1
General Questions and Answers / Re: 2017.1 Error on AnalysisBar Add-on
« on: September 25, 2017, 14:43 »
OK! I have sent it.
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2
General Questions and Answers / 2017.1 Error on AnalysisBar Add-on
« on: September 25, 2017, 04:37 »
Dear all,
When I plot the transmission eigenstate, there is an error during using the viewer to plot a 3D figure. How can I fix it? The version is 2017.1. Thanks!
My py file:
====================================================
path = 'ivcurve_selfconsistent_configuration_0.30000V.hdf5'
device_configuration = nlread(path, object_id='DeviceConfiguration_0')[0]
transmission_eigenstate = TransmissionEigenstate(
configuration=device_configuration,
energy=0.03*eV,
k_point=[0, 0],
quantum_number=0,
contributions=Left,
energy_zero_parameter=AverageFermiLevel,
)
nlsave('Trans_Eigenstate_E_0.03_vb_0.3_QN_0.hdf5', transmission_eigenstate)
=================================================================
The "hdf5" file is the size of about 215MB.
=================================================================
The error can be found in the attached figure.
Details of the error:
==============================================================
Exception message:
Traceback (most recent call last):
File "zipdir\NL\GUI\MainWindow\AnalysisBar\AnalysisBar.py", line 60, in widget
File "C:\Program Files (x86)\QuantumWise\VNL-ATK-2017.1\Lib\site-packages\AddOns\BasicAnalysis\ViewerPlugin.py", line 84, in createWidget
scene_window._addObjects(object_dict)
File "zipdir\NL\GUI\Tools\Viewer\Viewer.py", line 326, in _addObjects
File "zipdir\NL\GUI\Graphics\GL\Scene\Scene.py", line 812, in addGrid
File "zipdir\NLEngine.py", line 5103, in __init__
NotImplementedError: Wrong number or type of arguments for overloaded function 'new_Cartesian3D'.
Possible C/C++ prototypes are:
Cartesian3D::Cartesian3D()
Cartesian3D::Cartesian3D(double const &,double const &,double const &)
Cartesian3D::Cartesian3D(double const &)
When I plot the transmission eigenstate, there is an error during using the viewer to plot a 3D figure. How can I fix it? The version is 2017.1. Thanks!
My py file:
====================================================
path = 'ivcurve_selfconsistent_configuration_0.30000V.hdf5'
device_configuration = nlread(path, object_id='DeviceConfiguration_0')[0]
transmission_eigenstate = TransmissionEigenstate(
configuration=device_configuration,
energy=0.03*eV,
k_point=[0, 0],
quantum_number=0,
contributions=Left,
energy_zero_parameter=AverageFermiLevel,
)
nlsave('Trans_Eigenstate_E_0.03_vb_0.3_QN_0.hdf5', transmission_eigenstate)
=================================================================
The "hdf5" file is the size of about 215MB.
=================================================================
The error can be found in the attached figure.
Details of the error:
==============================================================
Exception message:
Traceback (most recent call last):
File "zipdir\NL\GUI\MainWindow\AnalysisBar\AnalysisBar.py", line 60, in widget
File "C:\Program Files (x86)\QuantumWise\VNL-ATK-2017.1\Lib\site-packages\AddOns\BasicAnalysis\ViewerPlugin.py", line 84, in createWidget
scene_window._addObjects(object_dict)
File "zipdir\NL\GUI\Tools\Viewer\Viewer.py", line 326, in _addObjects
File "zipdir\NL\GUI\Graphics\GL\Scene\Scene.py", line 812, in addGrid
File "zipdir\NLEngine.py", line 5103, in __init__
NotImplementedError: Wrong number or type of arguments for overloaded function 'new_Cartesian3D'.
Possible C/C++ prototypes are:
Cartesian3D::Cartesian3D()
Cartesian3D::Cartesian3D(double const &,double const &,double const &)
Cartesian3D::Cartesian3D(double const &)
3
Installation and License Questions / Re: error when install 2017: tk wasn't installed properly
« on: July 25, 2017, 14:52 »
Good news!
The installation is successful. But I do not know why, as too many settings I have tried and changed.
The installation is successful. But I do not know why, as too many settings I have tried and changed.
4
Installation and License Questions / Re: error when install 2017: tk wasn't installed properly
« on: July 25, 2017, 12:08 »
It is quite strange. Till now, I can not find out what is wrong. However, the installation of 2016.3 version is quite good.
