Chris,
The output you report for HOMo and LUMO values describes the situation at the beginning of the SCF process.
Non-variational initial energy
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Total energy = -548.336437
1-e energy = -1742.723191
2-e energy = 796.012396
HOMO = -0.555745
LUMO = -0.413072
Therefore, the HOMO and LUMO eigenvalues reported above do not correspond to the eigenvalues at the end of the (converged) SCF process.
The PDOS analysis, instead, utilizes the eigenvalues at the end of the SCF process
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