1
General Questions and Answers / Re: How to export graphic of bandstructure in given size?
« on: April 1, 2015, 10:22 »
Export the Bandstructure figure in EPS format and modify it by Adobe illustrator and so on.
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2
News and Announcements / 最新バージョンVNL-ATK-2014.1がリリースされました
« on: October 28, 2014, 10:04 »
各位
2014年10月最新バージョンVNL-ATK-2014.1がリリースされました。
最新バージョンではATK-Classicalのリリース、スピン軌道相互作用の考慮、計算スピードの改善、
VASPインターフェースなど多数の新機能を搭載しております。
新機能に関する詳細はこちら
http://quantumwise.co.jp/products/atk/release2014.1.html
をご覧ください。
以上
2014年10月最新バージョンVNL-ATK-2014.1がリリースされました。
最新バージョンではATK-Classicalのリリース、スピン軌道相互作用の考慮、計算スピードの改善、
VASPインターフェースなど多数の新機能を搭載しております。
新機能に関する詳細はこちら
http://quantumwise.co.jp/products/atk/release2014.1.html
をご覧ください。
以上
3
General Questions and Answers / Re: Optimization of two probe system
« on: October 6, 2014, 05:31 »
The energy of the system depends on several factors of the system you define.
I do not think one can specify a common reference energy.
I do not think one can specify a common reference energy.
4
General Questions and Answers / Re: Optimization of two probe system
« on: October 6, 2014, 04:37 »
You should choose a good initial structure to get a good final optimized structure.
for example
1. Optimize the molecule part.
2. Make bulk like structure like [Au-bulk]-Molecule-[Au-bulk] with optimized molecule
3. Change the Au-Molecule distance, calculate the total energy. And you can find the best distance between Au surfaces and S atoms.
4. Using the lowest energy structure of 3, make 2prove structure.
5 Starting with 4 structure start the optimization of 2 probe.
for example
1. Optimize the molecule part.
2. Make bulk like structure like [Au-bulk]-Molecule-[Au-bulk] with optimized molecule
3. Change the Au-Molecule distance, calculate the total energy. And you can find the best distance between Au surfaces and S atoms.
4. Using the lowest energy structure of 3, make 2prove structure.
5 Starting with 4 structure start the optimization of 2 probe.
5
Installation and License Questions / Re: Parallelization problem
« on: September 19, 2014, 02:16 »
Please check the memory usage of the calculation.
When the non-parallel calculation takes 2 GB, the 8-parallel calculation takes 16GB (2*8core).
When the non-parallel calculation takes 2 GB, the 8-parallel calculation takes 16GB (2*8core).
6
General Questions and Answers / Re: Eigenstate viusalize in VNL
« on: June 16, 2014, 08:43 »
Drag & Drop the structure icon to the 3D viewer which displays the eigenstate.
7
General Questions and Answers / Re: Required k-points are not available
« on: June 15, 2014, 03:41 »
I think you should convert your crystal structure to rhombohedral one.
This tutorial will be helpful
http://quantumwise.com/publications/tutorials/mini-tutorials/201.
This tutorial will be helpful
http://quantumwise.com/publications/tutorials/mini-tutorials/201.
8
General Questions and Answers / Re: How to give the bond length for two atoms initial guess value in the interface
« on: May 17, 2014, 04:39 »
I always use a covalent radius of each atom.
9
General Questions and Answers / Re: MOS2 Slater Koster
« on: April 23, 2014, 07:31 »
Your system is periodic in the directions B and C (Y and Z) so please increase ky and kz in SCF and DOS calculation
like
numerical_accuracy_parameters = NumericalAccuracyParameters(
k_point_sampling=(1, 27, 27),
)
(I am not sure k value 27 is the best one)
and
density_of_states = DensityOfStates(
configuration=bulk_configuration,
kpoints=MonkhorstPackGrid(1,101,101),
energy_zero_parameter=FermiLevel,
bands_above_fermi_level=None,
)
Usually we need lager values of ks in DOS calculation than SCF's ones.
like
numerical_accuracy_parameters = NumericalAccuracyParameters(
k_point_sampling=(1, 27, 27),
)
(I am not sure k value 27 is the best one)
and
density_of_states = DensityOfStates(
configuration=bulk_configuration,
kpoints=MonkhorstPackGrid(1,101,101),
energy_zero_parameter=FermiLevel,
bands_above_fermi_level=None,
)
Usually we need lager values of ks in DOS calculation than SCF's ones.
10
General Questions and Answers / Re: Bandgap vs. DOS curve
« on: April 8, 2014, 02:36 »
Dear Hassan
Try to increase k point value of Z direction like
dos = DensityOfStates(
configuration=configuration_obj,
kpoints=MonkhorstPackGrid(1,1,101),
bands_above_fermi_level=5,
energy_zero_parameter=FermiLevel,
)
In my experience it should be over one hundred to get good result.
And kx, ky should be one because the direction is not periodic.
BR
Try to increase k point value of Z direction like
dos = DensityOfStates(
configuration=configuration_obj,
kpoints=MonkhorstPackGrid(1,1,101),
bands_above_fermi_level=5,
energy_zero_parameter=FermiLevel,
)
In my experience it should be over one hundred to get good result.
And kx, ky should be one because the direction is not periodic.
