Search found 55 matches

by kai
Wed Dec 09, 2020 8:12 am
Forum: VTSTTools
Topic: nebmake.pl bug?
Replies: 5
Views: 5457

Re: nebmake.pl bug?

got it and thanks
by kai
Thu Dec 03, 2020 8:43 pm
Forum: VTSTTools
Topic: Illegal division by 0 with dymmatrix_v5.4.pl
Replies: 3
Views: 5261

Re: Illegal division by 0 with dymmatrix_v5.4.pl

vasp 5.4 changes the format, and you need to specify mass

add one line anywhere in OUTCAR (at the front):
POMASS = xxx; ZVAL =
POMASS = xxx; ZVAL =
POMASS = xxx; ZVAL =
.....
before use the scripts and have fun
by kai
Thu Dec 03, 2020 8:37 pm
Forum: VTSTTools
Topic: nebmake.pl bug?
Replies: 5
Views: 5457

nebmake.pl bug?

Hi, everyone, I have been using nebmake.pl to prepare my files, and everything went on fine until recently. Simply put, nebmake didnt interpolate good intermediate images any more. # image 00: POSCAR 0.6205393683339545 0.3748186251700154 0.6113134379103631 T T T 0.4407191996091184 0.3753464715751533...
by kai
Fri Jan 31, 2020 9:22 am
Forum: VTSTTools
Topic: from converged neb to dimer: ts goes away....
Replies: 2
Views: 7424

Re: from converged neb to dimer: ts goes away....

further update,

a contiuned neb at k221 successfully converged the ts to 0.02 ev/A....
by kai
Tue Jan 28, 2020 6:37 am
Forum: VTSTTools
Topic: from converged neb to dimer: ts goes away....
Replies: 2
Views: 7424

from converged neb to dimer: ts goes away....

Hi, all, I have such a problem to examine the barrier corresponds to the barrier of flipping the Si-dimer on the famous Si(001) surface. I started by climbing neb, using 3 images, gamma point k, and the calculation successfully converged to every image below 0.02 ev/A. TS is image #2 As a next step,...
by kai
Fri Mar 21, 2014 1:09 am
Forum: VTSTTools
Topic: initial velocities for MD after a normal mode calculation
Replies: 5
Views: 14543

Re: initial velocities for MD after a normal mode calculatio

thx, Graeme, I thought about the fixed bulk atoms too in the NVE....but i still have the same problem even putting a single CO molecule....dont know where the problem is from... a quick google guides me here, and you think that is relevant to vasp? http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2346486...
by kai
Thu Mar 20, 2014 6:21 pm
Forum: VTSTTools
Topic: initial velocities for MD after a normal mode calculation
Replies: 5
Views: 14543

Re: initial velocities for MD after a normal mode calculatio

thanks, Graeme. A question that sounds a bit off topic from this forum, but i am still assuming you are the right person to ask In a MD calculation, would the overal momentum conserved during the course of the process? say, in the N, V, E conserved scheme (IBRION = 0, SMASS = -3)? I thought naturall...
by kai
Thu Mar 06, 2014 10:28 pm
Forum: VTSTTools
Topic: initial velocities for MD after a normal mode calculation
Replies: 5
Views: 14543

initial velocities for MD after a normal mode calculation

Dear Prof. Graeme and others, i have a thought of using the results of wonderful normal mode calculation to run a molecular dynamics simulation. I plan to excite a specific mode of a molecule adsorbed on surface. based on my understanding, it goes as follows: 1 getting an equilibrium adsorbed geomet...
by kai
Fri Feb 28, 2014 4:32 pm
Forum: VTSTTools
Topic: normal modes from DYNAMICAL MATRIX
Replies: 6
Views: 12001

Re: normal modes from DYNAMICAL MATRIX

i am with you now, Graeme...thanks
by kai
Thu Feb 27, 2014 9:50 pm
Forum: VTSTTools
Topic: normal modes from DYNAMICAL MATRIX
Replies: 6
Views: 12001

Re: normal modes from DYNAMICAL MATRIX

thanks Graeme.....

when I looked at the modes at almost 0 cm-1, in addition to the expected rotation/translation, there is some stretch of bonds...is that because of the displacement in the cartesian coordinates....anyway to do it in vasp to work in the internal coordinates?
by kai
Wed Feb 26, 2014 4:21 pm
Forum: VTSTTools
Topic: normal modes from DYNAMICAL MATRIX
Replies: 6
Views: 12001

Re: normal modes from DYNAMICAL MATRIX

thank, Graeme, I have a further question, how does dyn matrix generate the set of normal modes and generate the movies? Does it have something to do with the way to set up the DISPLACECAR? In a naive thought of my case of C6H4I2, i pictured the modes as 3 trans +3 rotation +30 vibration; and in each...
by kai
Tue Feb 25, 2014 6:26 pm
Forum: VTSTTools
Topic: normal modes from DYNAMICAL MATRIX
Replies: 6
Views: 12001

normal modes from DYNAMICAL MATRIX

we followed the instruction to calculate an adsorbed ortho diiodoebenzene, C6H4I2 on Cu...In DISPLACAR, we ask all molecular atoms to move 0.015 by x, y, z, and used the wonderful scripts to visualize these modes. I thought each mode would corresponds to the motion of a single atom in the molecules,...
by kai
Thu Oct 03, 2013 7:45 pm
Forum: Bader
Topic: Bader failure for Si(100)-2x1
Replies: 1
Views: 12217

Re: Bader failure for Si(100)-2x1

I think i finally understand it now, perhaps....

Bader is talking about excess valence electron-charge. so this is a relative quantity; a positive bader charge could mean an absolute negative charge.
by kai
Thu Mar 08, 2012 12:48 am
Forum: VTSTTools
Topic: dimer calculation error message
Replies: 3
Views: 12154

Re: dimer calculation error message

further update, though i dont understand it seems to be associate with the gamma only version vasp; the regular one runs nicely. (the version we are running is 5.2.11) my labmate had similar experience when running NEB using ibrion=3 (with gamma only version), but fine with ibrion=1(again gamma only...
by kai
Wed Mar 07, 2012 9:09 pm
Forum: VTSTTools
Topic: dimer calculation error message
Replies: 3
Views: 12154

Re: dimer calculation error message

you are right....it is the electronic convergence...thx