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Messages - baizq

Pages: [1] 2 3 ... 7
1
Questions and Answers / Re: ionic dielectric constant
« on: July 23, 2021, 11:16 »
Thank you Anders. I have a couple of quuestions regarding the SiO2 tutorial in the webpage you suggested.

1. In the optical spectrum session, huge number of bands are used (1000 bands above the fermi level and 1000 below). Why we need so many bands for such calculation?

2. In the DFT calculator setup, occupation_method is set as FermiDirac(100.0*Kelvin*boltzmann_constant). Why electron temperature is set to low value?

2
Questions and Answers / ionic dielectric constant
« on: July 20, 2021, 10:05 »
Dear All,

May I know how to calculate the ionic contribution to dielectric constant of materials? I have noticed that there is Optical spectrum functionality which returns dielectric tensor; but I guess this is just for the electronic contribution (correct me if I am wrong). Thanks !

Regards,
baizq

3
Questions and Answers / error in the output nc file
« on: September 6, 2016, 22:56 »
Dear All,

I did a collinear calculation with fully relativistic pseudopotentials OMX-GGA.PBE (script attached) for a FePt system. There seemed to be some error in the output nc file: When I use VNL or nlread command to read in this nc file, the error message showed up:

Code
"The following error was generated during execution of the program: unexpected indent (, line 6) If the message is not clear or the error is caused by VNL itself, please report the issue to QuantumWise, and make sure to include the traceback (click "Show Details...") 
Traceback (most recent call last):
  File "./zipdir/NL/GUI/MainWindow/LabFloor/LabFloorModel.py", line 234, in load
  File "/home/bai_z/QuantumWise/VNL-ATK-2016/lib/python2.7/site-packages/AddOns/ATKNCImporter/ATKNCImporter.py", line 96, in load
    data = nlread(filename, object_id=object_id, read_state=read_full)[0]
  File "./zipdir/NL/IO/NLSaveUtilities.py", line 422, in nlread
  File "./zipdir/NL/ComputerScienceUtilities/Timer.py", line 45, in __call__
  File "./zipdir/NL/IO/NLSaveUtilities.py", line 422, in <lambda>
  File "./zipdir/NL/CommonConcepts/Configurations/ReadConfigurations.py", line 121, in nlreadBulkConfiguration
  File "./zipdir/NL/NanoLanguage/ScopeExecuter.py", line 214, in scope_execute
NLScopeExecutionError: unexpected indent (<string>, line 6)
"

But when I keep everything exactly the same except changing the pseudopotential to FHI-GGA.PBE, such error was eliminated. I am wondering whether there is anything wrong here.

Best,
baizq

4
Questions and Answers / Magnetic Anisotropy Calculation
« on: August 30, 2016, 18:49 »
A quick question: Is there a tutorial that talks about how to calculate magnetic anisotropy of bulks/films by ATK? If no, could anyone help to list a general procedure for calculating magnetic anisotropy? Thanks in advance!

baizq

5
Hi All,

Is there a way to calculate the exchange coupling constant between any pairs of atoms in a magnetic bulk system? E.g., If I have a Iron bulk system, how could I know the exchange coupling between the nearest neighbors, the second nearest neighbors, and so on? Thank you in advance.

baizq

6
Questions and Answers / export Fermi energy
« on: April 6, 2016, 02:17 »
Dear All,

How to export Fermi energy from a bulk calculation? I found there was a function from very old version.

http://quantumwise.com/documents/manuals/ATK-2008.10/ref.calculatefermienergy.html

Quote
from ATK.KohnSham import *
...
dft_calculation = dft_method.apply(water_molecule)
energy = calculateFermiEnergy( dft_calculation )
print "Fermi energy = %g eV" % ( energy.inUnitsOf(eV) )

But it does not work now.

Thanks,
baizq

7
Hi Ulrik,

Thank you for your answers.

We could reduce the thickness top XY layer to half in the model. Also there are EAM potentials available for the combination of X, Y and Z. Would this make it possible to simulate the diffusion?

