[DFTB-Plus-User] SK parameters for Phosphorus for LC-TD-DFTB
Thomas Niehaus
thomas.niehaus at univ-lyon1.fr
Mon Jan 29 10:12:06 CET 2024
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=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>
>
>
>
>
> On Fri, Jan 26, 2024 at 2:52 AM Thomas Niehaus
> <thomas.niehaus at univ-lyon1.fr <mailto: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
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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
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