Topics

1

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!

2

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)

3

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)

4

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

5

General Questions and Answers / Testing MPI

« on: June 2, 2016, 14:22 »

I followed the steps in installing  MPI as it was pointed out in the tutorial and I run a test script but I am not sure if it is working properly. I attached a snapshot of the log file. Can someone please confirm

I have single machine with a dual processor (10 cores each)

Thank you.

6

General Questions and Answers / Aluminium bonds

« on: May 10, 2016, 12:22 »

I can't seem to visualize the bonds between aluminium atoms. I know here in a previous post it is suggested to increase the radius of the bonds in the viewer, which i did but it did not work. I understand that this does not affect calculations, but I just want it for visualization purposes.

7

General Questions and Answers / Relaxation

« on: November 20, 2014, 13:14 »

Dear all,

Attached is the image of an already relaxed molecule on top of a Si-SiO2 substrate. I ran the optimization with a k-point sampling of (1,1,1). According to my understanding, because my structure size is fairly small, the reciprocal lattice should be even smaller, hence my choice of (1,1,1) k-points. My question is was this a right choice or not ?