, 10:49 »

Dear Sir,
Please find the attachment. Kindly help me out in setting the correct parameters for the smooth SCF run.
Regards,
Rebeda

rebeda · « **Reply #9 on:** February 12, 2016, 02:11 »

Dear Sir,
Finally the device calculation ends up with no convergence even after 300 iterations as this:
+------------------------------------------------------------------------------+
| 299 E = -631.898 dE = 1.208148e-02 dH = 3.087065e-02 |
+------------------------------------------------------------------------------+
################################################################################
# #
# Warning: The calculation did not converge to the requested tolerance! #
# #
###############################################################################
--------------------------------------------------------------------------------
Total : 350125.23 s (4d01h15m25.23s)

What parameters I should tune to get better dH convergence.
(i) Should I modify the K-points, which I did set as (3, 3, 100)?
(ii) Should I increase the circle_points, which I did set as 60?
(iii) Should I further reduce the damping_factor, which I took as the default value of 0.1?
(iv) Should I set the initial scaled spins reduced from 1.0 to say, 0.6?
I did try some of these already, but to no avail, as I continue to struggle for about a month to get it converged. Hence, I am really looking forward to your advice and kind cooperation in resolving this convergence issue, which I am sure, would help many others like me.
With warm regards,
Rebeda

Jess Wellendorff · « **Reply #10 on:** February 12, 2016, 08:44 »

That script cannot be the one you are really using. Lines 28-30, 62-64, and 130-132 are not valid Python code ([ ... ] is invalid):

Code

left_electrode_coordinates = [[  0.936693371666,   0.758276943974,   0.78499999998 ],
                              [ ... ],
                              [ 10.806693371665,  10.628276943974,   5.01500000002 ]]*Angstrom

Please upload a valid script so I can do a test run.

rebeda · « **Reply #11 on:** February 16, 2016, 17:31 »

Dear Dr. Wellendorff,
I am curious to know if you have done the test run successfully by now. Awaiting then your reply with the tips and tricks that has been needed to be adopted here, in particular, for the device convergence.
Thanks and warm regards,
Rebeda

rebeda · « **Reply #12 on:** February 19, 2016, 09:07 »

Dear Sir,
Even after a month or so, I am still struggling with the convergence issue for the above system. Please help me with some ideas so that I can make it converged at last.
With thanks and regards,
Rebeda

Anders Blom · « **Reply #13 on:** February 19, 2016, 12:22 »

What did you try? You can increase the damping factor a bit, and reduce the history steps perhaps.
I would also skip the equivalent bulk, it takes a lot of time for a system like this, but might give a bad starting guess because there is a stacking fault in the central region (your two electrodes are not identical).

Jess Wellendorff · « **Reply #14 on:** February 22, 2016, 10:51 »

Hi Rebeda. I am trying to run the calculation with a few changes: Thicker electrodes, more aggressive Pulay mixing, and NeutralAtoms instead of EquivalentBulk. Hope it helps, will let you know...

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Author Topic: electron-phonon interaction in two probe system (Read 8656 times)

rebeda

electron-phonon interaction in two probe system

Umberto Martinez

Re: electron-phonon interaction in two probe system

rebeda

electron-phonon coupling analyser

Umberto Martinez

Re: electron-phonon interaction in two probe system

rebeda

Re: electron-phonon interaction in two probe system

Jess Wellendorff

Re: electron-phonon interaction in two probe system

rebeda

Convergence issue with two-probe SCF run

Jess Wellendorff

Re: electron-phonon interaction in two probe system

rebeda

Re: electron-phonon interaction in two probe system

rebeda

Re: electron-phonon interaction in two probe system

Jess Wellendorff

Re: electron-phonon interaction in two probe system

rebeda

Re: electron-phonon interaction in two probe system

rebeda

Re: electron-phonon interaction in two probe system

Anders Blom

Re: electron-phonon interaction in two probe system

Jess Wellendorff

Re: electron-phonon interaction in two probe system