UT theoretical chemistry code forum

Dear Graeme,
Thanks for the reply. Just a quick question to clarify: While trying to calculating the diffusion coefficient, D=D0 exp(-Q/kbT), the factor D0 is approximated in the harmonic limit as:
D0 = 1/6 a^2 exp(-ds/Kb) v0 where v0 is the preexponential factor of the rate constant.

When I use ...

Hello:
I checked the akmc.submit.pl script. We have the LSF queuing system. I changed the script akmc_submit.pl accordingly.
Here is what I get when I submit akmc_submit.pl

bsub <akmc.sub |tail -1
Job <13038> is submitted to default queue <normal>.



Regards,
PG

Hello:
Does the prefactor calculated using dymprefactor include the vibrational entropy term? S_vib ( which is calculated as a sum of harmonic oscillators). I am interested in calculating the bulk diffusion coefficient in a fcc crystal. I would like to include the S_vib term which is approximated ...

Hello:
I am still struggling to run the akmc example code as given. I have modified my submission scripts to be compatible with my cluster. I have created a director akmc_sample and copied the files. The akmc.pl and the other akmc submit scripts are all located in the vtsscripts directory. When I ...

Dear all,
I am trying to run the akmc code using the scripts as suggested. I have modified the three files akmc_submit.pl akmc_check.pl and akmc_kill.pl according to my system. I am running it on a cluster using the LSF queueing system. I tried with the example code and when I try to run it using ...

Dear Graeme,
I have attached the 4 files.

Thanks,
PG

Dear All,
I have a question about the function of dymanalyze.pl. From the script description it is used to analyze the convergence of the dynamical matrices w.r.t displacements. In my calculation, I have two dynamial matrices generated for two displacements with the number of atoms same in both ...

Dear Graeme,
Thanks for the reply. I will try to restart my calculation with the new settings. The saddle point in my calculation are converged well until the force on each atom <0.005 eV/Ang. I guess this should be a good force convergence.

Regards,
PG

Hello,
I am trying to find the problem with my dynamical matrix calculation. In the previous calculations I did not set ISYM = 0 and I think that was the problem for getting so many imaginary frequencies in the initial state. I repeated the calculations with ISYM = 0 and calculated the Dynamical ...

Dear Kai,
Thanks for your reply. Could you please elaborate? I have never done these calculations before. How do we determine which of the frequencies are real? There seem to be a lot of imaginaory frequencies. Also, I am interested in calculating the prefactor for which I obtained the dynamical ...

Hello everyone,
I managed to set up the dynamical matrix calculation using the DISPLACECAR file obtained by the dymseldsph.pl script and I included 40 atoms. I ran two calculations one for the initial state and one for the saddle point using a displacement of 0.001. However for the initial state I ...

Hello everyone,
I am doing a simple vacancy-mediated diffusion calculation for a bulk system. I would like to calculate the prefactor ab-initio by generating the dynamical matrix and calculating the frequency modes. I have calculated the transition state using the NEB method. My question is.
If I ...

Dear all,
I would like to know how to merge more than one MEP curves. I have a diffusion path which takes place along a cyclic path and I would like to create one continuous plot all the jump-heights. So I want to get the energies from nebef.dat and then use nebspline.pl to fit the data.

Regards ...

Dear Graeme,
I started the calculations again by letting the atoms relax in a few layers below and above the defect. The initial run was ok with the energy and the forces of the saddle point converging well. Below is the nebef.dat for the first run.
0 0.01768400 -1083.01825100 0.00000000
1 0 ...

Dear Graeme,
Will It work if I let all the atoms near the vacancy relax (upto 2-3 layers) and constrain the x-y movement of all the remaining atoms? I am not sure if this is physical though? The other option is to treat the system as a substrate system with the top and bottom layers fixed ...