Search found 28 matches

by microomran
Sun May 24, 2020 1:10 pm
Forum: VTSTTools
Topic: DynamicMatrix_CH4
Replies: 4
Views: 5196

Re: DynamicMatrix_CH4

Thank you.Sorry,I just misread the numbers.I appreciate your kind help.
by microomran
Sat May 23, 2020 10:18 pm
Forum: VTSTTools
Topic: DynamicMatrix_CH4
Replies: 4
Views: 5196

Re: DynamicMatrix_CH4

Thank you...I have some doubts How I can calculate ZPE/Svib in presence of imaginary frequencies to reproduce calculations as attached? dymmatrix.pl will ignore them? In the case of of surface_adsorbate and clean surface calculations I managed to get all real frequency but never get same with molecu...
by microomran
Sat May 23, 2020 11:10 am
Forum: VTSTTools
Topic: DynamicMatrix_CH4
Replies: 4
Views: 5196

DynamicMatrix_CH4

Dear Dr.Graeme I am trying to use dynamic matrix to get vibratioonal frequencies for some simple molecules in box. I started with methane relaxation at PREC= High ,then followed by dynamic matrix calculations (files attached).However,the imaginary frequencies persist even after increasing the accura...
by microomran
Mon Dec 03, 2018 5:20 pm
Forum: VTSTTools
Topic: Vinyard formula in Arrhenius Eq. dymprefactor.pl
Replies: 3
Views: 8654

Re: Vinyard formula in Arrhenius Eq. dymprefactor.pl

Thank you for the explanation. In fact, I am working with temperature 800-1000K (that is considered in high Temperature,is n't it?) so I used that simple classical form k(T)=A exp (-Ea/KbT) where A is from dymprefactor.pl/Vineyard and I plug in the Ea directly from NEB results for few calculation.Va...
by microomran
Mon Dec 03, 2018 1:46 pm
Forum: VTSTTools
Topic: Vinyard formula in Arrhenius Eq. dymprefactor.pl
Replies: 3
Views: 8654

Vinyard formula in Arrhenius Eq. dymprefactor.pl

Dear Dr.Graeme, Currently I am calculating the rate constant for elementary reactions.I am using the simple harmonic TS theory and calculating the prefactor using dymprefactor.pl for that I use the simple form k(T)=A exp (-Ea/KbT) where A is prefactor form the script and Ea is the energy barrier fro...
by microomran
Mon Dec 03, 2018 1:17 pm
Forum: VTSTTools
Topic: Hydrogen association dynamic matrix
Replies: 7
Views: 12618

Re: Hydrogen association dynamic matrix

Dear Dr.Graeme ,

Crystal clear! ..Thank you very much for your help.

Regards,
A.Omran
by microomran
Fri Nov 30, 2018 8:43 am
Forum: VTSTTools
Topic: Hydrogen association dynamic matrix
Replies: 7
Views: 12618

Re: Hydrogen association dynamic matrix

Dear Dr.Graeme, I have continued with neb calculation more close to 0.01 eV Force as follow 0 0.007584 -183.098500 0.000000 1 0.006079 -182.749800 0.348700 2 0.003504 -182.516000 0.582500 3 0.001 476 -182.209900 0.888600 4 0.017795 -182.319100 0.779400 5 0.027094 -182.352200 0.746300 6 0.034287 -182...
by microomran
Sat Nov 24, 2018 6:06 pm
Forum: VTSTTools
Topic: Hydrogen association dynamic matrix
Replies: 7
Views: 12618

Re: Hydrogen association dynamic matrix

Dear Dr.Graeme, Thank you for advice. -Totally agree with your suggestion,I set up NEB calculation to continue further to less than -0.05 eV using FIRE. -Thanks for the tip about stopping reaction if Dimer cross from -ve to +ve curvature .In fact, I have just faced this problem with CH4 dissociation...
by microomran
Sat Nov 24, 2018 3:53 am
Forum: VTSTTools
Topic: Hydrogen association dynamic matrix
Replies: 7
Views: 12618

Re: Hydrogen association dynamic matrix

Thanks for your reply. Here is the calculation details First ,I have started with 6 images using QM and get 0 0.007584 -183.098500 0.000000 1 0.014441 -182.642100 0.456400 2 0.018104 -182.490600 0.607900 3 0.078443 -182.197500 0.901000 4 0.098946 -182.266200 0.832300 5 0.088267 -182.319200 0.779300 ...
by microomran
Fri Nov 23, 2018 8:54 pm
Forum: VTSTTools
Topic: Hydrogen association dynamic matrix
Replies: 7
Views: 12618

Hydrogen association dynamic matrix

Dear Dr.Graeme, For the reaction of H+H-->H2 over Ni-based catalyst,I have successfully performed cNEB followed by Dimer to get the T.S. with calculation converged to the given setting of -0.01eV. Trying to use dynamic matrix to find imaginary frequecy/ZPE ,multiple imaginarg frequencies are persist...
by microomran
Tue Oct 09, 2018 6:52 pm
Forum: VTSTTools
Topic: Transition state calculation for wealy bound molecules
Replies: 18
Views: 24334

Re: Transition state calculation for weakly bound molecules

Hi Andrew, Thank you very much for your insights and detail.I have already tried dimmin.pl with the 0.1 displacement and with now change in the result still same with "negative" barrier .I will give another chance with 0.2/0.3 displacements to see if any difference. Meanwhile,I will try a ...
by microomran
Sun Oct 07, 2018 5:42 am
Forum: VTSTTools
Topic: Transition state calculation for wealy bound molecules
Replies: 18
Views: 24334

Re: Transition state calculation for weakly bound molecules

Dear Prof.Graeme, Extending my gratitude for your kind support,I have gone for both ways to confirm the reaction mechanism. Initially,I confirmed that I got the right saddle point by dynamic matrix which resulted in only 1 imaginary vibrations @848.34 cm-1 .Then from that T.S.: (a)Dimer:Using dimmin...
by microomran
Fri Oct 05, 2018 7:27 pm
Forum: VTSTTools
Topic: Transition state calculation for wealy bound molecules
Replies: 18
Views: 24334

Re: Transition state calculation for weakly bound molecules

Dear Prof.Dr.Graeme, Thank you very much for your suggestion, (a)I have put your latest suggestion about intermediate convergence into action and waiting the results..just to clarify (please correct me if I am wrong): 1-I will minimize image 04 and consider it as my final state instead of my earlier...
by microomran
Wed Oct 03, 2018 5:21 am
Forum: VTSTTools
Topic: Transition state calculation for wealy bound molecules
Replies: 18
Views: 24334

Re: Transition state calculation for weakly bound molecules

Dear Prof.Graeme,

After reach below 0.1 force ,I switched to IOPT=1(LBFGS) as discussed ,After 450 steps the forces seems are not going down or very very slow (attached) .Should I consider FIRE or try DIMER better?

Thanks for your help
Omran
by microomran
Fri Sep 28, 2018 4:13 am
Forum: VTSTTools
Topic: Transition state calculation for wealy bound molecules
Replies: 18
Views: 24334

Re: Transition state calculation for wealy bound molecules

Please find attached calculations