BR
11
News and Announcements / Seebeck係数シミュレーション用の日本語チュートリアルを掲載しました【2014年2月12日】
« on: February 12, 2014, 10:35 »
お客様各位
Atomistix ToolKitを用いて熱電変換素子性能を示す数値的な指標の一つであるSeebeck係数をシミュレーション
するためのチュートリアルをWeb上にUpしました。本チュートリアルではグラフェンのゼーベック係数の解析手法を紹介します。
この結果は東京理科大学工学部山本研究室とQuantumWise Japan株式会社の共同研究により発表した論文
Jpn. J. Appl. Phys. 52, 06GD05 (2013).の一部を再現します。
チュートリアルのダウンロードは
http://quantumwise.co.jp/member_only/document/tutorial/TransportCoefficients_eshift.zipから
なおダウンロードにはレジストレーションが必要です。レジストレーションは以下からお願いいたします。
http://quantumwise.co.jp/member_only/regist/
Atomistix ToolKitを用いて熱電変換素子性能を示す数値的な指標の一つであるSeebeck係数をシミュレーション
するためのチュートリアルをWeb上にUpしました。本チュートリアルではグラフェンのゼーベック係数の解析手法を紹介します。
この結果は東京理科大学工学部山本研究室とQuantumWise Japan株式会社の共同研究により発表した論文
Jpn. J. Appl. Phys. 52, 06GD05 (2013).の一部を再現します。
チュートリアルのダウンロードは
http://quantumwise.co.jp/member_only/document/tutorial/TransportCoefficients_eshift.zipから
なおダウンロードにはレジストレーションが必要です。レジストレーションは以下からお願いいたします。
http://quantumwise.co.jp/member_only/regist/
12
General Questions and Answers / Re: Checking for Correct Optimized Structure
« on: February 6, 2014, 03:42 »
If you want to find a global minimum configuration for a drug like organic compound, just relaxing the structure from
one initial structure is not enough. Because the structure may lie in a local minimum by the optimization procedure.
It is depend on which structure you chose as an initial structure.
You should find a global minimum conformation of the compound, and this method is called "conformational search".
(Please search the word by google)
There are several methods of conformational search, general one will be
1. Find rotatable dihedral bonds in the system.
2. Generate the all structures by changing the values of the dihedral angles in the system
3. Optimize all structures and calculate total energies
4. The structure which has a minimum energy is global minimum configuration.
We hope you find it informative.
one initial structure is not enough. Because the structure may lie in a local minimum by the optimization procedure.
It is depend on which structure you chose as an initial structure.
You should find a global minimum conformation of the compound, and this method is called "conformational search".
(Please search the word by google)
There are several methods of conformational search, general one will be
1. Find rotatable dihedral bonds in the system.
2. Generate the all structures by changing the values of the dihedral angles in the system
3. Optimize all structures and calculate total energies
4. The structure which has a minimum energy is global minimum configuration.
We hope you find it informative.
13
Installation and License Questions / Re: Segmentation fault
« on: January 29, 2014, 02:35 »We have managed to find a temporary work around for this,
so if you want to run ATK or VNL, you will have to set this following environment variable before executing:QuoteLD_PRELOAD="libstdc++.so.6" atkpython my_script.pyorQuoteLD_PRELOAD="libstdc++.so.6" vnl
I could run ATK calculations on CentOS 6.5. Thank you.
14
General Questions and Answers / Re: Geometry optimization 3AGNR repeated 9 times in the z direction
« on: January 10, 2014, 03:59 »Dear Shinji,
Thanks for you promp reply. This was an ultra-narrow graphene nanorribon (not relizable experimentally until now). I set the width to 3 atoms because I could run calculations from seconds to minutes. I will be working however with much wider nanoribbons like 16-AGNR, 30-AGNR or 40-AGNR. In these type of NR the hydrogen atoms are not so close between each other, hence the NR will not experience the twisting phenomena, right?. So my question is .....
Even for wider NR (like 16-AGNR) should I start with C6H4-C6H4 (as you are suggesting me)?
As an electronic engineer I am worried because we do not study this kind of theory and will be very difficult for me to accomplish this (at least not in a short term). If I create the NR with VNL is this still OK, I mean, would I still have good and accurate results?
Regards,
Luis
If you want to calculate wider GNR like 16-AGNR, you do not have to start with two units cell system.
The final structure of wider GNRs will have complete plane structure.
(Ultra narrow 3-AGNR is called polybenzene and we can synthesize it)
BR
Shinji
15
General Questions and Answers / Re: Geometry optimization 3AGNR repeated 9 times in the z direction
« on: January 9, 2014, 10:44 »
Dear Luis M. Villamagua C.
I think your procedure of the optimization is perfect.
However, you will get a complete planar structure when you repeat the optimized one unit -C6H4- group.
Note that if two phenyl rings connect by single bond, the two plains will not lie in the same plane,
because of the repulsion between neighbor Hydrogen atoms.
This is the reason you could not get the optimized structure in the fifth step.
Try to use biphenyl structure -C6H4-C6H4- (two unit cells) in the first step, and you will get a twisted ring
configuration by relaxation. And then repeat the structure as the method you showed.
BR
Shinji
I think your procedure of the optimization is perfect.
However, you will get a complete planar structure when you repeat the optimized one unit -C6H4- group.
Note that if two phenyl rings connect by single bond, the two plains will not lie in the same plane,
because of the repulsion between neighbor Hydrogen atoms.
This is the reason you could not get the optimized structure in the fifth step.
Try to use biphenyl structure -C6H4-C6H4- (two unit cells) in the first step, and you will get a twisted ring
configuration by relaxation. And then repeat the structure as the method you showed.
BR
Shinji