Species Thermodynamics Dataset Generation

.gitignore

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 .old
 *.parquet
 
+data/thermo/*.csv
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

data/thermo/README.md

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+# QuantumPioneer Species Thermodynamics Dataset
+
+| Column                       | Type   | Units        | Description                                     |
+| ---------------------------- | ------ | ------------ | ----------------------------------------------- |
+| **`smiles`**                 | string | —            | Canonical SMILES representation of the species  |
+| **`H298`**                   | number | J/mol        | Standard enthalpy of formation at 298 K         |
+| **`S298`**                   | number | J/(mol·K)    | Standard entropy of formation at 298 K          |
+| **`Cp300`**                  | number | J/(mol·K)    | Constant pressure heat capacity at 300 K        |
+| **`dlpno_sp_hartree`**       | number | Hartree      | DLPNO-CCSD(T)-F12d single-point energy          |
+| **`dft_zpe_scaled_hartree`** | number | Hartree      | Scaled DFT zero-point energy (factor: 0.972387) |
+| **`CpInf`**                  | number | J/(mol·K)    | Heat capacity at infinite temperature           |
+| **`a0`**                     | number | —            | Zeroth-order Wilhoit polynomial coefficient     |
+| **`a1`**                     | number | —            | First-order Wilhoit polynomial coefficient      |
+| **`a2`**                     | number | —            | Second-order Wilhoit polynomial coefficient     |
+| **`a3`**                     | number | —            | Third-order Wilhoit polynomial coefficient      |
+| **`H0`**                     | number | J/mol        | Wilhoit integration constant for enthalpy       |
+| **`S0`**                     | number | J/(mol·K)    | Wilhoit integration constant for entropy        |
+| **`B`**                      | number | K            | Wilhoit scaled temperature coefficient          |
+| **`DHPM`**                   | number | J/mol        | Petersson-to-Melius enthalpy difference         |
+
+## Notes
+
+- All molecular structures are represented using canonical SMILES without atom map numbers
+
+- Thermodynamic properties (H298, S298, Cp300) are calculated from DFT-optimized geometries with
+DLPNO-CCSD(T)-F12d single-point calculations
+
+- The standard enthalpy of formation (`H298`) and Wilhoit integration constant for enthalpy (`H0`)
+derive from calculations using Petersson-type bond additivity corrections (BACs). Add `DHPM` to
+either of these in order to obtain their Melius-type BAC-corrected versions.
+
+## Wilhoit Model
+
+The Wilhoit model provides a physically meaningful representation of temperature-dependent heat capacity, guaranteeing correct limits at zero and infinite temperature. The model is defined by the following equations:
+
+### Heat Capacity
+
+$$
+        C_\mathrm{p}(T) = C_\mathrm{p}(0) + \left[ C_\mathrm{p}(\infty) -
+        C_\mathrm{p}(0) \right] y^2 \left[ 1 + (y - 1) \sum_{i=0}^3 a_i y^i \right]
+$$
+
+where $y \equiv T/(T + B)$ is a scaled temperature ranging from zero to one.
+
+$C_\mathrm{p}(0)$ is the heat capacity at zero temperature, whose value is equal to 33.2579 J/(mol·K) for all species in the dataset.
+
+### Enthalpy
+
+$$
+\begin{aligned}
+H(T) &= H_0 +
+        C_\mathrm{p}(0) T - \Bigg\{
+            \left(2 + \sum_{i=0}^3 a_i\right) \left[
+                \frac{y}{2} - 1 + \left( \frac{1}{y} - 1 \right) \ln \frac{T}{y}
+            \right] \\ &+ 
+            y^2 \sum_{i=0}^3 \frac{y^i}{(i+2)(i+3)} \sum_{j=0}^3 f_{ij} a_j
+        \Bigg\} \left[ C_\mathrm{p}(\infty) - C_\mathrm{p}(0) \right] T
+\end{aligned}
+$$
+
+where
+
+$$
+f_{ij} = \begin{cases}
+    0 & \text{if } i < j, \\
+    3 + j & \text{if } i = j, \\
+    1 & \text{if } i > j.
+\end{cases}
+$$
+
+### Entropy
+
+$$
+        S(T) = S_0 +
+        C_\mathrm{p}(\infty) \ln T - \left[ C_\mathrm{p}(\infty) - C_\mathrm{p}(0) \right]
+        \left[ \ln y + \left( 1 + y \sum_{i=0}^3 \frac{a_i y^i}{2+i} \right) y
+        \right]
+$$