UT theoretical chemistry code forum

Thank you Prof. Henkelman, for your time and efforts.

Dear Prof. Henkelman,

Please find attached a tar.gz archive of the whole run.

One more run of NSW=500 is complete without reaching accuracy.

I would greatly appreciate your valuable insights on my system.

Best regards,
mmg016

Dear Prof. Henkelman,

I have been simulating a system for a long time now. Each run of NSW=500 steps finished without reaching the accuracy set (EDIFFG = -0.01 and EDIFF = 1.0E-04) and I had to continue from the last run for more than 2 times.

As you can see from the attached vef.pl, the system ...

Dear all,

I am calculating the d-band center using the ''dosanalyze.pl' script.
For instance, I know that the surface atoms 2, 3, 8 are involved in the bonding of my adsorbate. Thus, I am interested in calculating the d-band center for these thee atoms.

Therefore,
dosanalyze.pl 2 3 8
No energy ...

Thank you Prof. Henkelman for your answer.

Dear Prof. Greame,
I am trying to use a force based conjugate gradient optimizer to find the ground state of a molecule (CH3OH) in a box. However, I see that the ions are not at all displacing. The positions of ions in CONTCAR are same as the positions in POSCAR. The same thing is observed after two ...

Dear all,

I am increasingly starting to read in recent papers that the "Improved force reversed method" is being used to locate the transition state. For example, some of the recent papers which say they use this method are:

1. https://www.sciencedirect.com/science/article/pii/S2211285517306985
2 ...

Dear Prof. Henkelman,

Thank you for your critical analysis of my job and the helpful suggestions to improve them. When you say [quote]
.... one H atom dissociates from CH4 to the surface leaving a radical CH3 above the surface, which then sequentially adsorbs. That is why you are seeing a barrier ...

Dear Prof. Henkelman and others,

I have been having issues with the convergence of a NEB calculation. I am attaching my calculation folders to this post. Any help to overcome convergence issues are welcome. Here are my calculation details:

I have been performing the NEB calculation in three stages ...

Dear Prof. Henkelman and all,

I am using dymseldsp.pl to make the DISPLACECAR to perform the dynamic matrix calculations. After getting the vibrational frequencies, I would like to use the Thermochemistry module in ASE package (https://wiki.fysik.dtu.dk/ase/ase/thermochemistry/thermochemistry.html ...

Thank You Prof. Henkelman, that was very helpful. I could reproduce the plot you posted.

Dear Prof. Henkelman and all,

I have run a NEB calculation and I wrapped it up with run of 'vfin.pl' . Inside the folder created by vfin.pl, I run the 'nebresults.pl' to produce all the results plots of my NEB calculation. But the 'mep.eps' plot produced is wierd (attached). I am also attaching the ...

Dear Prof. Henkelman,

I am observing that my dimer runs are abruptly stopping updating the output files. The worst part is that the job is still seen in the queue as running. Only when I go to check the status of the output files, I realize that the job has stopped updating a long time back.

I am ...

Dear Prof. Henkelman,

Thank you for your advice. I'll try to implement it now. This is what I plan to do now:

- I'll run a rough NEB calculation between initial_position and final_position POSCARS.
- After running vfin.pl on the result, I'll use neb2dim.pl script to create a dimer run folder and ...

Dear Prof. Henkelman and users,

I am trying to find the transition state of a simple reaction such as CH --> C + H on a Ni(111) slab. For this, I have optimized CH on the slab ( attached as POSCAR_01.tar.gz to this post) and I also optimize co-adsorbed 'C + H' ( attached as POSCAR_02.tar.gz to this ...