Code
# -------------------------------------------------------------
# AKMC
# -------------------------------------------------------------
saddle_search_parameters = SaddleSearchParameters(max_neb_images=5)
markov_chain = MarkovChain(bulk_configuration, TotalEnergy(bulk_configuration).evaluate())
akmc = AdaptiveKineticMonteCarlo(markov_chain,
                                 kmc_temperature=300.0*Kelvin,
                                 md_temperature=2000*Kelvin,
                                 calculator=calculator,
                                 saddle_search_parameters=saddle_search_parameters,
                                 write_searches=True,
                                 constraints=constraints,
                                 confidence=0.95)
akmc.run(50)

I have not used the AKMC solver much. There are no much explanations of this script as well. Could you please also advise me which functions/parameters should I modify for such a calculation?

baizq

8
Deal All,

Can we simulate atomic diffusion in solids using Monte Carlo simulation?

I have noticed a couple of tutorials talking about AKMC simulation of  Pt diffusion on Pt surface

http://quantumwise.com/publications/tutorials/item/872-adaptive-kinetic-monte-carlo-simulation-of-pt-on-pt-100
http://quantumwise.com/publications/tutorials/item/879-adaptive-kinetic-monte-carlo-simulation-of-pt-island-ripening

But my picture is a bit different. My system is a bilayer XY:Z(1nm)/XY(8nm) stack, where Z is metallic dopant to the lower 1nm XY alloy region. The upper layer (8nm) of XY is free of Z at the beginning.  We observe that, the more we increase the temperature, the more of Z diffuse to the the upper XY region. We would like to understand the temperature effect.

Is the current implementation in ATK able to tackle this simulation? Thank you in advance.

baizq

9
Questions and Answers / constrained Monte Carlo simulation
« on: March 17, 2016, 02:31 »
Hi All,

I just went through the tutorial of AKMC simulation of Pt diffusion on Pt surface. Is there a way to constrain the final configuration (may not be lowest energy or most stable ) so that we can see the path for the system to evolve from initial to final configurations, just as what the so called constrained MC does.

For example, for the Pt diffusion on Pt surface case, the results of example just have a few paths of diffusion across the surface. Is there anyway to force the Pt to penetrate the surface into Pt slab (by constrain the final configuration to be Pt inside Pt slab)?

Thanks in advance.

baizq

10
Hi Julian and All,

Thanks for the reply, Julian. I have read that PRB paper and also know the potential is already implemented as EAM_Zhou_2004 in ATK.

I am trying to simulate a similar growth process of a bilayer metal stack. The bottom layer is XY:Z (XY is a binary metallic alloy, where 10% X is randomly substituted by metal element Z), whereas the upper layer is pure XY. In experiment, we heat up the bottom layer XY:Z to around 500 K and grow the upper layer XY on top of it. It has been observed that significant amount of Z diffuse from the bottom layer into deep upper layer upon PVD growth. The diffusion is not observed in room temperature. We would like to understand the temperature effect on such growth and interdiffusion.

I am not an MD expert. Just keen to know whether  EAM_Zhou_2004 (all X, Y, Z elements are availaibe in this EAM potential ) or any other potentials available can be used to simulate the growth and interdiffusion process. Should we couple the bottom-layer of XY:Z to a Nose-Hoover chain thermostat of 500K, and leave the deposited atom in an NVE ensemble? I tried a similar calculation that grows amorphous carbon onto a diamond carbon template and did not see any diffusion of atom from "substrate" into the deposited layer. I am just worrying whether Z in XY:Z substrate would diffuse or not.

Any suggestion or comments would be appreciated. Thanks in advance.

baizq

11
Questions and Answers / Re: Estimate the convergence of NEB
« on: March 2, 2016, 20:15 »
Thank you, Jess. Sure, I have sent you the script.

