Author Topic: freeh - entropy  (Read 8233 times)

foea

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freeh - entropy
« on: October 18, 2011, 02:18:24 PM »
Hello,

I am trying to run freeh after a converged Numforce run to get the entropy but I always get the following message:

'number (0) of vibrational degrees of freedom with frequencies >0.000001 cm**(-1) does not agree with 3*natoms-6 this is a damn coincidence the programmer did not worry about.'


Unfortunately the manual doesn't give much information about freeh so I don't know if the problem lies in my structure or if I only don't use freeh correctly.
Please tell me what I can do to make sure that I don't get this message again.

Thanks for your help,
foea

Arnim

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Re: freeh - entropy
« Reply #1 on: October 18, 2011, 04:29:49 PM »
Hello,

is that a linear molecule calculated without symmetry?
For such cases inconsistencies could come up in older versions. The check for moments of interia can interpret it as a 3D molecule due to some small off-axis mass and then 3n-6 frequencies are expected and only 3n-5 are found.
This has been fixed in 6.3. Also, it shouldn't come up in c6v or d6h.

Cheers,

Arnim

foea

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Re: freeh - entropy
« Reply #2 on: October 19, 2011, 09:29:58 AM »
I am calculating a carbonnanotube (where most molecules are frozen) with an added OH-group without symmetry and I use version 6.2.

Arnim

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Re: freeh - entropy
« Reply #3 on: October 19, 2011, 10:36:52 AM »
Hi,

did you use NumForce with the -frznuclei option?
In that case, only the frequency components of the non-frozen atoms are calculated.
But for the calculation of the vibrational distribution function all 3*natoms-6 frequencies would be needed.
Also, in that case it is not defined how the translational and rotational distribution functions should look like.
I don't think, that the entropy can be calculated with these contraints.

Cheers,

Arnim

foea

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Re: freeh - entropy
« Reply #4 on: October 19, 2011, 10:53:08 AM »
Hello,

Yes I did use NumForce with the -frznuclei option. I will run NumForce again without the restraints. And then try if freeh works for me.

Thank you very much for your help,
foea

Arnim

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Re: freeh - entropy
« Reply #5 on: October 20, 2011, 08:03:52 PM »
Hello,

I am not sure, if that will do the trick.
If you have optimized the system with frozen atoms, NumForce might give imaginary frequencies, because you are not in the equilibrium. freeh might work technically, but in that case not even the ZPE would be well defined. (ZPEs are only defined on stationary points on the potential energy surface.)
So,  be careful what you do.

Best

Arnim

mpjohans

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Re: freeh - entropy
« Reply #6 on: September 01, 2016, 03:12:37 PM »
Bringing up old topic just because this became personally relevant, and perhaps useful for someone else as well.

You can do a NumForce calculation simulating the frozen state of the atoms by setting their mass to "infinite", and running a normal NumForce (without -frznuclei). Edit the control file and add very heavy masses to the frozen atoms. For example, assuming carbons 1 and 2 were frozen during optimisation:

Code: [Select]
c  1-2                                                                         \
   basis =c def2-SVP                                                           \
   jbas  =c def2-SVP                                                           \
   mass  =99999999999.9
c  3-6                                                                         \
   basis =c def2-SVP                                                           \
   jbas  =c def2-SVP

You'll get the same results as with NumForce and -frznuclei, except that the inactive modes will have (almost) zero frequencies. NumForce with -frznuclei sometimes produces some unphysical very high frequencies, these will also be "zero". The total number of vibrations, including translation and rotation, will be 3N.

This still doesn't make freeh happy, though. Most other programs ignore very low frequencies, but freeh includes them for computing thermodynamics, and will blow up. I have used Viewmol for computing thermodynamics from similar calcs (it ignores freqs below 10 cm-1, IIRC), but I'm sure there are other alternatives.

Note that, as Arnim mentioned, this might not be physically completely sound. But if you are interested in relative enthalpy/entropy contributions for systems with, say, the same frozen atoms, I don't see why this wouldn't be a good approach. If someone knows different, speak up :-)