Here is all my path
C:\>set path
Path=C:\Windows\system32;C:\Windows;C:\Windows\system32\wbem;C:\Program Files (x86)\QuantumWise\LMXTools v4.7.5 for VNL-ATK 2015.1\servertools;C:\ProgramData\Oracle\Java\javapath;C:\Program Files (x86)\CTEX\MiKTeX\miktex/bin\;C:\Program Files (x86)\CTEX\UserData\miktex\bin;C:\Program Files (x86)\CTEX\MiKTeX\miktex\bin;C:\Program Files (x86)\CTEX\CTeX\ctex\bin;C:\Program Files (x86)\CTEX\CTeX\cct\bin;C:\Program Files (x86)\CTEX\CTeX\ty\bin;C:\Program Files (x86)\CTEX\Ghostscript\gs9.05\bin;C:\Program Files (x86)\CTEX\GSview\gsview;C:\Program Files (x86)\CTEX\WinEdt;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Program Files\Intel\WiFi\bin\;C:\Program Files\Common Files\Intel\WirelessCommon\PATHEXT=.COM;.EXE;.BAT;.CMD;.VBS;.VBE;.JS;.JSE;.WSF;.WSH;.MSC
Here is all my path
C:\>set path
Path=C:\Windows\system32;C:\Windows;C:\Windows\system32\wbem;C:\Program Files (x86)\QuantumWise\LMXTools v4.7.5 for VNL-ATK 2015.1\servertools;C:\ProgramData\Oracle\Java\javapath;C:\Program Files (x86)\CTEX\MiKTeX\miktex/bin\;C:\Program Files (x86)\CTEX\UserData\miktex\bin;C:\Program Files (x86)\CTEX\MiKTeX\miktex\bin;C:\Program Files (x86)\CTEX\CTeX\ctex\bin;C:\Program Files (x86)\CTEX\CTeX\cct\bin;C:\Program Files (x86)\CTEX\CTeX\ty\bin;C:\Program Files (x86)\CTEX\Ghostscript\gs9.05\bin;C:\Program Files (x86)\CTEX\GSview\gsview;C:\Program Files (x86)\CTEX\WinEdt;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Program Files\Intel\WiFi\bin\;C:\Program Files\Common Files\Intel\WirelessCommon\PATHEXT=.COM;.EXE;.BAT;.CMD;.VBS;.VBE;.JS;.JSE;.WSF;.WSH;.MSC
5
Installation and License Questions / Re: error when install 2017: tk wasn't installed properly
« on: July 24, 2017, 16:13 »
The error remains.
Here are the outputs
====================================
C:\>echo %PYTHONPATH%
%PYTHONPATH%
C:\>echo %PYTHONHOME%
%PYTHONHOME%
C:\>set PYTHONHOME
Environment Variable PYTHONHOME not defined
C:\>set PYTHONPATH
Environment Variable PYTHONPATH not defined
Here is the bat file:
====================================
@echo off
set PYTHONPATH=
set PYTHONHOME=
cd E:\soft\atk\2017\
VNL-ATK-2017.0-Windows64.exe
When I copy the folder of tk8.5 from 2016.3's installed files to E:\soft\atk\lib, the error changed, see the picture
I think if I get the right version of tk8.5.15 and put it in E:\soft\atk\lib, the problem will be solved.
Here are the outputs
====================================
C:\>echo %PYTHONPATH%
%PYTHONPATH%
C:\>echo %PYTHONHOME%
%PYTHONHOME%
C:\>set PYTHONHOME
Environment Variable PYTHONHOME not defined
C:\>set PYTHONPATH
Environment Variable PYTHONPATH not defined
Here is the bat file:
====================================
@echo off
set PYTHONPATH=
set PYTHONHOME=
cd E:\soft\atk\2017\
VNL-ATK-2017.0-Windows64.exe
When I copy the folder of tk8.5 from 2016.3's installed files to E:\soft\atk\lib, the error changed, see the picture
I think if I get the right version of tk8.5.15 and put it in E:\soft\atk\lib, the problem will be solved.
6
Installation and License Questions / error when install 2017: tk wasn't installed properly
« on: July 22, 2017, 17:17 »
Hi,
A error comes out when I install VNL-2017 on win7, see the attached figure.
I have noticed there are several posts on the issue of "tk.tcl", and tried the solustions, e.g. BAT file method on https://quantumwise.com/forum/index.php?topic=2238.msg10504#msg10504
But the problem still exists. How can I solve it?
Thanks!
A error comes out when I install VNL-2017 on win7, see the attached figure.
I have noticed there are several posts on the issue of "tk.tcl", and tried the solustions, e.g. BAT file method on https://quantumwise.com/forum/index.php?topic=2238.msg10504#msg10504
But the problem still exists. How can I solve it?
Thanks!
7
General Questions and Answers / transmission pathway, is it valid?
« on: June 2, 2015, 18:12 »
Hi all,
I plot the pathway of my configuration in the manuscript. Two reviewers both raise questions about it. I am little confused on how to reply. I noticed there is a paper in the forum, e.g., http://www.nature.com/nchem/journal/v2/n3/pdf/nchem.546.pdf . I am going to read it.
But, is there any other suggestions?
