Dear Admin,
I have few questions regarding the dynamic calculation setup.
(1) Can we use CI-NEB run for dynamical matrix calculation just changing INCAR tags like ICHAIN NSW and POTIM etc as given in the website?. but the 00 folder contains the initial geometry, so how do i set up calculations for the initial POSCAR in 00 folder ? Do I increase the IMAGES to IMAGES in CINEB+2 and rename the folder 00 to 01 , 01 to 02 and so on ?
(2) Regarding the DISPLACECAR file, do I generate using POSCAR in 00 (CINEB) and the final POSCAR or the initial and TS state POSCAR/CONTCAR ?.
(3) I have the bottom 2 layers fixed and 3 top layers of the slab allowed to relax for CINEB calculations. Does it make sense to freeze the whole slab except the adsorbate taking part in reaction/ movement for dynamic calculation or just freeze all except top layer and the adsorbates ?
(4) to generate DISPLACECAR, if i use dymseldsp.pl (POSCAR 1) (POSCAR 2) (atoms to include) (displacement) , do I count frozen atoms also or just the unfrozen atoms in a POSCAR in(atoms to include)?
thank you
Best
Prefactor calculation setup
Moderator: moderators
Re: Prefactor calculation setup
(1) The dynamical matrix calculation, using the vtstcodes, can be done without any subdirectories. The simplest way to run it is by specifying ICHAIN, and setting NSW=DOF+1, where DOF is the number of degrees of freedom specified to displace in you OUTCAR file.
A more advanced mode is to use a set of images to calculate displacements in parallel. This is described here: http://theory.cm.utexas.edu/vtsttools/dynmat/
You can not just run a dynamical matrix calculation starting from a converged NEB. You must calculate the modes at the minimum and saddle in two separate dynamical matrix calculations in order to calculate the prefactor.
(2) Most simply, the DISPLACECAR can contain the displacement for x, y and z for every non-frozen atom in your system.
(3) You can, but check to make sure that your prefactor does not change if you also include the substrate degrees of freedom.
(4) Frozen atoms should not move and should not be included in your dynamical matrix calculations -- those degrees of freedom should be zero in your DISPLACECAR.
A more advanced mode is to use a set of images to calculate displacements in parallel. This is described here: http://theory.cm.utexas.edu/vtsttools/dynmat/
You can not just run a dynamical matrix calculation starting from a converged NEB. You must calculate the modes at the minimum and saddle in two separate dynamical matrix calculations in order to calculate the prefactor.
(2) Most simply, the DISPLACECAR can contain the displacement for x, y and z for every non-frozen atom in your system.
(3) You can, but check to make sure that your prefactor does not change if you also include the substrate degrees of freedom.
(4) Frozen atoms should not move and should not be included in your dynamical matrix calculations -- those degrees of freedom should be zero in your DISPLACECAR.