Search found 71 matches

by jianmin
Tue Feb 09, 2010 10:59 pm
Forum: VTSTTools
Topic: Can a DynMat calculation for an isolated molecule be done?
Replies: 2
Views: 6404

Re: Can a DynMat calculation for an isolated molecule be done?

Prof. Graeme, I appreciate your reply. I will follow your suggestions.
by jianmin
Tue Feb 09, 2010 7:50 pm
Forum: VTSTTools
Topic: Questions about DynMat calculation of gas-phase methanol
Replies: 16
Views: 25166

Re: Questions about DynMat calculation of gas-phase methanol

Hi Prof. Graeme, I have run 3 jobs from comparison. a 2x2x2 k mesh for the cubic box of 15 Angstrom side length, which has 2 k points. EDIFFG = -1.0E-8 EDIFF = 1.0E-8 ISMEAR = 1 DISPLACEMENT = 0.001 _______________________________________________ Job 1: When SIGMA = 0.1 k-point 1 : 0.2500 0.2500 0.2...
by jianmin
Tue Feb 09, 2010 6:17 pm
Forum: VTSTTools
Topic: Questions about DynMat calculation of gas-phase methanol
Replies: 16
Views: 25166

Re: Questions about DynMat calculation of gas-phase methanol

Hi Prof. Graeme, I have done the following tests according to your suggestions. (a) Increase the displacement to 0.005, and I got 177.080571 cm^{-1} ... 1 129.632840 cm^{-1} ... 1 48.307346 cm^{-1} ... 1 38.469833 cm^{-1} ... 1 26.444106 cm^{-1} ... 1 18.776305 cm^{-1} ... 1 12.635260 cm^{-1} ... 1 ...
by jianmin
Mon Feb 08, 2010 9:45 pm
Forum: VTSTTools
Topic: Questions about DynMat calculation of gas-phase methanol
Replies: 16
Views: 25166

Re: Questions about DynMat calculation of gas-phase methanol

Prof. Graeme, thanks a lot for your reply. I changed the EDIFFG to -1.0E-8 and then got all the frequencies as following: 352.208906 cm^{-1} ... 1 306.487546 cm^{-1} ... 1 87.364247 cm^{-1} ... 1 48.395025 cm^{-1} ... 1 35.040875 cm^{-1} ... 1 31.075402 cm^{-1} ... 1 9.693041 cm^{-1} ... 1 5.927690 ...
by jianmin
Mon Feb 08, 2010 9:07 pm
Forum: VTSTTools
Topic: Questions about DynMat calculation of gas-phase methanol
Replies: 16
Views: 25166

Questions about DynMat calculation of gas-phase methanol

Dear guys, I tried to get the vibrational frequeies of methanol (CH3-OH, which has 6 atoms). The following is what I did. Step 1: Fully relax one methanol molecule in a cubic box of 15 Angstroms side length. The key INCAR parameters are NBANDS = 10 NSW = 150 IBRION = 2 EIDFF = 1.0E-7 In the OUTCAR f...
by jianmin
Mon Feb 08, 2010 6:11 pm
Forum: VTSTTools
Topic: Questions about dosanalyze.pl
Replies: 4
Views: 13354

Re: Questions about dosanalyze.pl

Hi Prof. Graeme, thanks a lot for your note.
Is the new version of dosanalyze.pl script available for us at the moment?
by jianmin
Sat Feb 06, 2010 8:48 pm
Forum: VTSTTools
Topic: Can a DynMat calculation for an isolated molecule be done?
Replies: 2
Views: 6404

Can a DynMat calculation for an isolated molecule be done?

Dear guys, I need the zero point energy (ZPE) of a gas phase molecule like ethane. My quesitions are: 1. Can we get the vibration frequencies of an isolated molecule in a big box by a Dynamical Matrix calculation? 2. If we can, how do I prepare the DISPLACECAR file? Take ethane (8 atoms) as an examp...
by jianmin
Sat Feb 06, 2010 7:22 pm
Forum: VTSTTools
Topic: Questions about dosanalyze.pl
Replies: 4
Views: 13354

Re: Questions about dosanalyze.pl

Hi Wenjie, thank you very much for your answer.
Though, I still found that the values of NBANDS has a big effect on the calculated d-band center by the dosanalyze.pl.
by jianmin
Wed Feb 03, 2010 10:42 pm
Forum: VTSTTools
Topic: Questions about dosanalyze.pl
Replies: 4
Views: 13354

Questions about dosanalyze.pl

Dear guys, I tried to get the d-band center of Pd(111) surface and Pt(111) surface. I found that in the dosanalyze.pl script, "cut=0.25*$maxDOS", which means that the width of the quarter-height of maximum DOS times a value of "w" (the default value of "w" is 2.5) is us...
by jianmin
Wed Feb 03, 2010 6:38 pm
Forum: VTSTTools
Topic: How do I restart an NEB calculation?
Replies: 7
Views: 16055

Re: How do I restart an NEB calculation?

Hi, Prof. Graeme. Thank you so much for all the tips.
by jianmin
Wed Feb 03, 2010 2:31 pm
Forum: VTSTTools
Topic: How do I restart an NEB calculation?
Replies: 7
Views: 16055

How do I restart an NEB calculation?

Dear all: One of my NEB jobs was killed by the computer supervisor. It had been running for several days, finishing 27 ionic steps. My question is: Is that possible to restart this job using the configuration from 27th ionic step, instead of restarting it from stracth? If it's possible, how do I do ...
by jianmin
Wed Jan 27, 2010 2:40 pm
Forum: VTSTTools
Topic: Question about dynamical matrix calculation
Replies: 4
Views: 10393

Re: Question about dynamical matrix calculation

Hi Prof. Graeme, I setup a Pd(111) slab with 12 atoms (p(2x2) by 3 layers) and freeze all 12 Pd atoms and only relax the H atom. Is that fine with the calculation?
by jianmin
Tue Jan 26, 2010 3:01 pm
Forum: VTSTTools
Topic: Question about dynamical matrix calculation
Replies: 4
Views: 10393

Question about dynamical matrix calculation

Dear guys, To learn how to get the prefactor of a reaction by a dynamical matrix calculation, I have built a model of H difusion on Pd (111) surface. After performing two separate dynamical calculations for both initial state and transition state, I issued commands dymmatrix.pl DISPLACECAR OUTCAR to...
by jianmin
Mon Jan 25, 2010 10:55 pm
Forum: VTSTTools
Topic: Questions about the DISPLACECAR file
Replies: 2
Views: 9149

Re: Questions about the DISPLACECAR file

Hi Prof. Graeme, I appreciate you replies which help me so much.
by jianmin
Mon Jan 25, 2010 10:21 pm
Forum: VTSTTools
Topic: Error in the discription of DYNAMICAL MATRIX?
Replies: 2
Views: 6497

Re: Error in the discription of DYNAMICAL MATRIX?

Prof. Graeme, thank you very much for your prompt reply.

Now I understand that:
To do a serial calculation, use NSW=DOF+1 and do not set the IMAGES parameter;
To do a parallel calculation on N cores, use NSW=DOF/N+1 and set IMAGES=N.