Search found 1751 matches

by graeme
Wed Sep 19, 2018 1:06 pm
Forum: eOn
Topic: NEB terminated problems
Replies: 1
Views: 52

Re: NEB terminated problems

Again, as I mentioned in your other post, this is supposed to be about EON. In the EON code, you can in fact run the NEB image-by-image. But in VASP it must be parallel. Anyway, see my comments in your other post for possible solutions.
by graeme
Wed Sep 19, 2018 1:05 pm
Forum: eOn
Topic: NEB terminated problems
Replies: 1
Views: 27

Re: NEB terminated problems

First, this is posted on a forum related to the EON code. Is this really an EON calculation, or standard VASP-NEB? I assume it is the latter. If so, I think your assessment is correct, that you need to run each image on a sufficient number of cores to distribute the memory per core. To help with the...
by graeme
Mon Sep 17, 2018 2:50 pm
Forum: VTSTTools
Topic: Divergence of NEB calculation
Replies: 4
Views: 267

Re: Divergence of NEB calculation

You can see the current NEB forces using our script nebef.pl.

The time step is controlled by POTIM is you use the built-in vasp-optimizers and by the TIMESTEP tag if you use our vtst optimizers.
by graeme
Mon Sep 17, 2018 2:10 am
Forum: VTSTTools
Topic: Divergence of NEB calculation
Replies: 4
Views: 267

Re: Divergence of NEB calculation

There is some art to optimization, but there are also some sensible guidelines. When forces are high, use a conservative optimizer such as IBRION=3 and a small time step < 0.1. Once the forces are below 0.2 eV/Ang, you can switch to a second order optimizer (e.g. IBRION=1).
by graeme
Thu Sep 13, 2018 12:19 pm
Forum: VTSTTools
Topic: Transition state calculation for wealy bound molecules
Replies: 4
Views: 101

Re: Transition state calculation for wealy bound molecules

The problem is your initial paths. You have mechanisms in which molecules are being broken in the gas phase and then a fragment adsorbs on the surface (in the case of CO2 and CH4) or just left in gas phase (H2). If you are trying to understand dissociative adsorption, you need to find stable final s...
by graeme
Thu Sep 13, 2018 1:15 am
Forum: VTSTTools
Topic: Transition state calculation for wealy bound molecules
Replies: 4
Views: 101

Re: Transition state calculation for wealy bound molecules

Before getting into the dimer calculations, the NEB calculations do not looks right. I see jumps of over 2 eV between images in the first calculation and oscillations in the energy and high forces in the second. Check these paths to see if they are reasonable. I would not be surprised if you are loo...
by graeme
Tue Sep 11, 2018 6:49 pm
Forum: VTSTTools
Topic: Compile VASP 5.4.4 with VTST-176
Replies: 9
Views: 188

Re: Compile VASP 5.4.4 with VTST-176

the command for vasp is:
make veryclean

My concern is that there is an old chain.o object file in the src directory. If you clean the build there should be no .o files in the src subdirectory.
by graeme
Tue Sep 11, 2018 2:39 pm
Forum: VTSTTools
Topic: Compile VASP 5.4.4 with VTST-176
Replies: 9
Views: 188

Re: Compile VASP 5.4.4 with VTST-176

You do not need to modify makefile.include. Make sure that you do a make clean and check that chain.o is removed before making the vtst version.
by graeme
Tue Sep 11, 2018 1:31 am
Forum: VTSTTools
Topic: Compile VASP 5.4.4 with VTST-176
Replies: 9
Views: 188

Re: Compile VASP 5.4.4 with VTST-176

No, there is no secret rule. I just looked at my own makefile and stated where it was. To be honest, I'm not sure exactly where in the build order the vtst objects should go. I just figured that giving a specific place was better than suggesting that you place it by trial and error.
by graeme
Mon Sep 10, 2018 6:59 pm
Forum: VTSTTools
Topic: Compile VASP 5.4.4 with VTST-176
Replies: 9
Views: 188

Re: Compile VASP 5.4.4 with VTST-176

Make sure to add the VTST objects to your src/.objects file. This can be done by including a first line in the file: VTST_OBJS = bfgs.o dynmat.o instanton.o lbfgs.o sd.o cg.o dimer.o bbm.o \ fire.o lanczos.o neb.o qm.o opt.o chain.o and then add those objects after hamil_rot.o, as in: hamil_rot.o \ ...
by graeme
Mon Sep 03, 2018 6:56 pm
Forum: VTSTTools
Topic: Extracting Hessian Matrix from OUTCAR file
Replies: 2
Views: 94

Re: Extracting Hessian Matrix from OUTCAR file

With IBRION=5, vasp calculates the Hessian and the normal mode frequencies. Don't you just need the later for thermodynamic properties?

If you use the vtstcode, the dymmatrix.pl script generates the Hessian from forces printed in the OUTCAR file.
by graeme
Mon Sep 03, 2018 1:39 pm
Forum: VTSTTools
Topic: Continuous Run for Dimer Method
Replies: 11
Views: 764

Re: Continuous Run for Dimer Method

Yes, for sure. The dimer calculation should be continued with the CENTCAR file. If you use the vfin.pl script, the CENTCAR will be copied to the POSCAR, ready for another calculation.
by graeme
Sun Sep 02, 2018 12:46 pm
Forum: VTSTTools
Topic: Continuous Run for Dimer Method
Replies: 11
Views: 764

Re: Continuous Run for Dimer Method

Ah, you need a lower ediff for the dimer calculation. Using 1e-4 will result in too much noise in the forces so that the curvature calculation will be unreliable, as well as the dimer calculation. Use 1e-7 or 1e-8.
by graeme
Sun Sep 02, 2018 1:41 am
Forum: VTSTTools
Topic: Continuous Run for Dimer Method
Replies: 11
Views: 764

Re: Continuous Run for Dimer Method

Well, without having resolved the problems with the dimer calculation, I think that your continued ci-NEB calculation looks pretty good. You have a saddle point geometry at the 05 image with a barrier of 1.4 eV and a residual force of only 0.02 eV/Ang.
by graeme
Fri Aug 31, 2018 1:07 pm
Forum: VTSTTools
Topic: Continuous Run for Dimer Method
Replies: 11
Views: 764

Re: Continuous Run for Dimer Method

This looks strange - did you run the neb2dim.pl script to initialize your dimer calculation? Your dimer calculation starts with a much higher energy and force as compared to image 5 in your NEB calculation. You could try using the geometry from image 05 and a MODECAR generated from 04 and 06 as in: ...