Messages

121

General Questions and Answers / Running QATK on Multiple Nodes

« on: July 19, 2022, 19:44 »

Dear Admin, I want to run QATK on multiple nodes.
I have added paths of license, mpiexec.hydra (from libexec) & atkpython (bin) in ~/.bashrc added.
next I run the following commands on terminal.

1. mpiexec.hydra -f host_file -n 200 -ppn 40 atkpython filename.py > output.log
(host_file contains list of node information)
I get the following errors:
            i) /etc/tmi.conf: No such file or directory
 
              ii) DAPL startup: RLIMIT_MEMLOCK too small


2. mpiexec.hydra  -n 200 -ppn 40 atkpython filename.py > output.log
In this case although I mention 200/40= 5 nodes but it runs all calculation on single node & not on expected 5 nodes.


KIndly provide a solution!

122

General Questions and Answers / Re: Electrode Sizes fixed to mininal size

« on: July 9, 2022, 06:14 »

Ah Cool.
Thanks

123

General Questions and Answers / Re: Electrode Sizes fixed to mininal size

« on: July 7, 2022, 05:18 »

Dear Admin,
Can you kindly answer my question?
I am not able to resolve the issue of electrode length in electrode validator.

On the other hand, there seems no way to change length of electrode.

124

General Questions and Answers / Re: Hydrogen Molecule Dissociation energy calculation

« on: July 7, 2022, 05:10 »

That was helpful.
Thanks for your clarification.

125

General Questions and Answers / Re: Hydrogen Molecule Dissociation energy calculation

« on: July 6, 2022, 07:19 »

Dear Admin,
All units are in eV.
You probably misunderstood my question.

The mentioned values are not the dissociation energy values of H2 molecule but that of whole system i.e H2 molecule using PBE/B3LYP functionals.
As you can see when I calculate energy of H2 molecule using B3LYP whether unpolarized/polarized, I get -32 eV as total energy. Now, when I calculate same using PBE, I get different results for polarized/ unpolarized as -27.181 eV, -31.651 eV which should not happen because H2 anyways is unpolarized.

This questions the software because here in this case although I know H2 is unpolarized I can keep the unpolarized results & move on. However, when probing some unknown system for which I don't know prior whether its polarized or unpolarized, I may get incorrect results because PBE for polarized/unpolarized shows different results for H2 which should otherwise show same results.

126

General Questions and Answers / Re: Electrode Sizes fixed to mininal size

« on: July 6, 2022, 07:03 »

Thanks for your response.

But if I continue with 1 atom, the electrode validator shows not "NOT VALID Electrode & asks to increase number of atoms in Electrode" which unfortunately is not accessible to change as mentioned in my initial post?

Should I then ignore electrode validator message?

127

General Questions and Answers / Re: Bandstructures

« on: July 6, 2022, 06:59 »

Thanks or your response.
That said, wont it affect my other calculations when working with supercell of multiple of 3 unit cells? Should I be then avoiding a supercell of multiple of 3 unit cells or it is okay to continue with them?

128

General Questions and Answers / Electrode Sizes fixed to mininal size

« on: June 30, 2022, 12:47 »

Dear Admin/Others,
When doing device from bulk, it chooses minimal electrode length as one atom. However, I want to keep 2 or 3 atoms as my electrode I tried changing +/-  as shown in attachment, also tried changing left & right values below (see attachment) & electrode extension length but it does not help change the electrode length & keeps it fixed as one atom. How to rectify it? I found that changing left & right values below had no effect on the electrode size. Kindly help.
Check the attachments below.

(The reason why I want to change it to 2 or 3 atoms is because in electrode validator it says large matrix elements error & asks to increase electrode size)

129

General Questions and Answers / Bandstructures

« on: June 30, 2022, 11:28 »

Dear Admin/Anyone,
Could you kindly explain why any multiple of 3 chosen for a supercell (in this case for moS2) produces a different bandstructure than other sizes. It can be seen below that for a supercell of 3x3 & 9x9 we have VBM & CBM along G point whereas for other sizes such as 4x4,5x5 it is along KM points?
 Is it something with software or I am missing something here?
See the attachment below

130

General Questions and Answers / Re: convergence problem

« on: June 21, 2022, 14:17 »

You need to increase it thats the only way. I faced same issue some time ago but got results.
Try 300 maybe

131

General Questions and Answers / Re: convergence problem

« on: June 21, 2022, 14:11 »

If you are using Semiempirical calculator, then in that go to iteration control & if you have unticked no scf iteration then below it there will be maximum steps written as 100, change it to 400 & recompute. I am not sure but there is a way I guess to recompute only not converged points instead of rerunning whole calculations.

132

General Questions and Answers / Re: convergence problem

« on: June 20, 2022, 14:39 »

I see you are using Gold (as electrode I guess). From my experience with Gold adsorption calculations they taken long to optimize (converge). I normally run from command line & not from user interface & I see two files apart from .py during run. One is log file & another is name something like optimizationxxxxxx.log . Most infiormation of optimization were found in this optimizationxxx.log file.

133

General Questions and Answers / Re: convergence problem

« on: June 18, 2022, 12:00 »

Sometimes it doesn't converge because K points are not enough. 1x1x1 could be one problem. Check log file and save it then run with higher k points for same time & compare two log files to see if K point convergence is the issue

134

General Questions and Answers / Re: convergence problem

« on: June 18, 2022, 09:28 »

Depending on number of k points & size of device, transport calculations usually take long time.

135

General Questions and Answers / Hydrogen Molecule Dissociation energy calculation

« on: June 14, 2022, 14:56 »

I am calculating the dissociation energy of Hydrogen molecule.
The formula used is E(disso)=E(H2)-2E(H)
where E(H2) is the total energy calculated using two methods as:
1. Spin unpolarised/polarized using B3LYP functionals giving energies - 32, -32 respectively.
2. Spin unpolarised/polarised using PBE functionals giving energies - 31.651, -27.181 respectively.
Since H2 is spin unpolarised molecule & when choosing unpolarised/polarised using B3LYP both give same energy -32 which makes sense but why does PBE give different results for spin polarised & spin unpolarised?