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patonlab / GoodVibes

Calculate quasi-harmonic free energies from Gaussian output files with temperature and other corrections
http://www.patonlab.colostate.edu
MIT License
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! Dispersion Correction Failed #47

Closed calvanid13 closed 2 years ago

calvanid13 commented 2 years ago

Dear Robert Paton Group,

I'm writing you because I encountered a message of failed "! Dispersion Correction Failed" (see below) when I used GoodVibes on my optimized Gaussian output using the flag --d3bj for the dispersion estimation (the same failed also with --d3).

Please, could you help me with that or tell me if I did something wrong?

Really Thanks in advance for your work and time.

My Best Regards,

Dario

:~/anthracene/gaussian_analysis/gaussian_dimer$ python -m goodvibes --d3bj anthracene.out GoodVibes v3.0.1 2021/07/20 16:49:39 REF: Luchini, G.; Alegre-Requena J. V.; Guan, Y.; Funes-Ardoiz, I.; Paton, R. S. (2019). GoodVibes: GoodVibes 3.0.1 http://doi.org/10.5281/zenodo.595246 Requested: --d3bj

Temperature = 298.15 Kelvin Pressure = 1 atm All energetic values below shown in Hartree unless otherwise specified. Using vibrational scale factor 1.0 for PBEPBE/6-31G(d,p) level of theory

Entropic quasi-harmonic treatment: frequency cut-off value of 100.0 wavenumbers will be applied. QS = Grimme: Using a mixture of RRHO and Free-rotor vibrational entropies. REF: Grimme, S. Chem. Eur. J. 2012, 18, 9955-9964

D3-Dispersion energy with Becke-Johnson damping will be calculated and added to the energy terms. REF: Grimme S.; Ehrlich, S.; Goerigk, L. J. Comput. Chem. 2011, 32, 1456-1465

! Dispersion Correction Failed

Structure E ZPE H T.S T.qh-S G(T) qh-G(T)

o anthracene -1077.780669 0.378979 -1077.379051 0.074184 0.069930 -1077.453235 -1077.448981

bobbypaton commented 2 years ago

Hi Dario - thanks for the message,

Your command is correct - however, the python code for dftd3 is installed separately from goodvibes for this to work properly.

  1. First you should clone or download pydftd3 from here: https://github.com/bobbypaton/pyDFTD3

  2. Make sure that the location of this module is then added to your $PYTHONPATH - for example, depending on where you download the repository, you will need to add something like the following line to your .bashrc or .zshrc:

export PYTHONPATH=$PYTHONPATH:/Users/rpaton/Code/pyDFTD3

  1. Once that's done your python environment should be able to import dftd3. To check this try python -m dftd3

  2. That's it - goodvibes should now be able to call pydftd3 to get these corrections.

Sorry it's not easier - we'll look into making this installation a bit more straightforward, e.g. with pip or conda!

calvanid13 commented 2 years ago

Dear Bobby,

Really Thanks a lot for your fast and clear reply. I will follow your advice and try the installation also of the pyDFTD3.

My Best Regards,

Dario