Dear Philip James Hasnip
Hi, please, this is what energy is in the structure file output:
Pseudo atomic calculation performed for C 2s2 2p2
Converged in 19 iterations to a total energy of -145.7159 eV.
and
The values given in the phononDOS file output: E(eV) and F(eV) denote what?.
Thermodynamics
==============
Zero-point energy = 3.369180 eV
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T(K) E(eV) F(eV) S(J/mol/K) Cv(J/mol/K)
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298.0 3.541961 3.298459 78.840 170.326
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The first energy is the energy of an isolated atom of that species, calculated during the pseudopotential setup. It is not calculated in the plane-wave basis set, it uses a radial grid and assumes spherical symmetry (since it's an isolated atom).
The "thermodynamics" output uses the conventional notation from thermodynamics, so E is the internal energy and F is the Helmholtz free energy E-TS, where T is temperature and S is the vibrational entropy due to the phonons (note: no other entropic contributions are included here). The zero-point energy is the quantum mechanical zero-point energy of the phonons which, since we're working in the quasiharmonic approximation, is just 0.5 hbar omega per phonon (omega being the frequency).
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