12
Questions and Answers / Re: Estimate the convergence of NEB
« on: February 29, 2016, 20:03 »
The calculation is ongoing, giving out further odd results as follows. The number of max. energy image goes to zero, so does the max. energy. May I know whether this is a bug?


|       87     2.090e-02     3.245e-01                  4       0.133771      |
|        88     1.935e-02     3.313e-01                  4       0.118799      |
|        89     4.415e-02     4.111e-01                  4       0.092446      |
|        90     7.824e-02     1.277e+00                  3       0.050403      |
|        91     3.060e-02     1.084e+00                  3       0.050471      |
|        92     5.522e-02     4.922e-01                  4       0.057512      |
|        93     4.411e-02     4.008e-01                  4       0.047241      |
|        94     8.345e-02     5.668e-01                  0       0.000000      |
|        95     1.268e-01     9.273e-01                  0       0.000000      |
|        96     5.342e-02     2.655e+00                  0       0.000000      |
|        97     1.153e-01     2.513e+00                  0       0.000000      |
|        98     9.663e-02     3.551e+00                  0       0.000000      |

13
Questions and Answers / Re: Estimate the convergence of NEB
« on: February 29, 2016, 19:35 »
A further question: is there a way to resume an NEB calculation from nc file?

14
Questions and Answers / Re: Estimate the convergence of NEB
« on: February 29, 2016, 18:38 »
Thank you, Jess. Does that mean if we observe steady decrease of maximum energy, though the maximum force and the step length fluctuate, we should be positive and look forward to a convergence?

15
Questions and Answers / Estimate the convergence of NEB
« on: February 29, 2016, 06:02 »
I have very limited experience with NEB calculation. Just would like to know how one usually estimate (based on the runtime output) whether a NEB will achieve convergence or not. For example, if the output is as follows, should we expect a convergence or just give up?

