Quasi-RRHO Thermochemistry Analysis Module (#2028)

Alex Epstein · pre-commit-ci[bot] · rkingsbury · web-flow · commit 0d5eed0b6997 · 2023-08-21T15:02:26.000-07:00
* Linear molecules + units Tried to use more built-in units. Added functionality for checking if linear and adjusting rotational entropy accordingly. Added testing for linear molecule * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * pylint debugging Tried to make avg_mom_inertia an internal function * Pylint fixing Moved get_avg_mom_inertia outside the class * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * black * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * black 22.1.0 * QuasiRRHO: edits * QuasiRRHO: update tests * pre-commit auto-fixes * Incorporating comments - Cleaned up constants to use scipy.const - Created general __init__ and added functions from_GuassianOutput and from_QCOutput - Updated to google style docstrings * pre-commit Running pre-commit * Typos and doi fixed typo in units added duecredit decorator * docs update 1M in docs * duecredit fixing bugs * pre-commit auto-fixes * Remove Concentration Correction Removed solvent concentration corrections from the code so the class only deals with QuasiRRHO corrections * pre-commit auto-fixes * Changes to testing * pre-commit auto-fixes * add type hints and snake_case QuasiRRHO method names * rename single-letter module-scoped vars * fix tests following method renaming * add test_extreme_temperature_and_pressure() and test_get_avg_mom_inertia() --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Ryan Kingsbury <RKingsbury@lbl.gov> Co-authored-by: Janosh Riebesell <janosh.riebesell@gmail.com>
diff --git a/pymatgen/analysis/quasirrho.py b/pymatgen/analysis/quasirrho.py
@@ -0,0 +1,257 @@
+# Copyright (c) Pymatgen Development Team.
+# Distributed under the terms of the MIT License.
+
+
+"""
+A module to calculate free energies using the Quasi-Rigid Rotor Harmonic
+Oscillator approximation. Modified from a script by Steven Wheeler.
+See: Grimme, S. Chem. Eur. J. 2012, 18, 9955
+"""
+
+from __future__ import annotations
+
+__author__ = "Alex Epstein"
+__copyright__ = "Copyright 2020, The Materials Project"
+__version__ = "0.1"
+__maintainer__ = "Alex Epstein"
+__email__ = "aepstein@lbl.gov"
+__date__ = "August 1, 2023"
+__credits__ = "Ryan Kingsbury, Steven Wheeler, Trevor Seguin, Evan Spotte-Smith"
+
+from math import isclose
+from typing import TYPE_CHECKING
+
+import numpy as np
+import scipy.constants as const
+
+from pymatgen.core.units import kb as kb_ev
+from pymatgen.util.due import Doi, due
+
+if TYPE_CHECKING:
+    from pymatgen.core import Molecule
+    from pymatgen.io.gaussian import GaussianOutput
+    from pymatgen.io.qchem.outputs import QCOutput
+
+# Define useful constants
+kb = kb_ev * const.eV  # Pymatgen kb [J/K]
+light_speed = const.speed_of_light * 100  # [cm/s]
+h_plank = const.h  # Planck's constant [J.s]
+ideal_gas_const = const.R / const.calorie  # Ideal gas constant [cal/mol/K]
+R_ha = const.R / const.value("Hartree energy") / const.Avogadro  # Ideal gas
+
+# Define useful conversion factors
+amu_to_kg = const.value("atomic mass unit-kilogram relationship")  # AMU to kg
+# kcal2hartree = 0.0015936  # kcal/mol to hartree/mol
+kcal_to_hartree = 1000 * const.calorie / const.value("Hartree energy") / const.Avogadro
+
+
+def get_avg_mom_inertia(mol):
+    """
+    Calculate the average moment of inertia of a molecule
+
+    Args:
+        mol (Molecule): Pymatgen Molecule
+
+    Returns:
+        int, list: average moment of inertia, eigenvalues of the inertia tensor
+    """
+    centered_mol = mol.get_centered_molecule()
+    inertia_tensor = np.zeros((3, 3))
+    for site in centered_mol:
+        c = site.coords
+        wt = site.specie.atomic_mass
+        for dim in range(3):
+            inertia_tensor[dim, dim] += wt * (c[(dim + 1) % 3] ** 2 + c[(dim + 2) % 3] ** 2)
+        for ii, jj in [(0, 1), (1, 2), (0, 2)]:
+            inertia_tensor[ii, jj] += -wt * c[ii] * c[jj]
+            inertia_tensor[jj, ii] += -wt * c[jj] * c[ii]
+
+    # amuangs^2 to kg m^2
+    inertia_eigen_vals = np.linalg.eig(inertia_tensor)[0] * amu_to_kg * 1e-20
+
+    iav = np.average(inertia_eigen_vals)
+
+    return iav, inertia_eigen_vals
+
+
+class QuasiRRHO:
+    """
+    Class to calculate thermochemistry using Grimme's Quasi-RRHO approximation.
+    All outputs are in atomic units, e.g. energy outputs are in Hartrees.
+    Citation: Grimme, S. Chemistry - A European Journal 18, 9955-9964 (2012).
+
+    Attributes:
+        temp (float): Temperature [K]
+        press (float): Pressure [Pa]
+        v0 (float): Cutoff frequency for Quasi-RRHO method [1/cm]
+        entropy_quasiRRHO (float): Quasi-RRHO entropy [Ha/K]
+        entropy_ho (float): Total entropy calculated with a harmonic
+            oscillator approximation for the vibrational entropy [Ha/K]
+        h_corrected (float): Thermal correction to the enthalpy [Ha]
+        free_energy_quasiRRHO (float): Quasi-RRHO free energy [Ha]
+        free_energy_ho (float): Free energy calculated without the Quasi-RRHO
+            method, i.e. with a harmonic oscillator approximation for the
+            vibrational entropy [Ha]
+
+    """
+
+    def __init__(
+        self,
+        mol: Molecule,
+        frequencies: list[float],
+        energy: float,
+        mult: int,
+        sigma_r: float = 1,
+        temp: float = 298.15,
+        press: float = 101_317,
+        v0: float = 100,
+    ) -> None:
+        """
+        Args:
+            mol (Molecule): Pymatgen molecule
+            frequencies (list): List of frequencies (float) [cm^-1]
+            energy (float): Electronic energy [Ha]
+            mult (int): Spin multiplicity
+            sigma_r (int): Rotational symmetry number. Defaults to 1.
+            temp (float): