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Messages - Ji_BUF

Pages: [1]
1
General Questions and Answers / Re: Phonon Dispersion Spectrum of GNR (Geometry optimization and mode separation)
« on: April 24, 2019, 16:34 »
Quote from: Petr Khomyakov on April 24, 2019, 10:21
Quote from: Ji_BUF on April 24, 2019, 02:55
I am trying to calculate the phonon spectrum of a 8-dimer armchair graphene nanoribbon by following the example given by: https://docs.quantumwise.com/tutorials/phonon_calcs/phonon_calcs.html.

1. I want to optimize the geometry of the GNR and followed the exact procedure in the tutorial, but ended up with the error messages says: "The underlying configuration must be equal for the input  DynamicMatrix and the object being calculated.".

Please attach the script (and log) file that produced that error.

Log file:

+------------------------------------------------------------------------------+
|                                                                              |
| QuantumATK 2018.06-SP1-1[Build 3f8f0aa]                                      |
|                                                                              |
+------------------------------------------------------------------------------+
+----------------------------------------------------------+
| Bulk Bravais lattice                                     |
+----------------------------------------------------------+
Type:
UnitCell

Lattice constants:

Primitive vectors:
u_1 =     20.000000      0.000000      0.000000 Ang
u_2 =      0.000000     30.000000      0.000000 Ang
u_3 =      0.000000      0.000000      4.262580 Ang

+----------------------------------------------------------+
| Bulk: Cartesian (Angstrom) / fractional                  |
+----------------------------------------------------------+
16
Bulk
C     1.000000e+01  1.069325e+01  2.841720e+00    0.50000  0.35644  0.66667
C     1.000000e+01  1.192375e+01  3.552150e+00    0.50000  0.39746  0.83333
C     1.000000e+01  1.069325e+01  1.420860e+00    0.50000  0.35644  0.33333
C     1.000000e+01  1.315425e+01  2.841720e+00    0.50000  0.43847  0.66667
C     1.000000e+01  1.438475e+01  3.552150e+00    0.50000  0.47949  0.83333
C     1.000000e+01  1.192375e+01  7.104300e-01    0.50000  0.39746  0.16667
C     1.000000e+01  1.315425e+01  1.420860e+00    0.50000  0.43847  0.33333
C     1.000000e+01  1.561525e+01  2.841720e+00    0.50000  0.52051  0.66667
C     1.000000e+01  1.684575e+01  3.552150e+00    0.50000  0.56153  0.83333
C     1.000000e+01  1.438475e+01  7.104300e-01    0.50000  0.47949  0.16667
C     1.000000e+01  1.561525e+01  1.420860e+00    0.50000  0.52051  0.33333
C     1.000000e+01  1.807625e+01  2.841720e+00    0.50000  0.60254  0.66667
C     1.000000e+01  1.930675e+01  3.552150e+00    0.50000  0.64356  0.83333
C     1.000000e+01  1.684575e+01  7.104300e-01    0.50000  0.56153  0.16667
C     1.000000e+01  1.807625e+01  1.420860e+00    0.50000  0.60254  0.33333
C     1.000000e+01  1.930675e+01  7.104300e-01    0.50000  0.64356  0.16667
+----------------------------------------------------------+
| Bulk Bravais lattice                                     |
+----------------------------------------------------------+
Type:
UnitCell

Lattice constants:

Primitive vectors:
u_1 =     20.000000      0.000000      0.000000 Ang
u_2 =      0.000000     30.000000      0.000000 Ang
u_3 =      0.000000      0.000000      4.262580 Ang

+----------------------------------------------------------+
| Bulk: Cartesian (Angstrom) / fractional                  |
+----------------------------------------------------------+
16
Bulk
C     1.000000e+01  1.069325e+01  2.841720e+00    0.50000  0.35644  0.66667
C     1.000000e+01  1.192375e+01  3.552150e+00    0.50000  0.39746  0.83333
C     1.000000e+01  1.069325e+01  1.420860e+00    0.50000  0.35644  0.33333
C     1.000000e+01  1.315425e+01  2.841720e+00    0.50000  0.43847  0.66667
C     1.000000e+01  1.438475e+01  3.552150e+00    0.50000  0.47949  0.83333
C     1.000000e+01  1.192375e+01  7.104300e-01    0.50000  0.39746  0.16667
C     1.000000e+01  1.315425e+01  1.420860e+00    0.50000  0.43847  0.33333
C     1.000000e+01  1.561525e+01  2.841720e+00    0.50000  0.52051  0.66667
C     1.000000e+01  1.684575e+01  3.552150e+00    0.50000  0.56153  0.83333
C     1.000000e+01  1.438475e+01  7.104300e-01    0.50000  0.47949  0.16667
C     1.000000e+01  1.561525e+01  1.420860e+00    0.50000  0.52051  0.33333
C     1.000000e+01  1.807625e+01  2.841720e+00    0.50000  0.60254  0.66667
C     1.000000e+01  1.930675e+01  3.552150e+00    0.50000  0.64356  0.83333
C     1.000000e+01  1.684575e+01  7.104300e-01    0.50000  0.56153  0.16667
C     1.000000e+01  1.807625e+01  1.420860e+00    0.50000  0.60254  0.33333
C     1.000000e+01  1.930675e+01  7.104300e-01    0.50000  0.64356  0.16667
+------------------------------------------------------------------------------+
| Automatically detected repetitions = [1 1 5]                                 |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Geometry optimization using the LBFGS optimizer                              |
| Bravais Lattice: Unit Cell                                                   |
| External pressure: 0.000 GPa                                                 |
+------------------------------------------------------------------------------+
|       Step Step Length      Volume  Max. Force  Stress Error        Enthalpy |
|                  (Ang)    (Ang**3)    (eV/Ang)         (GPa)            (eV) |
+------------------------------------------------------------------------------+
| OPT      0  0.0000e+00    2557.548  5.5243e+00       0.83145     -121.497730 |
| OPT      1  9.2472e-02    2558.753  5.3353e+00       2.68902     -122.713293 |
| OPT      2  2.8905e-02    2560.234  1.3066e+00       2.06302     -123.296440 |
| OPT      3  1.6400e-02    2561.853  8.5016e-01       2.16680     -123.399393 |
| OPT      4  4.3608e-02    2566.991  5.1449e-01       2.13606     -123.513356 |
| OPT      5  5.6166e-02    2573.608  6.4237e-01       2.11419     -123.590251 |
| OPT      6  1.5705e-01    2592.110  7.8095e-01       1.88566     -123.751844 |
| OPT      7  4.1238e-02    2596.969  1.8093e+00       1.36723     -123.837476 |
| OPT      8  2.0723e-02    2599.410  5.6559e-01       1.46715     -123.885159 |
| OPT      9  2.8268e-03    2599.742  3.1653e-01       1.46115     -123.899648 |
| OPT     10  3.2920e-02    2603.620  3.6119e-01       1.39116     -123.939097 |
| OPT     11  9.4446e-02    2614.747  8.3807e-01       1.18355     -124.012071 |
| OPT     12  6.3825e-03    2615.499  4.5679e-01       1.24264     -124.037156 |
| OPT     13  6.4570e-03    2616.260  2.0636e-01       1.19434     -124.046906 |
| OPT     14  2.8009e-02    2619.560  3.0971e-01       1.08235     -124.068346 |
| OPT     15  4.8660e-02    2625.293  5.1829e-01       0.95292     -124.096410 |
| OPT     16  1.5392e-01    2643.426  7.7098e-01       0.59868     -124.169607 |
| OPT     17  9.0755e-03    2644.037  9.1345e-01       0.75792     -124.197892 |
| OPT     18  3.5366e-03    2644.453  1.9246e-01       0.68689     -124.212586 |
| OPT     19  5.2099e-03    2645.067  1.1090e-01       0.65509     -124.216511 |
| OPT     20  9.1618e-03    2646.146  1.6924e-01       0.62024     -124.220626 |
| OPT     21  3.1811e-02    2649.894  3.1806e-01       0.53683     -124.231473 |
| OPT     22  7.5396e-02    2658.777  4.3653e-01       0.38509     -124.252428 |
| OPT     23  1.4255e-01    2675.572  7.4041e-01       0.05542     -124.276380 |
| OPT     24  1.3229e-01    2691.157  6.1915e-01       0.13664     -124.283709 |
| OPT     25  5.3963e-02    2684.800  1.5280e-01       0.02938     -124.296767 |
| OPT     26  8.1788e-03    2683.836  4.7432e-02       0.00456     -124.297950 |
| OPT     27  1.5293e-03    2684.016  8.5408e-03       0.00130     -124.298067 |
+------------------------------------------------------------------------------+
| Geometry optimization converged in 27 steps.                                 |
+------------------------------------------------------------------------------+
+----------------------------------------------------------+
| Bulk Bravais lattice                                     |
+----------------------------------------------------------+
Type:
UnitCell

Lattice constants:

Primitive vectors:
u_1 =     20.000000      0.000000      0.000000 Ang
u_2 =      0.000000     30.000000      0.000000 Ang
u_3 =      0.000000      0.000000      4.473361 Ang

