1
General Questions and Answers / Re: How to design the gate electrode
« on: January 16, 2012, 02:50 »
Thank you, Anders Blom.
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2
General Questions and Answers / How to design the gate electrode
« on: January 11, 2012, 14:42 »
Dear Sir,
Can you give any suggestions about the gate electrode, e.g., in the graphene device tutorial, how to decide the thickness of metallic and dielectric region and the distance between the graphene and dielectric region?
Can you give any suggestions about the gate electrode, e.g., in the graphene device tutorial, how to decide the thickness of metallic and dielectric region and the distance between the graphene and dielectric region?
3
Installation and License Questions / Re: ATK can not work
« on: October 28, 2011, 03:41 »
Thank you for your advice, Anders Blom. It can work well now. 
I think I made one mistake when starting the license server. It should directly run it"lmx-serv-quantum -b -l /home/user1/bin/atk/license/qw_license.lic -lf /home/user1/bin/atk/license/lmxserver.log", not to rsh one node then run it. 
I think I made one mistake when starting the license server. It should directly run it"lmx-serv-quantum -b -l /home/user1/bin/atk/license/qw_license.lic -lf /home/user1/bin/atk/license/lmxserver.log", not to rsh one node then run it. 4
Installation and License Questions / ATK can not work
« on: October 27, 2011, 16:39 »
Dear Sir,
It works well before the restart of our server. However, unfortuantly, recently, our linux server had been restarted, and atk (11.2.3) can not work after the restart. I had tried to reinstall it, while it still does not work. After the installation, when I executive the commond "atkpython", it displays the error information
"License Error: (Internal: 292 Feature: ATKPython)
(Err: 9) Feature not found
For further assistance consult the manual or contact QuantumWise.
"
Note: The service license file had been put into the installation path /home/user1/bin/atk/license, and I had tried to start the license server using the commend "lmx-serv-quantum -b -l /home/user1/bin/atk/license/qw_license.lic -lf /home/user1/bin/atk/license/lmxserver.log".
Can you give any suggestion?
Thank you very much.
It works well before the restart of our server. However, unfortuantly, recently, our linux server had been restarted, and atk (11.2.3) can not work after the restart. I had tried to reinstall it, while it still does not work. After the installation, when I executive the commond "atkpython", it displays the error information
"License Error: (Internal: 292 Feature: ATKPython)
(Err: 9) Feature not found
For further assistance consult the manual or contact QuantumWise.
"
Note: The service license file had been put into the installation path /home/user1/bin/atk/license, and I had tried to start the license server using the commend "lmx-serv-quantum -b -l /home/user1/bin/atk/license/qw_license.lic -lf /home/user1/bin/atk/license/lmxserver.log".
Can you give any suggestion?
Thank you very much.
5
Gallery / Re: Energy dependent LDOS for a benzene device
« on: September 5, 2011, 16:38 »
Thank you, Dr. kstokbro.
6
Gallery / Re: Energy dependent LDOS for a benzene device
« on: September 4, 2011, 03:58 »
Dear Anders Blom,
I mean this new tutorial about the Au-DTB-Au system, i.e. http://quantumwise.com/documents/tutorials/latest/MolecularDevice/index.html/chap.analysis.html#sect1.analysis.transmission
Here, it only gave the PDOS of phenylene ring (the two S atoms not included), and compared that with the Transmission spectrum. Why not the whole sample molecule? So, I have the question how to reasonablely determine the projected atoms to analyze the transmission spectrum.
I mean this new tutorial about the Au-DTB-Au system, i.e. http://quantumwise.com/documents/tutorials/latest/MolecularDevice/index.html/chap.analysis.html#sect1.analysis.transmission
Here, it only gave the PDOS of phenylene ring (the two S atoms not included), and compared that with the Transmission spectrum. Why not the whole sample molecule? So, I have the question how to reasonablely determine the projected atoms to analyze the transmission spectrum.
7
Gallery / Re: Energy dependent LDOS for a benzene device
« on: September 1, 2011, 03:21 »
Dear Anders Blom，
Can you give any suggestions about the PDOS,how to determine the projected atoms of the central scattering region (or only the sample molecule) ? Like the example'Au-DTB-Au', it only gave the PDOS of phenylene ring (the two S atoms not included), and compared that with the Transmission spectrum? it is similar for the analysis of eigenstates. Thank you.
Can you give any suggestions about the PDOS,how to determine the projected atoms of the central scattering region (or only the sample molecule) ? Like the example'Au-DTB-Au', it only gave the PDOS of phenylene ring (the two S atoms not included), and compared that with the Transmission spectrum? it is similar for the analysis of eigenstates. Thank you.
8
Gallery / Re: Energy dependent LDOS for a benzene device
« on: August 31, 2011, 09:31 »
Thank you, Dr. kstokbro.
Another, when analysizing the Local Device Density of States, one can do it only at one energy value, whether is it possible to describe the LDOS at one optional energy range, e. g. from -1 to 1 eV. If so, the LDOS distribution (partial charge) on the real atom (atoms) can be viewed, not just the Z coordinate. right?
Another, when analysizing the Local Device Density of States, one can do it only at one energy value, whether is it possible to describe the LDOS at one optional energy range, e. g. from -1 to 1 eV. If so, the LDOS distribution (partial charge) on the real atom (atoms) can be viewed, not just the Z coordinate. right?