The questions:
reviewer 1:
"In transmission pathway analysis, the transmission coefficient is split into local bond contributions." How is this done? Details should be provided in the manuscript. The authors should notice that although the matrices involved in NEGF approach are defined in the basis of atomic orbitals, one cannot "split" the matrices by taking separate parts corresponding to specific atomic orbitals and expect to recover the overall transmission coefficient. It is therefore very important to specify exactly what is meant by "In transmission pathway analysis, the transmission coefficient is split into local bond contributions."
reviewer 2:
Page *, the bottom line mentions contribution of local bonds to transmission. There are multiple approaches addressing this issue, but not all of them turn out valid. Authors may better describe their method specifically.
I plot the pathway of my configuration in the manuscript. Two reviewers both raise questions about it. I am little confused on how to reply. I noticed there is a paper in the forum, e.g., http://www.nature.com/nchem/journal/v2/n3/pdf/nchem.546.pdf . I am going to read it.
But, is there any other suggestions?
The questions:
reviewer 1:
"In transmission pathway analysis, the transmission coefficient is split into local bond contributions." How is this done? Details should be provided in the manuscript. The authors should notice that although the matrices involved in NEGF approach are defined in the basis of atomic orbitals, one cannot "split" the matrices by taking separate parts corresponding to specific atomic orbitals and expect to recover the overall transmission coefficient. It is therefore very important to specify exactly what is meant by "In transmission pathway analysis, the transmission coefficient is split into local bond contributions."
reviewer 2:
Page *, the bottom line mentions contribution of local bonds to transmission. There are multiple approaches addressing this issue, but not all of them turn out valid. Authors may better describe their method specifically.
8
General Questions and Answers / Re: About the gate electrode
« on: May 12, 2014, 04:02 »
Dear kstokbro,
Thank you for your answer! It really helps me a lot!
Thank you for your answer! It really helps me a lot!
9
General Questions and Answers / About the gate electrode
« on: May 6, 2014, 10:13 »
Dear all,
Using ATK 2008.10, I studied the transport of a transition matel-doped Si structure contacted with Cu electrodes. A gate electrode is introduced in my system. I describe Vg in my manuscript like this (I use ATK 2008.10):
"Gate voltage is introduced by adding an external electro-static potential into the effective potential Veff[n](r) in the one-electron Kohn-Sham Hamiltonian."
However, the reviewer asked me to provide more about Vg, see below.
1. The author should describe what kind of external electro-static potentials added into the effective potential Veff(r) in the one-electron Kohn-Sham Hamiltonian as the gate voltage Vg.
2. The author should comment on the effects of gate electrodes on to the electronic structures and the spin dependent transport of the Si structure in the realistic system.
As for Point 1, I know "the electrostatic effect of the gate electrode is simulated by simply shifting the scattering region part of the Hamiltonian with the gate voltage (converted into an electrostatic potential energy)", and "only shift the diangonal terms H_ii, and all (selected) atoms were shifted by the same, fixed amount".
Here, I want to know the quantitative expression of this "fixed amount", is it -e*Vg ? or something else?
As for Point 2, would you please give me some suggestions?
Thank you!
Using ATK 2008.10, I studied the transport of a transition matel-doped Si structure contacted with Cu electrodes. A gate electrode is introduced in my system. I describe Vg in my manuscript like this (I use ATK 2008.10):
"Gate voltage is introduced by adding an external electro-static potential into the effective potential Veff[n](r) in the one-electron Kohn-Sham Hamiltonian."
However, the reviewer asked me to provide more about Vg, see below.
1. The author should describe what kind of external electro-static potentials added into the effective potential Veff(r) in the one-electron Kohn-Sham Hamiltonian as the gate voltage Vg.
2. The author should comment on the effects of gate electrodes on to the electronic structures and the spin dependent transport of the Si structure in the realistic system.
As for Point 1, I know "the electrostatic effect of the gate electrode is simulated by simply shifting the scattering region part of the Hamiltonian with the gate voltage (converted into an electrostatic potential energy)", and "only shift the diangonal terms H_ii, and all (selected) atoms were shifted by the same, fixed amount".
Here, I want to know the quantitative expression of this "fixed amount", is it -e*Vg ? or something else?
As for Point 2, would you please give me some suggestions?
Thank you!
10
General Questions and Answers / The calculation of the Hamiltonian
« on: January 6, 2014, 17:46 »
I noticed there is a tutorial of ATK about single-electron transistor (SET).
http://quantumwise.com/documents/tutorials/latest/BenzeneSET/index.html/
I intend to do some studies on the molecule in the SET environment.
The Hamiltonian of a molecule is
H=Sumi(EiC+iCi)+Sumij(Uijninj)
I wonder: How to obtain Ei and Uij for each i or (i, j) using ATK within (and without) the SET environment?
Any help will be appreciated!
http://quantumwise.com/documents/tutorials/latest/BenzeneSET/index.html/
I intend to do some studies on the molecule in the SET environment.
The Hamiltonian of a molecule is
H=Sumi(EiC+iCi)+Sumij(Uijninj)
I wonder: How to obtain Ei and Uij for each i or (i, j) using ATK within (and without) the SET environment?
Any help will be appreciated!
Pages: [1]