| NEB Optimization using the LBFGS optimizer                                   |
+------------------------------------------------------------------------------+
| Iteration   Step Length    Max. Force  Max. Energy Image    Max. Energy      |
+------------------------------------------------------------------------------+
|         0     0.000e+00     8.290e+00                  3       4.074025      |
|         1     1.677e-01     1.750e+00                  3       2.338270      |
|         2     5.741e-02     1.806e+00                  3       2.006154      |
|         3     7.919e-02     1.724e+00                  3       1.740350      |
|         4     1.725e-01     1.884e+00                  4       1.449709      |
|         5     1.772e-01     2.875e+00                  3       1.344200      |
|         6     9.295e-02     1.463e+00                  4       1.175542      |
|         7     1.124e-01     1.656e+00                  4       1.041492      |
|         8     1.060e-01     1.814e+00                  3       0.952107      |
|         9     8.552e-02     1.329e+00                  3       0.839494      |
|        10     5.592e-02     2.038e+00                  4       0.849147      |
|        11     4.137e-02     9.464e-01                  4       0.726946      |
|        12     1.717e-01     2.818e+00                  5       0.636764      |
|        13     6.338e-02     1.331e+00                  5       0.629938      |
|        14     8.958e-02     1.144e+00                  5       0.601600      |
|        15     1.613e-01     1.488e+00                  5       0.554602      |
|        16     1.832e-01     1.961e+00                  5       0.532888      |
|        17     1.883e-01     1.876e+00                  5       0.532621      |
|        18     1.609e-01     2.334e+00                  4       0.520117      |
|        19     1.114e-01     3.481e+00                  5       0.434571      |
|        20     7.493e-02     4.892e+00                  5       0.449733      |
|        21     1.290e-01     2.424e+00                  5       0.438712      |
|        22     1.147e-01     7.662e+00                  5       0.402852      |
|        23     7.109e-02     1.921e+00                  5       0.392863      |
|        24     5.848e-02     1.709e+00                  5       0.380071      |
|        25     1.549e-01     1.580e+00                  4       0.381998      |
|        26     1.625e-01     2.766e+00                  4       0.382241      |
|        27     6.413e-02     2.175e+00                  4       0.393642      |
|        28     5.137e-02     1.453e+00                  4       0.365978      |
|        29     1.266e-01     2.768e+00                  4       0.352593      |
|        30     4.086e-02     9.296e-01                  4       0.348628      |
|        31     1.287e-01     1.989e+00                  4       0.339829      |
|        32     4.591e-02     1.452e+00                  4       0.340066      |
|        33     7.947e-02     9.345e-01                  4       0.341770      |
|        34     1.462e-01     1.747e+00                  4       0.353379      |
|        35     1.292e-01     3.906e+00                  4       0.381371      |
|        36     6.650e-02     2.056e+00                  4       0.378206      |
|        37     8.992e-02     7.477e-01                  4       0.372127      |
|        38     5.721e-02     4.661e-01                  4       0.361421      |
|        39     7.983e-02     7.730e-01                  4       0.342288      |
|        40     4.963e-02     8.188e-01                  4       0.324326      |
|        41     4.704e-02     8.541e-01                  4       0.306461      |
|        42     8.092e-02     8.304e-01                  4       0.292080      |
|        43     9.223e-02     9.421e-01                  4       0.287996      |
|        44     3.542e-02     6.786e-01                  4       0.286875      |
|        45     6.534e-02     6.013e-01                  4       0.281882      |
|        46     7.977e-02     7.766e-01                  4       0.291941      |
|        47     8.681e-02     5.456e-01                  4       0.289363      |
|        48     5.494e-02     5.299e-01                  3       0.288635      |
|        49     3.637e-02     5.101e-01                  3       0.273450      |
|        50     3.460e-02     5.031e-01                  4       0.267689      |
|        51     6.985e-02     9.933e-01                  4       0.265413      |
|        52     2.029e-02     5.936e-01                  4       0.264947      |
|        53     3.018e-02     3.944e-01                  4       0.262447      |
|        54     3.141e-02     2.750e-01                  4       0.258681      |
|        55     4.305e-02     2.439e-01                  4       0.256390      |
|        56     7.651e-02     3.663e-01                  4       0.257563      |
|        57     2.460e-02     2.903e-01                  4       0.251078      |
|        58     7.070e-02     2.161e-01                  4       0.251786      |
|        59     3.378e-02     3.596e-01                  4       0.252871      |
|        60     1.819e-02     2.611e-01                  4       0.251387      |
|        61     1.766e-02     1.481e-01                  4       0.251193      |
|        62     1.322e-02     1.567e-01                  4       0.250207      |
|        63     2.475e-02     1.361e-01                  4       0.249766      |
|        64     3.006e-02     2.371e-01                  4       0.250092      |
|        65     7.935e-03     1.005e-01                  4       0.248043      |
|        66     7.304e-03     9.936e-02                  4       0.246630      |
|        67     2.141e-02     1.508e-01                  4       0.244856      |
|        68     4.312e-02     4.002e-01                  4       0.242708      |
|        69     5.923e-02     6.326e-01                  4       0.241984      |
|        70     6.366e-02     6.439e-01                  4       0.241400      |
|        71     5.622e-02     8.051e-01                  4       0.238383      |
|        72     1.006e-01     6.955e-01                  5       0.256355      |
|        73     3.685e-02     4.516e-01                  4       0.237830      |
|        74     4.681e-02     3.641e-01                  4       0.232630      |
|        75     4.393e-02     5.761e-01                  4       0.224798      |
|        76     7.176e-02     1.222e+00                  5       0.260728      |
|        77     5.037e-02     7.388e-01                  5       0.225165      |
|        78     4.955e-02     3.884e-01                  4       0.218996      |
|        79     1.978e-02     3.305e-01                  4       0.212795      |
|        80     3.705e-02     3.893e-01                  4       0.204375      |
|        81     1.532e-02     4.015e-01                  4       0.201892      |
|        82     1.262e-02     3.243e-01                  4       0.197980      |
|        83     1.170e-02     2.455e-01                  4       0.194299      |
|        84     6.470e-02     5.046e-01                  5       0.182382      |
|        85     4.025e-02     6.853e-01                  5       0.163395      |
|        86     2.841e-02     7.090e-01                  4       0.151578      |

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