+----------------------------------------------------------+
| Bulk: Cartesian (Angstrom) / fractional                  |
+----------------------------------------------------------+
16
Bulk
C     1.000000e+01  1.085563e+01  2.880052e+00    0.50000  0.36185  0.64382
C     1.000000e+01  1.186827e+01  3.787804e+00    0.50000  0.39561  0.84675
C     1.000000e+01  1.085563e+01  1.593309e+00    0.50000  0.36185  0.35618
C     1.000000e+01  1.313061e+01  2.987488e+00    0.50000  0.43769  0.66784
C     1.000000e+01  1.438038e+01  3.735839e+00    0.50000  0.47935  0.83513
C     1.000000e+01  1.186827e+01  6.855571e-01    0.50000  0.39561  0.15325
C     1.000000e+01  1.313061e+01  1.485873e+00    0.50000  0.43769  0.33216
C     1.000000e+01  1.561962e+01  2.974202e+00    0.50000  0.52065  0.66487
C     1.000000e+01  1.686939e+01  3.722553e+00    0.50000  0.56231  0.83216
C     1.000000e+01  1.438038e+01  7.375217e-01    0.50000  0.47935  0.16487
C     1.000000e+01  1.561962e+01  1.499159e+00    0.50000  0.52065  0.33513
C     1.000000e+01  1.813173e+01  2.922237e+00    0.50000  0.60439  0.65325
C     1.000000e+01  1.914437e+01  3.829989e+00    0.50000  0.63815  0.85618
C     1.000000e+01  1.686939e+01  7.508077e-01    0.50000  0.56231  0.16784
C     1.000000e+01  1.813173e+01  1.551123e+00    0.50000  0.60439  0.34675
C     1.000000e+01  1.914437e+01  6.433717e-01    0.50000  0.63815  0.14382

2
General Questions and Answers / Re: Phonon Dispersion Spectrum of GNR (Geometry optimization and mode separation)
« on: April 24, 2019, 16:18 »
# -*- coding: utf-8 -*-
# -------------------------------------------------------------
# Bulk Configuration
# -------------------------------------------------------------

# Set up lattice
vector_a = [20.0, 0.0, 0.0]*Angstrom
vector_b = [0.0, 30.0, 0.0]*Angstrom
vector_c = [0.0, 0.0, 4.26258]*Angstrom
lattice = UnitCell(vector_a, vector_b, vector_c)

# Define elements
elements = [Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon,
            Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon]

# Define coordinates
fractional_coordinates = [[ 0.5           ,  0.356441566891,  0.666666666667],
                          [ 0.5           ,  0.397458262065,  0.833333333333],
                          [ 0.5           ,  0.356441566891,  0.333333333333],
                          [ 0.5           ,  0.438474957239,  0.666666666667],
                          [ 0.5           ,  0.479491652413,  0.833333333333],
                          [ 0.5           ,  0.397458262065,  0.166666666667],
                          [ 0.5           ,  0.438474957239,  0.333333333333],
                          [ 0.5           ,  0.520508347587,  0.666666666667],
                          [ 0.5           ,  0.561525042761,  0.833333333333],
                          [ 0.5           ,  0.479491652413,  0.166666666667],
                          [ 0.5           ,  0.520508347587,  0.333333333333],
                          [ 0.5           ,  0.602541737935,  0.666666666667],
                          [ 0.5           ,  0.643558433109,  0.833333333333],
                          [ 0.5           ,  0.561525042761,  0.166666666667],
                          [ 0.5           ,  0.602541737935,  0.333333333333],
                          [ 0.5           ,  0.643558433109,  0.166666666667]]

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

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

potentialSet = Tersoff_C_2010()
calculator = TremoloXCalculator(parameters=potentialSet)
calculator.setVerletListsDelta(0.25*Angstrom)

bulk_configuration.setCalculator(calculator)
nlprint(bulk_configuration)
bulk_configuration.update()
nlsave('Phonon_AGNR_W8.hdf5', bulk_configuration)

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

potentialSet = Tersoff_C_2010()
calculator = TremoloXCalculator(parameters=potentialSet)
calculator.setVerletListsDelta(0.25*Angstrom)

bulk_configuration.setCalculator(calculator)
nlprint(bulk_configuration)
nlsave('Phonon_AGNR_W8.hdf5', bulk_configuration)

# -------------------------------------------------------------
# Dynamical Matrix
# -------------------------------------------------------------
dynamical_matrix = DynamicalMatrix(
    bulk_configuration,
    filename=u'Phonon_AGNR_W8.hdf5',
    object_id='dynamical_matrix',
    repetitions=Automatic,
    atomic_displacement=0.01*Angstrom,
    acoustic_sum_rule=True,
    finite_difference_method=Central,
    force_tolerance=1e-08*Hartree/Bohr**2,
    processes_per_displacement=1,
    log_filename_prefix='forces_displacement_',
    use_wigner_seitz_scheme=False,
    )
dynamical_matrix.update()

