Topics

31

General Questions and Answers / Multiple Node issue

« on: July 23, 2022, 15:16 »

Dear Admin,

When using the following command for 2 node with 25 cores per node:
mpiexec -n 50 -ppn 25 atkpython test.py > test.log
I see from CPU activity all calculations run on single node.

& when I use following command (host_names is a file that contains compute node addresses):
mpiexec -f host_names -n 50 -ppn -25 atkpython test.py > test.log
I see this error:
bash: /opt/QuantumATK/QuantumATK-T-2022.03-SP1/libexec/pmi_proxy: No such file or directory
bash: /opt/QuantumATK/QuantumATK-T-2022.03-SP1/libexec/pmi_proxy: No such file or directory


Kindly help resolve this error.

32

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!

33

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)

34

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

35

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?

36

General Questions and Answers / Interface between Nickel and Graphene

« on: May 8, 2022, 09:19 »

I was learning to make an interface between graphene and nickel from the QATK Tutorials. I exactly followed the steps but didn't get the end structure as expected from tutorials. Kindly help and let me know where am I possibly doing wrong.

The one with black background is what I get. It is seen during shift surfaces when i use z=2, the nickle atom lifts with graphene but in tutorials nothing such happens.

37

General Questions and Answers / Convergence issues

« on: April 25, 2022, 11:26 »

I see in some paper they use surface energy convergence to check how many layers of active material is needed for proper calculations however when electrode convergence is required they use LDOS, local density of states to check after how many layers it is not changing.
My question is why LDOS is used for electrode convergence and surface energy for active material?

38

General Questions and Answers / Interface between Graphene & Mos2

« on: April 17, 2022, 09:54 »

I am trying to optimize the shift between MoS2 & Graphene interface but there is no forcefield. How do I find the optimum distance between the two surfaces?