problem about pxaid2 Tut1_basics/ step3

[Zhiyong Zhang]

when i  using Pyxaid2 /Tut1_basics/step2, It calculated and completed well. It create dir " Tut1_basics/step2/res/ "

however, I have encountered a problem while using Pyxaid2 for step3.

namd_7.localhost show that:

"

Maximal Hamiltonian file to read is /home/zzy-x220/chemsoft/pyxaid2-master/scratch/Tut1_basics/step2/res/0_Ham_250_re

Error: Can not open file Haa0_re. Check if this file exists"

but in " Tut1_basics/step2/res/ ", there are not any file named "Haa0_re".!

how to resolve this problem?

thanks

 

[Alexey Akimov]

Dear Zhiyong,

Could you please provide sufficient details? Your input file at least. If you have the Error saying there is not "Haa0_re" file, then I guess you might have input the prefix and/or suffix parameters wrong. Please check that you didn't mistyped the prefixes as "Haa" instead of "Ham".

Best,

Alexey

[Zhiyong Zhang]

Dear Alexey, 

Thanks.

I use the tutorial input, and there was a little change according to my sysytem.

the input  and pbs files are appended below . I  didn't mistype the prefixes as "Haa" instead of "Ham"..

namd_8.localhost is the error information file.

thanks for your attention. Please help me.

Best,

Zhiyong.

[Wei Li]

Hi Zhiyong,

if you just want to try the pyxaid2 example, I would suggest you look into the examples at https://github.com/Quantum-Dynamics-Hub/pyxaid2/tree/master/example

Since pyxaid2 has changed a lot with respect to pyxaid1, i.e., the vibronic Ham files reading, and the tutorials you are looking into are outdated and adapted with the original pyxaid.

best,

Wei

[Zhiyong Zhang]

Dear wei,

 thanks for your help. I will try the new example or pyxaid I .

 I have another question, I can not find any example on PYXAID2- DFTB. Where can i get it?

 thanks a lot.

Best

 Zhiyong

[Wei Li]

Hi Zhiyong,

PYXAID2 has never interfaced with DFTB.

Wei

[Zhiyong Zhang]

Dear Wei,

 I has read a paper :

Nonadiabatic Molecular Dynamics for Thousand Atom Systems: A Tight-Binding Approach toward PYXAID

Sougata Pal†, Dhara J. Trivedi∥, Alexey V. Akimov§, Bálint Aradi‡, Thomas Frauenheim‡, and Oleg V. Prezhdo

J. Chem. Theory Comput., 2016, 12 (4), pp 1436–1448

DOI: 10.1021/acs.jctc.5b01231

It said "By combining PYXAID with DFTB, we have integrated the advanced techniques for simulating NA-MD within the tight binding approximation (DFTB-NA-MD)."

is there any PYXAID branches other than PYXAID2 to combine DFTB?

Best

Zhiyong

[Wei Li]

Zhiyong,

At present no branch in PYXAID 1/2 to interface DFTB.

Perhaps you can write the scripts yourself, using DFTB to run electronic structure calculation and NA coupling calculation, then PYXAID for NA-MD.

Wei

[Alexey Akimov]

Hi Zhiyong,

In fact, the interface of DFTB+ with Pyxaid does exist, but it is distributed solely by Dr. Pal (not an open-source). Please contact him if you want to use it. 

Best,

Alexey

[Roland Gillen]

Just in case someone else runs into this problem:  The error is caused by the fact that the namd function always attempts to read the Haa and Hbb Hamiltonians (at least in the version of PYXAID2 that I downloaded). Those files, however, are only generated for nac_method = 3 in step 2. As Haa and Hbb are only required if spin-orbit interaction is to be included in step 3, this can be easily fixed by only reading those files in case of alph_bet=1.

[Zhiyong Zhang]

Dear Roland Gillen,

  can you give me more information? I don't know how to "only reading those files in case of alph_bet=1". What should I do? Which file should be changed?

Thanks a lot.

your sinceresly,

                    zhiyong zhang

[Wei Li]

Hi Zhiyong,

I would say not try "alph_bet=1" for this moment since couple different spin multiplicity in electronic excitation is still under development.

best,

Wei