Messages

1

General Questions and Answers / Re: Bandgaps of Anthracene Based SAMs

« on: February 26, 2019, 12:50 »

Apologies if I wasn't entirely clear. In terms of conjugation, I was refering to the single A1, A2, and A3mono. The addition of the lateral substituent groups (and their size) would lead to slightly smaller band gaps, which is rightly observed. This might not be the case comparing the "packed" configurations with their single counterparts, as there will be energy level splitting (this also has been observed for 2 ,3, and 4 adjacent molecules). I was interested to include the packed configuraitons in my analysis because when I move towards the "on substrate" anaylsis including boundary conditions, I try to mimic a thin film of SAMs (eventhough the nature of the overlap isn't exactly known!!).

On the substrate I am a bit puzzled by why the A3 massively decreased comparing it to the A2 and A1 (either in a single or packed configuration).

Regarding the script, I attached the one for the single A3 on substrate for the geometry optimization. Once finished I projected the MES only on the molecule

2

General Questions and Answers / Bandgaps of Anthracene Based SAMs

« on: February 25, 2019, 15:32 »

Hello All,

I would like a second opinion on some band gap analysis I carried out on 3 different types of Anthracene based SAMs. Their illustrations are attached ("SAMs.png"). I also investigated packed versions of the A2- & A3mono (i.e. with an overlap at the side chains). The band gap analysis was done both in standalone and on a substrate configurations ("Standalone.pdf" and "On Substrate.pdf"). One would expect with the increased conjugation, the band gap would decrease. And indeed this is the case either in gas phase or on substrate. But what puzzles me a bit, is the rather significant decrease in the gap in the case of the A3mono (either single or packed). To double check the MES anaylsis, I also did a PDOS simulaiton which returned more or less the same results

A second opinon on why the large decrease is observed would be greatly appreciated. Thank You!

3

General Questions and Answers / Re: Generating the log file from the command line

« on: July 10, 2018, 10:56 »

Thank you Petr. Greatly appreciate you help 

4

General Questions and Answers / Re: Generating the log file from the command line

« on: July 9, 2018, 17:24 »

Thank you for this explanation. But following from there, if I want to use this spectrum to compute the I-V characteristics between an applied bias of  +2V to -2V, then this T(E) is not sufficient. Well at least for the negative bias because -4.296750-2 = 6.29750 eV. I have to increase my energy window in the transmission analysis ? As I only run it between -5eV and 5 eV.

5

General Questions and Answers / Re: Generating the log file from the command line

« on: July 9, 2018, 11:44 »

The reason for my question was because during the simulation nothing was being printed on screen to track the progress. The "calculating transmission" line only appeared after it had finished. But in any case the simulation was completed and I viewed the log file (or results), and this brings me to a more important question If I may ask. (Apologies if I am of topic from when I started the post)

As you can see from the code in my first post I specify that my energy zero parameter should be the AverageFermiLevel, yet by looking at the results I am getting an absolute value !! Any explanation  why ? For simplicity I only show the first part of the transmission file.

+------------------------------------------------------------------------------+
|                                                                              |
| Transmission Spectrum Analysis                                               |
|                                                                              |
+------------------------------------------------------------------------------+

                            |--------------------------------------------------|
Calculating Transmission   : ==================================================

+----------------------------------------------------------+
| Transmission Spectrum Report                             |
| -------------------------------------------------------- |
| Left electrode Fermi level  = -4.296750e+00 eV           |
| Right electrode Fermi level = -4.296750e+00 eV           |
| Energy zero                 = -4.296750e+00 eV           |
+----------------------------------------------------------+
   energy       T(up)
     eV
 -5.000000e+00   3.191915e-01
 -4.975000e+00   1.090114e-01
 -4.950000e+00   7.421144e-02
 -4.925000e+00   3.715330e-02
 -4.900000e+00   3.610812e-02
 -4.875000e+00   2.874695e-02
 -4.850000e+00   9.024125e-03
 -4.825000e+00   3.491315e-03
 
 .
 .
 .
 .
 .
 .
 .

6

General Questions and Answers / Generating the log file from the command line

« on: July 4, 2018, 11:03 »

I am running my .py script from the command line while using a SLURM. So basically my command is:

srun -p quantis -c 16 --mem=60G -t 10-1 -o transmissionA2.log mpiexec.hydra -n 16 atkpython NEW_Device_Sub_Ox_A2mono.py &

the transmissionA2.log defined above gives me the terminal output, but I was looking for log file that is usually generated when I run a .py from the job manager on the GUI . My script is as follows (I am using an already generated device .nc file and running a transmission spectrum block on it)

# -*- coding: utf-8 -*-
# -------------------------------------------------------------
# Analysis from File
# -------------------------------------------------------------
path = u'/mnt/share/gfsVolume/mohammed/Atomistics/Device SubOx_A2mono.nc'
configuration = nlread(path, object_id='gID000')[0]

# -------------------------------------------------------------
# Transmission Spectrum
# -------------------------------------------------------------
kpoint_grid = MonkhorstPackGrid(
    na=15,
    nb=15,
    )

transmission_spectrum = TransmissionSpectrum(
    configuration=configuration,
    energies=numpy.linspace(-5,5,401)*eV,
    kpoints=kpoint_grid,
    energy_zero_parameter=AverageFermiLevel,
    infinitesimal=1e-06*eV,
    self_energy_calculator=RecursionSelfEnergy(),
    )
nlsave('/mnt/share/gfsVolume/mohammed/Atomistics/NEW_Device_Sub_Ox_A2mono.hdf5', transmission_spectrum)
nlprint(transmission_spectrum)

7

General Questions and Answers / Re: Error regarding the self energies when calculating transmission pathways

« on: March 1, 2018, 13:15 »

Yes I did

8

General Questions and Answers / Re: Error regarding the self energies when calculating transmission pathways

« on: February 27, 2018, 16:56 »

The email has been sent.

