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Refresh README Example 2 values for the split zpe_fac/harm_fac scaling
The ethane_spc / ethane SPC examples in README and docs/source/README were last regenerated under pre-refactor v3.x (zpe_fac applied uniformly). The split scaling that landed in 4409b86 leaves ZPE matching that pre-refactor value but shifts H_SPC, T·S, and G_SPC by ~0.001 Hartree (those columns now use harm_fac for the vibrational contribution while ZPE keeps zpe_fac). Updated both README.md and docs/source/README.md (the latter is the copy RTD serves; not auto-synced from the project root, so both need the change). Also refreshed the explanatory text under Example 2 to mention both factors (0.991 harmonic / 0.977 ZPE for B3LYP/6-31G(d)) and to point at --zpe-vscal for ZPE-only override. Examples 7 and 8 are unchanged: they pass mixed levels of theory, so auto-lookup falls back to 1.0 for both factors and the values are identical to before.
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README.md

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@@ -99,11 +99,11 @@ goodvibes examples/ethane_spc.out --spc link
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Structure E_SPC E ZPE H_SPC T.S T.qh-S G(T)_SPC qh-G(T)_SPC
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***********************************************************************************************************************
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o ethane_spc -79.858399 -79.830421 0.073508 -79.780448 0.027569 0.027570 -79.808017 -79.808019
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o ethane_spc -79.858399 -79.830421 0.073508 -79.779414 0.027540 0.027542 -79.806954 -79.806956
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***********************************************************************************************************************
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```
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This calculation contains a multi-step job: an optimization and frequency calculation with a small basis set followed by (--Link1--) a larger basis set single point energy. Note the use of the `--spc link` option. The standard harmonic and quasi-harmonic corrected thermochemical data are obtained from the small basis set partition function combined with the larger basis set single point electronic energy. In this example, GoodVibes automatically recognizes the level of theory used in the frequency calculation, B3LYP/6-31G(d), and applies the appropriate scaling factor of 0.977 (this can be suppressed to apply no scaling with -v 1.0)
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This calculation contains a multi-step job: an optimization and frequency calculation with a small basis set followed by (--Link1--) a larger basis set single point energy. Note the use of the `--spc link` option. The standard harmonic and quasi-harmonic corrected thermochemical data are obtained from the small basis set partition function combined with the larger basis set single point electronic energy. In this example, GoodVibes automatically recognizes the level of theory used in the frequency calculation, B3LYP/6-31G(d), and applies the [Truhlar group scaling factors](https://t1.chem.umn.edu/freqscale/index.html) of 0.991 (harmonic, used for H<sub>vib</sub> and S<sub>vib</sub>) and 0.977 (ZPE). Use `-v 1.0` to suppress all scaling, or `--zpe-vscal Y` to override only the ZPE factor.
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Alternatively, if a single point energy calculation has been performed separately, provided both file names share a common root e.g. `ethane.out` and `ethane_TZ.out` then use of the `--spc TZ` option is appropriate. This will give identical results as above.
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@@ -112,7 +112,7 @@ goodvibes examples/ethane.out --spc TZ
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Structure E_SPC E ZPE H_SPC T.S T.qh-S G(T)_SPC qh-G(T)_SPC
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***********************************************************************************************************************
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o ethane -79.858399 -79.830421 0.073508 -79.780448 0.027569 0.027570 -79.808017 -79.808019
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o ethane -79.858399 -79.830421 0.073508 -79.779414 0.027540 0.027542 -79.806954 -79.806956
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***********************************************************************************************************************
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```
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docs/source/README.md

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@@ -99,11 +99,11 @@ goodvibes examples/ethane_spc.out --spc link
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Structure E_SPC E ZPE H_SPC T.S T.qh-S G(T)_SPC qh-G(T)_SPC
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***********************************************************************************************************************
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o ethane_spc -79.858399 -79.830421 0.073508 -79.780448 0.027569 0.027570 -79.808017 -79.808019
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o ethane_spc -79.858399 -79.830421 0.073508 -79.779414 0.027540 0.027542 -79.806954 -79.806956
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***********************************************************************************************************************
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```
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This calculation contains a multi-step job: an optimization and frequency calculation with a small basis set followed by (--Link1--) a larger basis set single point energy. Note the use of the `--spc link` option. The standard harmonic and quasi-harmonic corrected thermochemical data are obtained from the small basis set partition function combined with the larger basis set single point electronic energy. In this example, GoodVibes automatically recognizes the level of theory used in the frequency calculation, B3LYP/6-31G(d), and applies the appropriate scaling factor of 0.977 (this can be suppressed to apply no scaling with -v 1.0)
106+
This calculation contains a multi-step job: an optimization and frequency calculation with a small basis set followed by (--Link1--) a larger basis set single point energy. Note the use of the `--spc link` option. The standard harmonic and quasi-harmonic corrected thermochemical data are obtained from the small basis set partition function combined with the larger basis set single point electronic energy. In this example, GoodVibes automatically recognizes the level of theory used in the frequency calculation, B3LYP/6-31G(d), and applies the [Truhlar group scaling factors](https://t1.chem.umn.edu/freqscale/index.html) of 0.991 (harmonic, used for H<sub>vib</sub> and S<sub>vib</sub>) and 0.977 (ZPE). Use `-v 1.0` to suppress all scaling, or `--zpe-vscal Y` to override only the ZPE factor.
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Alternatively, if a single point energy calculation has been performed separately, provided both file names share a common root e.g. `ethane.out` and `ethane_TZ.out` then use of the `--spc TZ` option is appropriate. This will give identical results as above.
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@@ -112,7 +112,7 @@ goodvibes examples/ethane.out --spc TZ
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Structure E_SPC E ZPE H_SPC T.S T.qh-S G(T)_SPC qh-G(T)_SPC
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***********************************************************************************************************************
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o ethane -79.858399 -79.830421 0.073508 -79.780448 0.027569 0.027570 -79.808017 -79.808019
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o ethane -79.858399 -79.830421 0.073508 -79.779414 0.027540 0.027542 -79.806954 -79.806956
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***********************************************************************************************************************
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```
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