# -------------------------------------------------------------
# Optimize Geometry
# -------------------------------------------------------------

constraints = [FixStrain(x=True, y=True, z=False)]

bulk_configuration = OptimizeGeometry(
    bulk_configuration,
    max_forces=0.01*eV/Ang,
    max_stress=0.0001*eV/Ang**3,
    max_steps=200,
    max_step_length=0.2*Ang,
    constraints=constraints,
    trajectory_filename=None,
    optimizer_method=LBFGS(),
    constrain_bravais_lattice=False,
)
nlsave('Phonon_AGNR_W8.hdf5', bulk_configuration)
nlprint(bulk_configuration)

# -------------------------------------------------------------
# Phonon Bandstructure
# -------------------------------------------------------------
phonon_bandstructure = PhononBandstructure(
    configuration=bulk_configuration,
    dynamical_matrix=dynamical_matrix,
    route=['G', 'Z'],
    points_per_segment=100,
    number_of_bands=All
    )
nlsave('Phonon_AGNR_W8.hdf5', phonon_bandstructure)

3
General Questions and Answers / Phonon Dispersion Spectrum of GNR (Geometry optimization and mode separation)
« on: April 24, 2019, 02:55 »
Dear all,

I am trying to calculate the phonon spectrum of a 8-dimer armchair graphene nanoribbon by following the example given by: https://docs.quantumwise.com/tutorials/phonon_calcs/phonon_calcs.html.

1. I want to optimize the geometry of the GNR and followed the exact procedure in the tutorial, but ended up with the error messages says: "The underlying configuration must be equal for the input  DynamicMatrix and the object being calculated.".

2. I want to seperate the phonon spectrum calculated into longitudinal, transverse, and flexural modes. Has anyone done this before?

Thank you for your time!

4
General Questions and Answers / Re: Output the Electron Phonon Scattering Rate in Graphene Nanoribbons
« on: March 6, 2019, 17:21 »
Quote from: Ulrik G. Vej-Hansen on March  1, 2019, 08:48
Sounds like you need the method .inverseRelaxationTime(), which can be invoked in a script - see the manual page for more details: https://docs.quantumatk.com/manual/Types/Mobility/Mobility.html

Does it look like the properties you need?

Dear Dr. Vej-Hansen,

I also have a problem when trying to run the mobility_isotropic_scattering_rate2.py code in the link you provided.

I got an error message says "The length of inverse_relaxation_time'  does not match the length of 'energies'". However, I check the code and found they have the same length which is 100.

I don't know what do I need to change for the parameters in the script and need your help on this problem.

Thank you for your time!

Best,
Ji

5
General Questions and Answers / Re: Output the Electron Phonon Scattering Rate in Graphene Nanoribbons
« on: March 6, 2019, 16:12 »
Quote from: Ulrik G. Vej-Hansen on March  1, 2019, 08:48
Sounds like you need the method .inverseRelaxationTime(), which can be invoked in a script - see the manual page for more details: https://docs.quantumatk.com/manual/Types/Mobility/Mobility.html

Does it look like the properties you need?

Dear Dr. Vej-Hansen,

I have calculated the electron-phonon coupling matrix terms and they can be shown in the Electron Phonon Coupling Analyzer. I would like to output the data that is stored in the hdf5 file and rearrange it into matrices to be used in Matlab.

I used HDFView to access the directory in the HDF5 file and think the e-ph coupling matrix should be under the directory of ElectronPhononCoupling/Coupling Matrix Block Basis.

Would you please help me on output the data of the e-ph coupling matrix terms?

Thank you for your time!
Ji

6
General Questions and Answers / Re: Output the Electron Phonon Scattering Rate in Graphene Nanoribbons
« on: March 1, 2019, 21:05 »
Quote from: Ulrik G. Vej-Hansen on March  1, 2019, 08:48
Sounds like you need the method .inverseRelaxationTime(), which can be invoked in a script - see the manual page for more details: https://docs.quantumatk.com/manual/Types/Mobility/Mobility.html

Does it look like the properties you need?

Dear Dr. Vej-Hansen,

Thank you for your information!

It looks like the .inverseRelaxationTime() is the scattering rate that I am interested in.  In the link you offered, the energy-dependent inverse relaxation time/scattering rate will be calculated.

I will try following the example in the link and see how the result goes.

Thank you!
Ji

7
General Questions and Answers / Output the Electron Phonon Scattering Rate in Graphene Nanoribbons
« on: February 28, 2019, 16:30 »
Dear all,

I am interested in calculating the electron phonon scattering rate for each possible scattering event in a metallic 10-dimer wide zigzag graphene  nanoribbon. I have followed the tutorial in this link: https://docs.quantumatk.com/tutorials/mobility/mobility.html but did not get the information about the scattering rate/inverse relaxation time information from the VNL lab floor.

Does anyone know how to output the data for the scattering rate for each possible scattering event from the hdf5 file?

Thank you!

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