pewald3D

[tobiaskoc...@gmail.com]

Hello,

I want to calculate refined charge transfer rates for a KMC simulations for an organic semiconductor in a 3D periodic box in VOTCA, using the long-range embedding of molecular ions and excitations in a polarizable molecular environment.
(J. Chem. Theory Comput., 2016, 12 (9), pp 4516–4523)

I suppose it is done via the pewald3D options. However, I think the information in the VOTCA-CTP manual, regarding this aspect is quite limited.

Can anyone give me some hints about the workflow for these calculations?
Which input files are necessary?
How can I determine the self-consistent background / foreground polarization? 
What is a suitable cutoff for the polarization cloud?

Thank you and best wishes

Tobias

[Jens Wehner]

Hallo Tobias,

Again not a ctp developer so take this info with a grain of salt, as I did this last 5 years ago.

So:

1) yes

2) nothing apart from the options files and the stuff you typically need to calculate side energies

3) a) run ctp_run -e ewdbgpol

this creates a background.ptop file

b) run ctp_parallel -e pewald3d and specify the above produced file in the options

b2) you probably have to create a jobfile first, using jobwriter, but I am not sure about that anymore

4) typcial is 3nm

[Denis Andrienko]

Hi Tobias,

I am updating the manual right now to include Carl's developments. Will push it to the repository sometime next week.

Meantime you could try to run (if you are familiar with the CTP workflow)

ewdbgpol, then jobwriter, then pewald3d.

I attach typical input files.

Best,

Denis

[Denis Andrienko]

Hi Tobias,

I have added Ewald schemes description to the manual.

You can pull and compile it with

cmake -DBUILD_CTP_MANUAL=ON

I also attach it for your convenience.

Denis

[tobiaskoc...@gmail.com]

Dear Jens and Denis,

Thank you very much for your efforts and useful hints.
The Ewald scheme with ewdbgpol, jobwriter and pewald3d, as presented in the manual, works well.

Thank you and best wishes,
Tobias

Am Mittwoch, 23. Januar 2019 17:27:09 UTC+1 schrieb tobiaskoc...@gmail.com:

[tobiaskoc...@gmail.com]

Hello,

I have got a further question concerning the use of pewald3d for a polymer.

So far I can calculate the energy contributions with the long-range embedding in a polarizable environment,
I treat an entire polymer chain as one conjugated segment and hopping site.
However, I want to partition the polymer into conjugated segments of varying number of chain elements.

1) I suppose for QM calculations to obtain the orbitals or the *.mps files for segments, one needs to saturate the segment with "artificial, ghost" hydrogen atoms, which do not appear in the initial *.gro morphology.
This way the number of atoms or polarizable sites in the QM file might differ from the number of atoms in the *.gro file.
Is there a way or workaround how to treat such dummy atoms / sites in VOTCA-CTP?
Can one exclude certain "ghost" atoms in the Ewald summation?

2) Furthermore, or I have got a CDFT-based parametrization of the charge transfer integrals for intra-chain charge transport.
    Is there a way how to set the J values?

    how to use a relation like Jintra = J0 cos(theta) for intrachain transport.

Best wishes,
Tobias

[Denis Andrienko]

Hi Tobias,

It is easy to answer (2):Everything is stored in an sql file, you can access all fields with, e.g,, sqlpython module. Let me know if you need an example. Alternatively, you can prepare an xmlfile similar to the output of the idft calculator (see ctp_parallel -j write) and read it in with the ctp_parallel -j read command, as described in the manual.

Regarding (2): we have done this before, this is what different segment mappings are for. Let me see if this is still in the code.

Best,

Denis

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[Denis Andrienko]

Virtual sites are still in the code.

In the mapping file, you have to tell whether the mps atom is virtual (1) or real (0):

<virtual_mps> 0 0 0 0 0 0 1 </virtual_mps>

The last atom here is virtual.

[tobiaskoc...@gmail.com]

Hello Denis,

So far I did not figure out how to include your suggestions.
Do you have an example, where one fragment is divided, into two conjugated segments, including the treatment of the ghost H atoms for the QM calculations?

Best wishes,
Tobias