16
General Questions and Answers / Re: Significance and meaning of LDDOS Plot
« on: February 9, 2016, 13:34 »
PFA
Show Posts
This section allows you to view all posts made by this member. Note that you can only see posts made in areas you currently have access to.
Pages: 1 [2]
17
General Questions and Answers / Significance and meaning of LDDOS Plot
« on: February 8, 2016, 13:37 »
Hi All,
I was trying to plot LDDOS plot for a device structure and end up with a plot looks like multiple LDDOS plots are merged onto same plot. I can't figure out if it a real plot or i went wrong somewhere while plotting it. Also tell me what is the significance of plotting it. Is it for the counter-check of the results obtained by Transmission spectra? what does Transmission coefficient T(E)>1 signifies in context of LDDOS plot.
Thank you
I was trying to plot LDDOS plot for a device structure and end up with a plot looks like multiple LDDOS plots are merged onto same plot. I can't figure out if it a real plot or i went wrong somewhere while plotting it. Also tell me what is the significance of plotting it. Is it for the counter-check of the results obtained by Transmission spectra? what does Transmission coefficient T(E)>1 signifies in context of LDDOS plot.
Thank you
18
General Questions and Answers / Re: Molecular Dynamics Error
« on: January 28, 2016, 13:12 »
Hi again
After geometry optimization i was checking transmission spectra and device density of states. for that I take reference of Molecular device tutorial (https://www.quantumwise.com/documents/tutorials/latest/MolecularDevice/index.html/chap.analysis.html). In Energy dependent LDDOS I got following plot. Do you think that it's a valid plot? It looks like two plots are overlapped over one another. PFA
After geometry optimization i was checking transmission spectra and device density of states. for that I take reference of Molecular device tutorial (https://www.quantumwise.com/documents/tutorials/latest/MolecularDevice/index.html/chap.analysis.html). In Energy dependent LDDOS I got following plot. Do you think that it's a valid plot? It looks like two plots are overlapped over one another. PFA
19
General Questions and Answers / Re: Molecular Dynamics Error
« on: January 25, 2016, 06:00 »
Thank you for your suggestion. I gave run with Langvin type MolecularDynamics and for geometry optimization as well. I have some doubts about both results.
1) Langvin MD
In results i got one device configuration file and one MD trajectory file. In MD trajectory file I got following results, PFA. can you tell me what does it signify and what does it optimize?
2) Geometry Optimization
In results i got two device configuration files and when i drag .nc file into stash it generated two device structure there. Then I checked their coordinates and i found that two device structures have different coordinates. Do you think that changed coordinates are geometry optimized one. Also I checked it for only 10 steps, do you think that increasing steps will give much better results.
1) Langvin MD
In results i got one device configuration file and one MD trajectory file. In MD trajectory file I got following results, PFA. can you tell me what does it signify and what does it optimize?
2) Geometry Optimization
In results i got two device configuration files and when i drag .nc file into stash it generated two device structure there. Then I checked their coordinates and i found that two device structures have different coordinates. Do you think that changed coordinates are geometry optimized one. Also I checked it for only 10 steps, do you think that increasing steps will give much better results.
20
General Questions and Answers / Re: Molecular Dynamics Error
« on: January 19, 2016, 13:27 »
I didn't find any option in New calculator :-> ATK-DFT calculator or in molecular dynamics for classical potential. please tell where shall i find these potential values
In ATK-classical calculator it shows warning. PFA
In ATK-classical calculator it shows warning. PFA
21
General Questions and Answers / Re: Molecular Dynamics Error
« on: January 19, 2016, 05:57 »
Dear Jess and Julian
this time i tried NVT Berendsen molecular dynamics. But i am confused with the results, as the bonds are breaking apart in the molecule. I am surprised why this is happening at room temperature.
so far i was thinking that by doing optimization (OG or MD) we will get a molecule which is supposed to be at those environmental conditions. i was expecting tiny little change in bond-length not breaking of bonds.
Please help me with the little i know.
Due to size constraints i can't attach .nc file
this time i tried NVT Berendsen molecular dynamics. But i am confused with the results, as the bonds are breaking apart in the molecule. I am surprised why this is happening at room temperature.
so far i was thinking that by doing optimization (OG or MD) we will get a molecule which is supposed to be at those environmental conditions. i was expecting tiny little change in bond-length not breaking of bonds.
Please help me with the little i know.
Due to size constraints i can't attach .nc file
22
General Questions and Answers / Re: Molecular Dynamics Error
« on: January 14, 2016, 07:30 »
i also tried optimize Geometry but i think that, change in molecular structure is not conceptually correct at room temperature.
Please check trajectory file
Please check trajectory file
23
General Questions and Answers / Molecular Dynamics Error
« on: January 11, 2016, 09:08 »
Hi All,
I was trying to make minimum energy state Metal-Insulator-Metal (MIM) structure with insulator being an organic molecule. But i got this error after execution completed.
