Messages

1

General Questions and Answers / geometry optimization of bulk configuration error

« on: September 14, 2021, 00:26 »

Dear all,
I have been trying to optimize the bulk configuration. every time I submit the job. it runs for some time and return back with this error;

/opt/local/atk/2016.0/lib/python27.zip/NL/CommonConcepts/Configurations/Utilities.py:212: RuntimeWarning: invalid value encountered in less
/var/lib/torque/mom_priv/jobs/88764.gibbs.gibbs.alliance.unm.edu.SC: line 39:  4351 Segmentation fault      (core dumped) /opt/local/atk/2016.0/bin/atkpython 2mephthp_opt5.py

what can I do to overcome this error?
Thank you so much
Ranjana

2

General Questions and Answers / PLDDOS

« on: September 14, 2021, 00:20 »

hello,
I have generated the .nc file for the projected local device density of states. I can get the heat map of that PLDDOS by using projected local density of states. I would also like to have the spatial distribution of PLDDOS on molecule at particular energy projected on the molecule so that I can compare the it with the molecular orbital of isolated molecule.
Any suggestions and comments will be highly appreciated.
Thank you so much in advance
Ranjana

3

General Questions and Answers / Re: 3/3 vs 4/4 gold lattice and (one thiol vs two thiols)

« on: April 4, 2018, 21:58 »

Thank you so much for the response, If you don't mind , could you explain in little bit about  this:
 ''transport calculations should be checked for convergence with respect to the lateral unit cell size'' copied from your response.
How do I do that?

4

General Questions and Answers / 3/3 vs 4/4 gold lattice and (one thiol vs two thiols)

« on: March 29, 2018, 21:39 »

Hello,
I would like to do the transport calculation on a little bit big complex so for that to make a large enough surface for the molecule  I would like to repeat the structure 4*4*2 times instead of 3*3*2(mentioned in the tutorial building a molecular junction). Because in the 3*3*2 my molecule gets connected only on the terminal gold atom.

So I am thinking with 4*4*2, this situation would not occur.My questions are:
1. Does the 4*4*2 repeat gold surface make any change on transport calculation? If yes then would you mind to explain how?
2. What could be the difference in transport properties between the molecule that connected to the gold electrode by using two thiols(in my case I have used 2thiols that connects molecules to the two gold atoms) vs only one thiol(most of the studies have used only one thiol)?

little bit of long questions but I hope you will me on these issues.
Thank you so much in advance,
Ranjana Dangi