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Topics - baizq

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1
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

2
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

3
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

4
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

5
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

6
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

7
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

8
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      |

9
Dear All,

I recently saw a paper (PRB 69, 144113 (2004)) which describes an MD simulation (using EAM potential) of vapor-deposition of CoFe/NiFe/CoFe multilayer on a Cu substrate. The main idea is to throw "hot" atoms onto the substrate at a specific rate, and let MD to determine the final position of the atoms.

This is an old work published more than 10 years ago. Just wondering whether/how we are able to model this with ATK.

Thanks,
baizq

10
Questions and Answers / NEB path
« on: January 28, 2016, 18:41 »
Dear all,

I would like to set up an NEB path between two geometries (in both geometries there is a MgO slab with one oxygen vacancy inside. A carbon atom is diffusing from the surface (initial) into the vacancy in the slab (final)). However, when I put the two geometries into the VNL NEB builder, it complains "invalid". I have tried both relaxed and unrelaxed pairs.

Could anyone suggest me what happens here and how to solve the problem? I have attached the relaxed geometries for your reference.

Thanks in advance!
baizq

11
Questions and Answers / dissociation temperature of solids
« on: January 27, 2016, 02:50 »
Hi All,

We are recently looking into the dissociation temperature of a few solids (amorphous). Anyone knows whether there is a way to calculate it with ATK? Thanks in advance

Best,
baizq

12
Hi All,

I was trying to do a phonon transport calculation on a gold/vacuum/carbon system while encountering an error at the phonon transport step after dynamic matrix calculation had been done:

** Back Engine Exception : Dimension mismatch
** Location of Exception : complexmatrix.cpp:319

1. Does anyone have an idea what the problem is? I tried a similar system of gold/vacuum/gold and the problem did not appear.

2. How could one resume a phonon calculation from the previous calculation where the dynamic matrix is available?

I have attached the phonon transport script for your reference.

Thanks,
baizq

13
General Questions / generating gif movie
« on: November 9, 2015, 20:52 »
Hi All,

I am trying to generate an animation gif file for the relaxation process of a system from the nc file. Although it says "generating movie - please wait", it does not generate a movie at all even after several hours waiting

May I know whether it is a bug? I am running VNL 15.0 on Ubuntu 14.04.

Thanks,
baizq

14
Questions and Answers / comb potential
« on: October 23, 2015, 02:24 »
Dear ATK developers,

I find from the ATK 2015 release note that the COMB classic potential is available. However, in the reference manual, no information about COMB is included. May I know whether there is any way to use this potential?

In addition, is there a way to use semi-empirical potential for MD calculation?

Thank you,
baizq

15
Dear all,

I remember that, in some previous version (maybe ver 2008.x), it is possible to extract isovalues of transmission eigenstates using VNL for plotting with other software. Is the functionality still available in the current versions (ver. 12.x)? Or is there any other way for the extraction?

Thanks&regards,
baizq

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