Thank you Petr for your assistance 

9

General Questions and Answers / Re: Error regarding the self energies when calculating transmission pathways

« on: February 22, 2018, 11:47 »

They are attached.  I zipped the log file because its size was too large

10

General Questions and Answers / Re: Error regarding the self energies when calculating transmission pathways

« on: February 21, 2018, 17:06 »

I am using ATK 2017.12, and I ran the calculation through the GUI.

The script is attached (same as in my first message) and the log file with the error message as well

11

General Questions and Answers / Re: Error regarding the self energies when calculating transmission pathways

« on: February 21, 2018, 11:49 »

Any help ??

12

General Questions and Answers / Error regarding the self energies when calculating transmission pathways

« on: February 20, 2018, 13:58 »

I am trying to run a script calculating the transmission pathways at 3 different energies. I am using a Recursion self energy calculator. At first I didnt specify any arguments and it gave me the error "save_self_energies is deprecated, use storage_strategy". I returned and added this argument to the calculator and still getting this error. Generally the simualation ran when I was using the Direct self energy but I understand that Recursion is a more accurate approach, hence I want to keep with it.

The scrpit is shown below / attached.

# -------------------------------------------------------------
# Analysis from File
# -------------------------------------------------------------
path = u'/home/ads.mwn.de/ga37juw/Anthracene Chains/Device/Device SubOx_2A2mono.nc'
configuration = nlread(path, object_id='gID000')[0]

# -------------------------------------------------------------
# Transmission Pathways
# -------------------------------------------------------------
kpoint_grid = MonkhorstPackGrid(
    na=15,
    nb=15,
    )

transmission_pathways = TransmissionPathways(
    configuration=configuration,
    energy=-0.36*eV,
    kpoints=kpoint_grid,
    energy_zero_parameter=AverageFermiLevel,
    infinitesimal=1e-06*eV,
    contributions=Left,
    self_energy_calculator=RecursionSelfEnergy(storage_strategy=SaveInMemory()),
    )
nlsave('/home/ads.mwn.de/ga37juw/Anthracene Chains/Device/Device SubOx_2A2mono.nc', transmission_pathways)
nlprint(transmission_pathways)

# -------------------------------------------------------------
# Transmission Pathways
# -------------------------------------------------------------
kpoint_grid = MonkhorstPackGrid(
    na=15,
    nb=15,
    )

transmission_pathways = TransmissionPathways(
    configuration=configuration,
    energy=-1.48*eV,
    kpoints=kpoint_grid,
    energy_zero_parameter=AverageFermiLevel,
    infinitesimal=1e-06*eV,
    contributions=Left,
    self_energy_calculator=RecursionSelfEnergy(storage_strategy=SaveInMemory()),
    )
nlsave('/home/ads.mwn.de/ga37juw/Anthracene Chains/Device/Device SubOx_2A2mono.nc', transmission_pathways)
nlprint(transmission_pathways)

# -------------------------------------------------------------
# Transmission Pathways
# -------------------------------------------------------------
kpoint_grid = MonkhorstPackGrid(
    na=15,
    nb=15,
    )

transmission_pathways = TransmissionPathways(
    configuration=configuration,
    energy=-2.46*eV,
    kpoints=kpoint_grid,
    energy_zero_parameter=AverageFermiLevel,
    infinitesimal=1e-06*eV,
    contributions=Left,
    self_energy_calculator=RecursionSelfEnergy(storage_strategy=SaveInMemory()),
    )
nlsave('/home/ads.mwn.de/ga37juw/Anthracene Chains/Device/Device SubOx_2A2mono.nc', transmission_pathways)
nlprint(transmission_pathways)

13

General Questions and Answers / Re: Choosing the right functional

« on: December 5, 2016, 15:17 »

Thank you for your replies.

I will try with the Meta-GGA functional and see the output. I understand that the band gap would be underestimated compared to experimental values but a difference of more than 1 eV seems quite large to me.

On a different note I wont be able to use the FHI-Aims calculator as it is not included in our license.

14

General Questions and Answers / Choosing the right functional

« on: December 2, 2016, 13:38 »

Hello,

I am running a DFT simualtion on anthracene molecules with a phosphonate anchor group. In order to get an agreement with experimental results I wanted to use the B3LYP but I understand its not included in the functional library in ATK. I used BLYP instead but I get a much smaller band gap (2.2eV sim compared to 3.5eV exp). I not familiar with all the functionals included but I am trying different sets to see if I can retain the correct band gap.

But I would greatful if you can guide me on how to get the correct value.

Thank You

15

General Questions and Answers / Re: Testing MPI

« on: June 6, 2016, 11:31 »

thanks for the confirmation. Hence will keep to what the VNL scripts are showing