[DFTB-Plus-User] SK parameters for Phosphorus for LC-TD-DFTB

Mon Jan 29 23:18:01 CET 2024

Thanks, Thomas, I've attached the input file and the corresponding
structure file.
best,
David

Dr Kathleen A Durkin,  Dr Dave Small and Dr. Azhagiya Singam
Molecular Graphics and Computation Facility, College of Chemistry
University of California, Berkeley, CA 94720-1460
https://mgcf.cchem.berkeley.edu/

On Mon, Jan 29, 2024 at 1:16 AM Thomas Niehaus <thomas.niehaus at univ-lyon1.fr>
wrote:

> Dear David,
>
> OpenMP is not very effective for TD-DFTB. I am currently working on an MPI
> parallel code. Can you send me your structure/input file? Then I can have a
> quick look what might be going on.
>
> Best Thomas
> On 1/26/24 10:58 PM, Mgcf Departmental via DFTB-Plus-User wrote:
>
> Hi Thomas,
>
> Thanks for your reply.  I totally understand, regarding the difficulty of
> creating new parameters, so I think I'll look into creating an analogue of
> my molecule that contains e.g. a nitrogen atom instead of P.  By the way, I
> was wondering if I could ask you another question about TD-LC-DFTB.  A test
> on a small molecule (21 atoms) went smoothly, but I then tried adding 40
> solvent molecules (for 261 atoms in total), and the calculation gets stuck
> after the SCC (which itself finishes in only a minute or so).  I figured
> that I'm perhaps missing something in the input file, or in the
> environment variables.  I'm using a fairly simply input file, with a TD
> section like this:
>
> ExcitedState {
>
>     Casida {
>
>         NrOfExcitations = 4
>
>         Symmetry = Singlet
>
>         Diagonaliser = Stratmann {SubSpaceFactor = 5}
>
>     }
>
> I'm using "ulimit -s unlimited", and I've tried setting OMP_NUM_THREADS to
> either 4, 8, 16, or 32 core, and both with or without setting
> MKL_NUM_THREADS to the same number.  I've also tried the calculation both
> with and without the following:
>
> export OMP_STACKSIZE=6G
>
> export OMP_MAX_ACTIVE_LEVELS=1
>
>
> In each case, the calculation gets stuck at the point in the output file
> where it writes "Stratmann diagonalisation of response matrix", and appears
> to make no progress for several hours.  Do you have any suggestions?
>
> best,
> David
>
>
> Dr Kathleen A Durkin,  Dr Dave Small and Dr. Azhagiya Singam
> Molecular Graphics and Computation Facility, College of Chemistry
> University of California, Berkeley, CA 94720-1460
> https://mgcf.cchem.berkeley.edu/
> <https://MailInBlack.univ-lyon1.fr/securelink/?url=https://mgcf.cchem.berkeley.edu&key=eyJsYW5nIjoiRlIiLCJ1cmwiOiJodHRwczovL21nY2YuY2NoZW0uYmVya2VsZXkuZWR1LyIsInRva2VuIjoiZ0FBQUFBQmx0Q3N0TGo4TlEzZW13THdsamMyRzlvUUJQM0ljWTQ4NmhnTGpTaG9KR1FJSERMWDZuWGptOElfLVo3dXI5WjhVWmVtdmwzTTFrOXVhOXJmMFg3bVdNbk5GaHFsVUxzV25leFpadWVmQTJoQlVMcWl4eElaZ3pDUFE3X2w0c0lfOUdlejRaLS1RWGRXN2NJTmYyWG0zMXA0Wm41UXprelFvQ200bUtnRjRyLUtDQ1Vyb1lzbl83NzJuUU5NZm4yY2lUc05aX20xU0V6TzBvWlcwMU40OUdYUmJYQndrbXVXbTdraHBoRUpPejVFUGhZclJEeENxc05LZnduejNiNzNhZ1NNYkxISXRfS1lqdHJ5dWdqTkRSaktpMm5jbkNmWUV1UkphcVNGQy13X3d3Nk43QVFWLTJjYWVnN1pmN0MtNnBPQUwifQ==>
>
>
>
> On Fri, Jan 26, 2024 at 2:52 AM Thomas Niehaus <
> thomas.niehaus at univ-lyon1.fr> wrote:
>
>> Dear David,
>>
>> there are currently no parameters for P. I can create them, but this
>> might take some time and work.
>>
>> Best Thomas
>> On 1/26/24 12:55 AM, Mgcf Departmental via DFTB-Plus-User wrote:
>>
>> Hi,
>>
>> I'm interested in doing LC-TD-DFTB calculations on a molecule that
>> contains (C, H, N, O, P) atoms.  I've used the ob2 slater-koster set for a
>> related molecule with just C,H,N,O atoms, and the results were promising,
>> so I'd like to apply the method to the P-containing molecule as well.  Does
>> anyone know if there exist compatible SK parameters for this?  I've tried
>> searching the web but didn't find anything.
>>
>> thanks,
>> David Small
>>
>>
>> Dr Kathleen A Durkin,  Dr Dave Small and Dr. Azhagiya Singam
>> Molecular Graphics and Computation Facility, College of Chemistry
>> University of California, Berkeley, CA 94720-1460
>> https://mgcf.cchem.berkeley.edu/
>> <https://MailInBlack.univ-lyon1.fr/securelink/?url=https://MailInBlack.univ-lyon1.fr&key=eyJsYW5nIjoiRlIiLCJ1cmwiOiJodHRwczovL01haWxJbkJsYWNrLnVuaXYtbHlvbjEuZnIvc2VjdXJlbGluay8_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>
>>
>>
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>>
>> --
>> Prof. Dr. Thomas Niehaus
>> Institut Lumière Matière
>> UMR5306 CNRS
>> Université Claude Bernard Lyon 1
>> Domaine Scientifique de La Doua
>> 10 rue Ada Byron
>> 69622 Villeurbanne CEDEX, France
>> --
>> Office: Brillouin building, 4th floor, room 006
>> Tel: +33 472 431 571
>> Home page: http://ilm-perso.univ-lyon1.fr/~tniehaus <https://MailInBlack.univ-lyon1.fr/securelink/?url=http://ilm-perso.univ-lyon1.fr&key=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>
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>
> --
> Prof. Dr. Thomas Niehaus
> Institut Lumière Matière
> UMR5306 CNRS
> Université Claude Bernard Lyon 1
> Domaine Scientifique de La Doua
> 10 rue Ada Byron
> 69622 Villeurbanne CEDEX, France
> --
> Office: Brillouin building, 4th floor, room 006
> Tel: +33 472 431 571
> Home page: http://ilm-perso.univ-lyon1.fr/~tniehaus
> Lab: http://ilm.univ-lyon1.fr
>
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