File "/tmp/5701470339676073.py", line 27, in <module>
method=method
File "./zipdir/NL/Dynamics/MolecularDynamics/MolecularDynamics.py", line 215, in MolecularDynamics
File "./build/atkpython/lib/python2.7/site-packages/ase/md/nptberendsen.py", line 110, in step
File "./build/atkpython/lib/python2.7/site-packages/ase/md/nptberendsen.py", line 100, in scale_positions_and_cell
File "./zipdir/NL/Dynamics/ASEAtomsInterface.py", line 352, in set_cell
AttributeError: 'DeviceConfiguration' object has no attribute '_setBravaisLattice'
I did following modifications
1) convert bulk structure to device structure
2) Apply Fit Cell in Bulk Tools
3) Sent it to script generator
4) Add New calculator
5) Add MolecularDynamics from optimization
6) In New calculator i take ATK-DFT calculator
7) In Molecular Dynamics I take NPT Berendsen Type
8 ) in constraints i select left and right electrode metal atoms
9) keep all other parameters as default.
I want to ask you why i am facing this problem. Is that because of asymmetry of device or anything else. Please help
I was trying to make minimum energy state Metal-Insulator-Metal (MIM) structure with insulator being an organic molecule. But i got this error after execution completed.
File "/tmp/5701470339676073.py", line 27, in <module>
method=method
File "./zipdir/NL/Dynamics/MolecularDynamics/MolecularDynamics.py", line 215, in MolecularDynamics
File "./build/atkpython/lib/python2.7/site-packages/ase/md/nptberendsen.py", line 110, in step
File "./build/atkpython/lib/python2.7/site-packages/ase/md/nptberendsen.py", line 100, in scale_positions_and_cell
File "./zipdir/NL/Dynamics/ASEAtomsInterface.py", line 352, in set_cell
AttributeError: 'DeviceConfiguration' object has no attribute '_setBravaisLattice'
I did following modifications
1) convert bulk structure to device structure
2) Apply Fit Cell in Bulk Tools
3) Sent it to script generator
4) Add New calculator
5) Add MolecularDynamics from optimization
6) In New calculator i take ATK-DFT calculator
7) In Molecular Dynamics I take NPT Berendsen Type
8 ) in constraints i select left and right electrode metal atoms
9) keep all other parameters as default.
I want to ask you why i am facing this problem. Is that because of asymmetry of device or anything else. Please help
24
Gallery / Re: Energy dependent LDOS for a benzene device
« on: November 3, 2015, 13:35 »The attached figure shows the LDOS along z (averaged over x and y), for DTB coupled with gold electrodes. Note how the high density of states coincides with the resonances in the transmission spectrum. I also attach the scripts used for generating the figure.
i was trying same for 1.6V but didn't get much success. so far i was changing left electrode and right electrode potentials in new calculator. is there anything else that i can do to get the LDOS image at 1.6V?
25
General Questions and Answers / Re: THE LDDOS AT 1.6 V (Molecular Device Reference) script Error
« on: November 2, 2015, 14:05 »
Thank you Jess for your valuable suggestion.
i got a think over it and i go to script generator and modify it accordingly by placing 1.6V to left electrode and 0V to right electrode in the new calculator and then sent it to editor and modify it accordingly too. And now i am running it with the help of job manager.
will this modification give me authentic results?
i got a think over it and i go to script generator and modify it accordingly by placing 1.6V to left electrode and 0V to right electrode in the new calculator and then sent it to editor and modify it accordingly too. And now i am running it with the help of job manager.
will this modification give me authentic results?
26
General Questions and Answers / THE LDDOS AT 1.6 V (Molecular Device Reference) script Error
« on: November 2, 2015, 12:30 »
i was trying to run this script already given in molecular device reference at http://quantumwise.com/documents/tutorials/latest/MolecularDevice/index.html/chap.iv.html#sect1.iv.lddos
the script is under headline of THE LDDOS AT 1.6V
configuration = nlread('au_dtb_au.nc', DeviceConfiguration)[8]
# make list of energies to be used for ldos
energies = numpy.linspace(-3,3,31)
# calculate ldos for each energy in the list
for e in energies:
local_device_density_of_states = LocalDeviceDensityOfStates(
configuration=configuration,
energy=e*eV,
kpoints=MonkhorstPackGrid(3,3),
contributions=All,
energy_zero_parameter=AverageFermiLevel,
infinitesimal=1e-06*eV,
self_energy_calculator=RecursionSelfEnergy(),
spin=Spin.Sum,
)
nlsave(r'lddos16.nc', local_device_density_of_states)
when i run this script with the help of job manager, it return me a log file with error
Traceback (most recent call last):
File "/tmp/2438853653008193.py", line 20, in <module>
spin=Spin.Sum,
TypeError: __init__() got an unexpected keyword argument 'spin'
please suggest me what shall i modify.
Thank you
the script is under headline of THE LDDOS AT 1.6V
configuration = nlread('au_dtb_au.nc', DeviceConfiguration)[8]
# make list of energies to be used for ldos
energies = numpy.linspace(-3,3,31)
# calculate ldos for each energy in the list
for e in energies:
local_device_density_of_states = LocalDeviceDensityOfStates(
configuration=configuration,
energy=e*eV,
kpoints=MonkhorstPackGrid(3,3),
contributions=All,
energy_zero_parameter=AverageFermiLevel,
infinitesimal=1e-06*eV,
self_energy_calculator=RecursionSelfEnergy(),
spin=Spin.Sum,
)
nlsave(r'lddos16.nc', local_device_density_of_states)
when i run this script with the help of job manager, it return me a log file with error
Traceback (most recent call last):
File "/tmp/2438853653008193.py", line 20, in <module>
spin=Spin.Sum,
TypeError: __init__() got an unexpected keyword argument 'spin'
please suggest me what shall i modify.
Thank you
Pages: 1 [2]