Search found 14 matches

by tp.joe
Thu Jan 26, 2017 5:31 pm
Forum: VTSTTools
Topic: NEB Energy fluctuating without trend towards convergence
Replies: 8
Views: 15895

Re: NEB Energy fluctuating without trend towards convergence

Thank you Joshua, I will do it longer. And yes I did change a system a bit to make it a little simpler molecule. Also, I have tried Dimer method before using NEB image as the starting point, but the forces keep increasing with out decreasing trend at all, so I stopped. Did you have the same issue in...
by tp.joe
Fri Jan 20, 2017 6:28 am
Forum: Bader
Topic: Analysis "only when with core charges" yields unexpected results
Replies: 0
Views: 18557

Analysis "only when with core charges" yields unexpected results

Hello Prof. Henkelman, I am dealing with charge analysis of an oxygenated aromatic compound adsorbing on Ni surface, using VASP 5.4.1 with optB88-vdW for dispersion force correction. In short, the issue I encountered with is that when I included core electrons, the carbon atoms in the ring become po...
by tp.joe
Fri Jan 20, 2017 6:07 am
Forum: VTSTTools
Topic: NEB Energy fluctuating without trend towards convergence
Replies: 8
Views: 15895

Re: NEB Energy fluctuating without trend towards convergence

Yes please Prof. Attached is the detail of the calculation. Note that initially I used more than one picture for NEB, but the results were initially the same, so I reduced the number of picture to just the one with the highest energy (for quicker calculation) to see in a long run where does it lead ...
by tp.joe
Thu Jan 19, 2017 6:52 pm
Forum: VTSTTools
Topic: NEB Energy fluctuating without trend towards convergence
Replies: 8
Views: 15895

Re: NEB Energy fluctuating without trend towards convergence

Unfortunately, it does not. I have tried suggestions from other posts extensively, including doing damped MD with time step of 0.002, but it still fluctuates heavily with no tendency toward convergence. I have also tried using FIRE method. The results of both of these are attached.
by tp.joe
Thu Nov 17, 2016 5:01 am
Forum: Bader
Topic: Very quick question regarding using weight method in VASP
Replies: 1
Views: 7786

Very quick question regarding using weight method in VASP

Hi, I know that in VASP for accurate bader analysis, we need to include core charges and hence we do, bader CHGCAR -ref CHGCAR_sum I am wondering if we want to use the weight method is typing bader -b weight CHGCAR -ref CHGCAR_sum the correct way to do it or would this result in weight method of onl...
by tp.joe
Sun Nov 13, 2016 11:16 am
Forum: Bader
Topic: Error when using CHGCAR_sum
Replies: 4
Views: 13585

Re: Error when using CHGCAR_sum

Just an extra information regarding question no. 3 in the previous reply, I did an integration of no. of core electrons from AECCAR0 of a simpler system (just phenol), which is C6H6O1, therefore principally the core electrons should be 14 electrons using the maximum accuracy, the core electrons are ...
by tp.joe
Sun Nov 13, 2016 9:16 am
Forum: Bader
Topic: Error when using CHGCAR_sum
Replies: 4
Views: 13585

Re: Error when using CHGCAR_sum

I found a way to "alleviate" the issue. For future new users that may encounter the same issue, you should increase NG(X,Y,Z)F by MANY MANY folds, at least in my case. Increasing this should reduce the negative values in CHGCAR_sum significantly, and hence eradicate oscillation. In my case...
by tp.joe
Sat Nov 12, 2016 9:16 am
Forum: Bader
Topic: Error when using CHGCAR_sum
Replies: 4
Views: 13585

Re: Error when using CHGCAR_sum

I think I know now, it's likely to be because negative values in AECCAR0 correct?, if so do you have any suggestion of what may be the cause, my INCAR is, SYSTEM = Ni_slab_phenol PREC = Accurate ENCUT = 500 IBRION = 2 NSW = 0 ISIF = 2 NELMIN = 6 EDIFF = 1.0e-04 EDIFFG = -0.02 VOSKOWN = 1 NELM = 250 ...
by tp.joe
Sat Nov 12, 2016 6:32 am
Forum: Bader
Topic: Error when using CHGCAR_sum
Replies: 4
Views: 13585

Error when using CHGCAR_sum

Hi Prof., I have read through other thread regarding having an error "ERROR: should be no new maxima in edge refinement", I tried checking that the cause of this error is not as you mentioned earlier. My setup is a slab model with spin polarization, van der Waals interaction (optB88-vdW). ...
by tp.joe
Thu Oct 13, 2016 1:58 am
Forum: VTSTTools
Topic: Short questions regarding dimer method (it stops at one ionic run)
Replies: 2
Views: 6969

Re: Short questions regarding dimer method (it stops at one ionic run)

Hello sir, I attached the file (Dimer.tar.gz) that shows DIMCAR only 1 step. The POSCAR is the initial structure file, and the MODECAR file is generated from modemake.pl of the presumably transition structure from NEB and the initial state. I think this could have been much easier if I use neb2dim.p...
by tp.joe
Thu Oct 13, 2016 12:04 am
Forum: VTSTTools
Topic: Short questions regarding dimer method (it stops at one ionic run)
Replies: 2
Views: 6969

Short questions regarding dimer method (it stops at one ionic run)

Hello, I generated a modecar file using modemake.pl on initial structure and the likely transition state from CNEB. However, when I started it only run once and finished, the energy given is apparently the initial structure energy (POSCAR). In DIMCAR, this is what written Step Force Torque Energy Cu...
by tp.joe
Wed Oct 12, 2016 7:53 am
Forum: VTSTTools
Topic: General questions regarding CNEB followed by dimer method protocol
Replies: 2
Views: 7089

Re: General questions regarding CNEB followed by dimer method protocol

Thank you Prof. Graeme. Appreciated your quick reply.
by tp.joe
Tue Oct 11, 2016 11:56 pm
Forum: VTSTTools
Topic: General questions regarding CNEB followed by dimer method protocol
Replies: 2
Views: 7089

General questions regarding CNEB followed by dimer method protocol

Hello all, I am very new to vtst calculation. I am looking if anyone has encountered similar system as I currently do. The system is a reaction on a surface which is fairly large and also have to take into account van der Waals force. Convergence by CNEB using 5 images took a very long time (roughly...
by tp.joe
Fri Oct 07, 2016 10:05 am
Forum: VTSTTools
Topic: NEB Energy fluctuating without trend towards convergence
Replies: 8
Views: 15895

NEB Energy fluctuating without trend towards convergence

Hi, I am doing NEB calculation for a reaction of a rather complicated molecule on a fixed reaction surface. Preliminarily, I am using 3 images with LBFGS method. However, it seems like the molecule just moved back and forth so I used nebconverge.pl to generate the force. And as seen in the attachmen...