Search found 24 matches

by mmg016
Thu May 09, 2019 12:19 pm
Forum: VTSTTools
Topic: system very near to the ground state
Replies: 4
Views: 5043

Re: system very near to the ground state

Thank you Prof. Henkelman, for your time and efforts.
by mmg016
Thu May 02, 2019 7:47 am
Forum: VTSTTools
Topic: system very near to the ground state
Replies: 4
Views: 5043

Re: system very near to the ground state

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
by mmg016
Wed May 01, 2019 5:11 pm
Forum: VTSTTools
Topic: system very near to the ground state
Replies: 4
Views: 5043

system very near to the ground state

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 seem...
by mmg016
Sun Mar 17, 2019 7:05 am
Forum: VTSTTools
Topic: negative d-band center
Replies: 1
Views: 3893

negative d-band center

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 range...
by mmg016
Tue Oct 02, 2018 1:02 pm
Forum: VTSTTools
Topic: Ions are not moving between POSCAR and CONTCAR
Replies: 2
Views: 5990

Re: Ions are not moving between POSCAR and CONTCAR

Thank you Prof. Henkelman for your answer.
by mmg016
Mon Oct 01, 2018 1:47 pm
Forum: VTSTTools
Topic: Ions are not moving between POSCAR and CONTCAR
Replies: 2
Views: 5990

Ions are not moving between POSCAR and CONTCAR

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...
by mmg016
Sun Jun 03, 2018 10:15 pm
Forum: VTSTTools
Topic: Improved force reversed method
Replies: 0
Views: 13800

Improved force reversed method

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. h...
by mmg016
Wed Mar 21, 2018 7:42 am
Forum: VTSTTools
Topic: NEB calculation
Replies: 3
Views: 7466

Re: NEB calculation

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 ov...
by mmg016
Thu Mar 15, 2018 11:08 am
Forum: VTSTTools
Topic: NEB calculation
Replies: 3
Views: 7466

NEB calculation

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 o...
by mmg016
Wed Feb 28, 2018 5:36 pm
Forum: VTSTTools
Topic: Thermochemistry from ASE for dynamic matrix calculations
Replies: 0
Views: 12198

Thermochemistry from ASE for dynamic matrix calculations

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) ...
by mmg016
Mon Jan 08, 2018 10:15 am
Forum: VTSTTools
Topic: wrong mep.eps
Replies: 2
Views: 6351

Re: wrong mep.eps

Thank You Prof. Henkelman, that was very helpful. I could reproduce the plot you posted.
by mmg016
Sun Jan 07, 2018 7:15 pm
Forum: VTSTTools
Topic: wrong mep.eps
Replies: 2
Views: 6351

wrong mep.eps

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 ...
by mmg016
Wed Oct 18, 2017 2:01 pm
Forum: VTSTTools
Topic: DIMER run stops updating abruptly
Replies: 1
Views: 4048

DIMER run stops updating abruptly

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 at...
by mmg016
Tue Oct 03, 2017 7:11 pm
Forum: VTSTTools
Topic: Dimer run converging to the initial state
Replies: 2
Views: 5165

Re: Dimer run converging to the initial state

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 run...
by mmg016
Mon Oct 02, 2017 9:56 pm
Forum: VTSTTools
Topic: Dimer run converging to the initial state
Replies: 2
Views: 5165

Dimer run converging to the initial state

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 ...