Search found 71 matches

by jianmin
Thu Apr 18, 2013 1:22 pm
Forum: Bader
Topic: Problem related to Bader Charge Analysis
Replies: 5
Views: 22500

Re: Problem related to Bader Charge Analysis

Thanks a lot for your reply, Prof. Graeme. In the TeO2 unit cell, there are 4 Te atoms and 8 O atoms. One of my questions would be: Since VASP uses the pseudopotential method, there are only 4*6+8*6=72 electrons in the system (all these 72 electrons are valence eletrons.), not 4*52+8*8=272 eletrons,...
by jianmin
Wed Apr 17, 2013 8:52 pm
Forum: Bader
Topic: Problem related to Bader Charge Analysis
Replies: 5
Views: 22500

Problem related to Bader Charge Analysis

We are trying to use the VTST Bader Charge Analysis (BCA) program for the TeO2 crystal. What we want to find out is the complete spatial charge distribution for each atom in the crystal. There are 4 Te and 8 O in the TeO2 unit cell. So in total, we want to know the charge distribution of 4*52+8*8=27...
by jianmin
Thu Apr 29, 2010 9:48 pm
Forum: VTSTTools
Topic: Question about calculated vibrational frequecies
Replies: 3
Views: 8483

Re: Question about calculated vibrational frequecies

I still got some imaginary vibrational frequencies for molecules which strongly bind to Pd(111) surface, such as CO.
One thing I haven't tried is to include some Pd atoms into the dyn_matr calculation. Could you tell me which Pd atoms I should include? The Pd atoms binding to the molecules?
by jianmin
Fri Apr 16, 2010 9:11 pm
Forum: VTSTTools
Topic: NEWMODECAR from a Dimer calculation
Replies: 5
Views: 12094

Re: NEWMODECAR from a Dimer calculation

Thanks a lot for your reply, Prof. Graeme.
by jianmin
Fri Apr 16, 2010 4:02 pm
Forum: VTSTTools
Topic: NEWMODECAR from a Dimer calculation
Replies: 5
Views: 12094

NEWMODECAR from a Dimer calculation

Dear Prof. Graeme, I noticed that a file named NEWMODECAR is generated after a Dimer calculation is done. Does it mean that we could use this NEWMODECAR file for next run if the former run is not complete? In some cases, the Dimer calculation (let name it Job 1) is not complete after 50 NSW steps. I...
by jianmin
Thu Apr 08, 2010 10:09 pm
Forum: VTSTTools
Topic: Calculation of d-band center
Replies: 2
Views: 28740

Re: Calculation of d-band center

Thanks a lot for the explanation. I am learning it.
by jianmin
Tue Apr 06, 2010 6:17 pm
Forum: VTSTTools
Topic: Calculation of d-band center
Replies: 2
Views: 28740

Calculation of d-band center

Hi Prof. Graeme, Is there any new progress on the method of calculating the d-band center by VTST (the dosanalyze.pl script)? If there is, I would be glad to use it. Continue the topic in http://theory.cm.utexas.edu/forum/viewtopic.php?f=2&t=632&p=2070&hilit=center#p2070. According to th...
by jianmin
Mon Mar 08, 2010 7:06 pm
Forum: VTSTTools
Topic: Question about calculated vibrational frequecies
Replies: 3
Views: 8483

Re: Question about calculated vibrational frequecies

Prof. Graeme, thank you so much for all the tips. I will follow your suggestions.
I use EDIFF=1.0E-7 and displacement=0.01. I assume these values are accurate enough for dyn_matr calculations.
by jianmin
Fri Mar 05, 2010 6:55 pm
Forum: VTSTTools
Topic: Question about calculated vibrational frequecies
Replies: 3
Views: 8483

Question about calculated vibrational frequecies

Dear Prof. Graeme, I have calculated the vibrational frequencies of propanoic acid (CH3CH2COOH) adsorbed onto Pd(111). Since the molecule has 11 atoms, I got 33 modes as follows: 33.514594 cm^{-1} ... 1 15.126440 cm^{-1} ... 1 37.403031 cm^{-1} ... 0 64.535768 cm^{-1} ... 0 73.538973 cm^{-1} ... 0 9...
by jianmin
Mon Mar 01, 2010 9:21 pm
Forum: VTSTTools
Topic: Can a Dyn_Matr calculation be restarted?
Replies: 4
Views: 7783

Re: Can a Dyn_Matr calculation be restarted?

Thank you so much, Prof. Graeme. I will try that.
by jianmin
Sun Feb 28, 2010 10:14 pm
Forum: VTSTTools
Topic: Can a Dyn_Matr calculation be restarted?
Replies: 4
Views: 7783

Re: Can a Dyn_Matr calculation be restarted?

Hi Prof. Graeme, I am not sure I understand your idea of "zero the displacements that have been done". Let's assume that there is a 5-atom molecule adsorbing onto the 10-atom slab, and I set displacement to 0.001 to the molecule but not to the slab, then the DISPLACECAR looks like: 0.001 0...
by jianmin
Fri Feb 26, 2010 10:35 pm
Forum: VTSTTools
Topic: Can a Dyn_Matr calculation be restarted?
Replies: 4
Views: 7783

Can a Dyn_Matr calculation be restarted?

Hi Prof. Graeme, As my former post mentioned, I have to perform a dynamical matrix calculation for a big system. The job cannot be finished within the time limit of the supercomputer, e.g., 24 hours. Let's assume that the NSW = 31, if the first run has calculated 10 NSW steps, and I restart the job,...
by jianmin
Fri Feb 26, 2010 10:27 pm
Forum: VTSTTools
Topic: Questions about EDIFF for DynMat calculation
Replies: 3
Views: 7443

Re: Questions about EDIFF for DynMat calculation

Hi Prof. Graeme, thank you so much for your reply. Now I know that setting EDIFF to 1.0E-7 is unneccesary to get the optimized structure, but is neccesary for dynamical matrix calculations. I am calculating a system with a molecule adsorbing onto a 48-atom Pd slab. I think it's a big system for dyna...
by jianmin
Thu Feb 25, 2010 6:42 pm
Forum: VTSTTools
Topic: Questions about EDIFF for DynMat calculation
Replies: 3
Views: 7443

Questions about EDIFF for DynMat calculation

Hi Prof. Graeme, 1. To get the relaxed structure for a dynamical matrix calculation, should I really have to set EDIFF to such a small value as 1.0E-7? 2. When I use the relaxed structure from question 1 to perform a dynamical matrix calculation in order to get the vibrational frequecies, should I r...
by jianmin
Thu Feb 11, 2010 2:44 pm
Forum: VTSTTools
Topic: Questions about DynMat calculation of gas-phase methanol
Replies: 16
Views: 25168

Re: Questions about DynMat calculation of gas-phase methanol

Hi Prof. Graeme, thank you so much for all of your help. I set ISYM to 0 and it worked. The following is results from my job: 64.784000 cm^{-1} ... 1 50.187061 cm^{-1} ... 1 25.267127 cm^{-1} ... 1 4.768032 cm^{-1} ... 1 36.103207 cm^{-1} ... 0 43.456248 cm^{-1} ... 0 281.443955 cm^{-1} ... 0 1009.9...