9
Gallery / Re: Energy dependent LDOS for a benzene device
« on: August 31, 2011, 08:41 »
Dear Dr. kstokbro,
Can you give any suggestions to extract the date of the energy relevent LDOS, and then plot the Z-Energy figure by other software, e.g. origin. Another, the scale of the color bar could be helpful to understand this figure.
Thank you.
Can you give any suggestions to extract the date of the energy relevent LDOS, and then plot the Z-Energy figure by other software, e.g. origin. Another, the scale of the color bar could be helpful to understand this figure.
Thank you.
10
General Questions and Answers / two-probe model in new version
« on: July 10, 2011, 09:28 »
Dear Sir,
In the new version 11.2.3, when building one two-probe model like the Au-S-alkene-S-Au (the example in Custom->Molecular Junction, as shown inthe attachment), it seems that the central molecule is always tilted (the X and Y positions of the two end S atoms are not same).
Whether is there one convemient way to tune the molecule position, so that when one new molecule (like S-molecule-S) is dropped to "Drop configure here" the two end S atoms are automatically moved to one hollow site near the center of the electrode sections,respectively, and have same X and Y positions.
Thank you.
In the new version 11.2.3, when building one two-probe model like the Au-S-alkene-S-Au (the example in Custom->Molecular Junction, as shown inthe attachment), it seems that the central molecule is always tilted (the X and Y positions of the two end S atoms are not same).
Whether is there one convemient way to tune the molecule position, so that when one new molecule (like S-molecule-S) is dropped to "Drop configure here" the two end S atoms are automatically moved to one hollow site near the center of the electrode sections,respectively, and have same X and Y positions.
Thank you.
11
General Questions and Answers / Re: One error occured when calculating the DOS
« on: March 25, 2011, 03:15 »
It still can not get the DOS information in serial calculation for my 3-dimensional Au-molecule-Au system.
12
General Questions and Answers / Re: One error occured when calculating the DOS
« on: March 24, 2011, 03:22 »
Dear Sir,
Fortunately, the problem of LDOS parallel calculation is solved, but I still encounter some problems when calculating the DOS using the newest version 11.2.1 in parallel by 2X2 nodes because the output of DOS only prints "nan" like the folllowing.
PS: My mpi is mpich2.1.0.8. The command is
"/home/user1/bin/mpich2/bin/mpiexec -machinefile node -n 4 /home/user1/bin/atk112/atkpython/bin/atkpython test.py >& test.txt"
Can you give any advance? Thank you.
output:
|--------------------------------------------------|
Calculating DOS : ==================================================
+----------------------------------------------------------+
| Density of States Report |
| -------------------------------------------------------- |
| Left electrode Fermi level = -2.244959e+00 |
| Right electrode Fermi level = -2.244959e+00 |
| Energy zero = -2.244959e+00 |
| Units = eV 1/eV |
+----------------------------------------------------------+
-2.000000e+00 nan
-1.990000e+00 nan
-1.980000e+00 nan
-1.970000e+00 nan
-1.960000e+00 nan
-1.950000e+00 nan
.......................................
1.950000e+00 nan
1.960000e+00 nan
1.970000e+00 nan
1.980000e+00 nan
1.990000e+00 nan
2.000000e+00 nan
Fortunately, the problem of LDOS parallel calculation is solved, but I still encounter some problems when calculating the DOS using the newest version 11.2.1 in parallel by 2X2 nodes because the output of DOS only prints "nan" like the folllowing.
PS: My mpi is mpich2.1.0.8. The command is
"/home/user1/bin/mpich2/bin/mpiexec -machinefile node -n 4 /home/user1/bin/atk112/atkpython/bin/atkpython test.py >& test.txt"
Can you give any advance? Thank you.
output:
|--------------------------------------------------|
Calculating DOS : ==================================================
+----------------------------------------------------------+
| Density of States Report |
| -------------------------------------------------------- |
| Left electrode Fermi level = -2.244959e+00 |
| Right electrode Fermi level = -2.244959e+00 |
| Energy zero = -2.244959e+00 |
| Units = eV 1/eV |
+----------------------------------------------------------+
-2.000000e+00 nan
-1.990000e+00 nan
-1.980000e+00 nan
-1.970000e+00 nan
-1.960000e+00 nan
-1.950000e+00 nan
.......................................
1.950000e+00 nan
1.960000e+00 nan
1.970000e+00 nan
1.980000e+00 nan
1.990000e+00 nan
2.000000e+00 nan
13
General Questions and Answers / how to hide the unit cell
« on: March 18, 2011, 03:57 »
Dear Sir,
For the newest version 11.2.1, I want to know how to hide the unit cell like that the Axes can be hiden. Thank you.
For the newest version 11.2.1, I want to know how to hide the unit cell like that the Axes can be hiden. Thank you.
14
General Questions and Answers / Re: losing the configure when displaying the LDOS
« on: March 15, 2011, 03:20 »
Thank you Norland, It works fine by your method although only the device configure can be controled, but the left or right leads not.
15
General Questions and Answers / Re: losing the configure when displaying the LDOS
« on: March 14, 2011, 02:34 »
Thank you Nordland. The configure can be displayed with the LDOS by your method, but the radius (atom or bond) of the configure seems unable to be controled, beacuse it only shows "The composite plot takes no parameters" for "Device configure" when controling the display of LDOS.
Thanks, do you have more advice to control the configure.
Thanks, do you have more advice to control the configure.