UT theoretical chemistry code forum

It may be because the nebresults.pl is looking for the CONTCAR files. Once an ionic step has completed, the distances should be there.

The distances are RMS distances between all the atoms, in Angstoms.

Can you make sure that the new objects: dimer.o dynmat.o neb.o lanczos.o sd.o cg.o qm.o lbfgs.o bfgs.o fire.o opt.o are all listed before chain.o in the makefile. My guess is that they are after, so that chain.o is being built before opt.o, and it is complaining about not finding the opt module. The...

The harmonic rate is R=v exp(-dE/kT) where dE is the activation energy and v is the prefactor.

Try setting EDIFFG to a very small value (1e-6 for example). If your minimum has a force below your stopping criteria of 0.01 eV/Ang, vasp will think it is converged and quit.

v0.22b 03/07

Fixed distances within cube files with a non-zero origin (again).
Added an OS X, Intel binary

Ok, that makes sense. If you start a dimer calculation near a saddle, it should converge to that saddle, irrespective of the modecar that you choose. To find other saddles, you need to use other initial starting configurations.

You need to say a little more about how you are starting the dimer calculations. The dimer calculation only requires an initial configuration (POSCAR) and an initial guess at the lowest mode (MODECAR). The final state configuration is not an input, unless you are using it to generate one of these tw...

Do you have an independent way of determining the total charge from the cube file? In principle, this is simply a matter of adding up all the numbers in the file, and possibly normalizing by the voxel size. If you get the same charge that the bader program outputs, the problem is probably due to how...

Yes, it was this segfault problem that prompted me to make the change which introduced the cube file bug. If you look in the cube_mod.f90, you try making the following change to the code. It just replaces an array multiplication with an explicit loop. For some reason, the array function has given me...

v0.22a 03/07

Minimum distance reporting is fixed, as well as a bug for non-cubic cube files.

Ok, there was a silly mistake in the cube reader which was causing problems for non-cubic cells. I've updated the tar.gz file. The results look much better for the pentanethiol partial charges: # X Y Z CHARGE MIN DIST ---------------------------------------------------------------- 1 0.0000 -0.1666 ...

We're still looking into the cube file problem. I think you have clearly shown that there is a problem interpreting the SEISTA->CUBE type file. We'll post back when we know what's going on, and update the code at the same time (with the min-dist fix included).

What you suggest would be fine. Slightly better is to copy the CENTCAR to the POSCAR. Because of the finite different steps, the current position (CONTCAR) could be displaced from the center of the dimer (CENTCAR) by the finite difference displacement distance (typically 0.01 Ang or less). In the co...

I don't think that it makes sense to break up the optimization into two steps. These kind of approaches usually introduce inefficiencies. One way to speed up the convergence of the NEB is to use our new force based optimizers. In particular, the FIRE optimizer is similar to quick-min, but tends to b...

v0.22 03/07 has been released.

Added the -ref option to allow for using a total charge density file for the Bader partitioning and a CHGCAR file to get the atomic charges. This option was added to work with the total charge density files that can be generated in the latest version of VASP.