rotational: There is no external rotation in periodic systems.

[Xenhua Zhang]

Dear Toon,

I am trying to calculate the thermodynamic quantities of a gas phase molecule which has been optimized in the VASP software (in a large box).  The following is the script I am using:

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from tamkin import *
from molmod import *

molecule = load_molecule_vasp("CONTCAR", "OUTCAR")
# normal mode analysis
nma = NMA(molecule)#, ConstrainExt())
# Construct a partition function object with the typical gas phase contributions.
pf = PartFun(nma, [ExtTrans(), ExtRot()])

# Write some general information about the molecule
# and the partition function to a file.
pf.write_to_file("partfun.txt")
print pf.free_energy(973.15)/(kjmol)

# Write an extensive overview of the thermodynamic properties to a file:
ta = ThermoAnalysis(pf, [673.15,723.15,773.15,823.15,873.15,923.15,973.15,1023.15,1073.15,1123.15,1173.15])
ta.write_to_file("thermo.csv")

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The following is the error I am encountering.

--------------------------------------------------------------------------------------------------

Traceback (most recent call last):
  File "Tamkin_script_final.py", line 9, in <module>
    pf = PartFun(nma, [ExtTrans(), ExtRot()])
  File "/home/xenhua/anaconda3/envs/py27/lib/python2.7/site-packages/tamkin/partf.py", line 1353, in __init__
    term.init_part_fun(nma, self)
  File "/home/xenhua/anaconda3/envs/py27/lib/python2.7/site-packages/tamkin/partf.py", line 1006, in init_part_fun
    raise ValueError("There is no external rotation in periodic systems.")
ValueError: rotational: There is no external rotation in periodic systems.

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Could you please help me to solve this error. Thank you so much.

Best regards

Xenhua Zhang

[Toon Verstraelen]

Dear Xenhau,

I suppose your system has periodic boundary conditions. In that case, you can remove ExtRot() when creating the partition function.

Best regards,

Toon

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[Xenhua Zhang]

Dear Toon,

My system is a gas-phase CO molecule. The way CO gas is calculated in VASP is to put it in a large box of vacuum (analogous to gas-phase).

If  I remove ExtRot() in partition function, I believe rotational contributions will not be accounted for in the resulting partition functions. I would like the thermodynamical properties to have all translational, rotational and vibrational contributions.

Best regards,

Xenhua Zhang

To view this discussion on the web visit https://groups.google.com/d/msgid/tamkin/CAB9k2YkD6eBrCMGo4S4ibBxpEZUYK30_BvZx%2B%2BNi%2BzNWxqy%2Bnw%40mail.gmail.com.

[Toon Verstraelen]

Dear Xenhau,

In that case, you have to override the periodicity flag after loading the data. This is not very convenient at the moment in TAMkin. It can be done as follows:

molecule = load_molecule_vasp("CONTCAR", "OUTCAR").copy_with(periodic=False)

Best regards,

Toon

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For more options, visit https://groups.google.com/d/optout.

[Minhaj Ghouri]

Dear Toon,

Thank you. That worked!

But  now, when I use the same script  for just  "C' atom, I get the following error:

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Traceback (most recent call last):
  File "Tamkin_script_final.py", line 9, in <module>

    pf = PartFun(nma, [ExtTrans(), ExtRot()])#symmetry_number=None)])

  File "/home/xenhua/anaconda3/envs/py27/lib/python2.7/site-packages/tamkin/partf.py", line 1353, in __init__
    term.init_part_fun(nma, self)

  File "/home/xenhua/anaconda3/envs/py27/lib/python2.7/site-packages/tamkin/partf.py", line 1016, in init_part_fun
    self.symmetry_number = tmp_mol.compute_rotsym()
  File "/home/xenhua/anaconda3/envs/py27/lib/python2.7/site-packages/molmod/molecules.py", line 292, in compute_rotsym
    raise ValueError("The rotational symmetry number can only be computed when the graph is fully connected.")
ValueError: rotational: The rotational symmetry number can only be computed when the graph is fully connected.

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Best regards,

Xenhua

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[Toon Verstraelen]

Dear Xenhau,

For an isolated atom, you can drop the rotational partition function. (The moments of inertia due to the finite extent of the nucleus and the electron cloud is usually ignored.)

Best regards,

Toon

To view this discussion on the web visit https://groups.google.com/d/msgid/tamkin/CA%2Bxhm9CL%3DsQkHc9H7y0ZVY-KUFYQhoDHE-7473La%2BxBu2R2sgA%40mail.gmail.com.

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[Xenhua Zhang]

Dear Toon,

Thank you so much for your assistance. It was very helpful.

Best regards,

Xenhua Zhang

To view this discussion on the web visit https://groups.google.com/d/msgid/tamkin/CAB9k2Yk150kvnAP1k_4ddSiUS88qRAHXLT1F6MgRwHZh5L6oHg%40mail.gmail.com.