Show Posts

This section allows you to view all posts made by this member. Note that you can only see posts made in areas you currently have access to.


Messages - rebeda

Pages: 1 2 [3] 4
31
General Questions and Answers / Re: Negative inelastic transmission
« on: June 9, 2016, 07:10 »
Dear Sir,

According to my knowledge transmission, being a probability, can have minimum value of 0 and maximum of 1 (though it depends on the no. of channels available for conduction) and hence,  is always positive, but refering to one of your quantumwise tutorial-
link: http://quantumwise.com/support/tutorials/item/877-inelastic-electron-spectroscopy-of-h-molecule-between-1d-au-chains
I observe negative inelastic transmission at mode 0 and mode 5 in the IETS study of H molecule between 1D Au chains. I am not able to interpret this "negative inelastic transmission". In other words, how transmission can have negative values in this case, though for IETS, one can understand to have both positive and negative values.
Will you please help me?

Regards,
Rebeda :( :( :(

32
General Questions and Answers / Re: mode assignment for negative bias for IETS of hydrogen molecule
« on: June 7, 2016, 14:38 »
In the tutorial given in the link below to calculate the IETS of  hydrogen molecule-
http://quantumwise.com/publications/tutorials/item/877-inelastic-electron-spectroscopy-of-h-molecule-between-1d-au-chains
1. why vibrational modes were not assign for the negative bias?
2. I calculated the same for my system[Au(111)-single molecular magnet-Au(111)] within the bias -0.1 to 0.1 volt and I got asymmetric IETS. How can I find the modes for the negative bias?
     In my vibrational analyser, mode zero lie at -53.99 meV which is -0.05399 volt, what about the IETS peaks within -0.1 to -0.05399 volt? How can we identify them?

Please help me. I will be waiting for your kind reply.
Regards,
Rebeda

33
General Questions and Answers / Re: electron-phonon interaction in two probe system
« 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

34
General Questions and Answers / Re: electron-phonon interaction in two probe system
« 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

35
General Questions and Answers / Re: electron-phonon interaction in two probe system
« 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   


36
General Questions and Answers / Re: electron-phonon interaction in two probe system
« 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

37
General Questions and Answers / Convergence issue with two-probe SCF run
« 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

38
General Questions and Answers / Re: electron-phonon interaction in two probe system
« 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)"


39
General Questions and Answers / electron-phonon coupling analyser
« 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

40
General Questions and Answers / Re: Tremolox Package
« on: September 28, 2015, 13:14 »
Thank you for your kind reply.

With best regards,
Rebeda

41
General Questions and Answers / Re: Tremolox Package
« on: September 25, 2015, 06:59 »
1. I have been trying to generate ReaxFF potential for my system consisting of Au,S,C and H. But, I am facing some problem locating the potential file (i.e. FField_AuSCH) which I got from this link
http://ttj.kapsi.fi/publ/ffield_AuSCH   
Since  it is not there in the quantumwise file which have been installed (i.e. VNL-ATK-2015.rc2), how can I fetch this file into my python script for execution?


2. Can I use two different types of ReaxFF potential ? will you please check the python file that I have made

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

# Create a new potential set
potentialSet.addTremoloXPotentialSet(name='ReaxFF_HOAu_2010')
potentialSet.addTremoloXPotentialSet(name='ReaxFF_CHONS_2010')

# Add the particle type to the potential set
potentialSet.addParticleType(ParticleType(symbol='Au',
                                          mass=196.96655*atomic_mass_unit))
potentialSet.addParticleType(ParticleType(symbol='S',
                                          mass=32.065*atomic_mass_unit))
potentialSet.addParticleType(ParticleType(symbol='C',
                                          mass=12.0107*atomic_mass_unit))
potentialSet.addParticleType(ParticleType(symbol='H',
                                          mass=1.00794*atomic_mass_unit))

# Add the ReaxFF potential to the potential set
potentialSet.addPotential(ReaxFFPotential(file='ffield_AuSCH',
                                          qeq=True,
                                          qeqEps=1.000000e-06,
                                          qeqMaxIter=200,
                                          lgvdw=False,
                                          bond_rcut=5.0*Angstrom,
                                          hbond_rcut=7.5*Angstrom,
                                          thb_bond_rcut=0.001000,
                                          thb_bond_rcutsq=0.000010,
                                          multiwell=False,
                                          strict_bondpairs=True))

# Create a new TremoloX calculator from the potential set
calculator = TremoloXCalculator(parameters=potentialSet)

42
General Questions and Answers / Re: Tremolox Package
« on: September 4, 2015, 12:08 »
Thank you for your kind reply.

Regards,
Rebeda

43
General Questions and Answers / Re: Tremolox Package
« on: September 2, 2015, 13:27 »
I have tried doing it, but if you go through the below link  which is for EAMsetflPotential as an example
http://quantumwise.com/documents/manuals/latest/ReferenceManual/index.html/ref.eamsetflpotential.html


"# Add the EAM potential to the potential set
potentialSet.addPotential(EAMsetflPotential(file='Cu-Mishin-2001.eam.alloy',
                                            splineType='natural'))"

In the above script, where do I find in the source code the file: 'Cu-Mishin-2001.eam.alloy', as I could not trace it.  Similarly how to locate the file:'Ti-Ackland-1992.eam.fs' for 'EAMFS_Ti_1992' potential set.
 
Please help me.

Regards,
Rebeda


44
General Questions and Answers / Re: Tremolox Package
« on: September 2, 2015, 08:58 »
I am unable to find the potential files for the potential parameter sets which are already present in the given  list. Would you please tell me how can I trace these files?

Thank you for your kind corporation.

Regards,
Rebeda

45
General Questions and Answers / Tremolox Package
« on: August 31, 2015, 11:32 »
How do I generate interatomic potential parameter sets for a system consisting of Au, S, C, N, Cr and H ?

Pages: 1 2 [3] 4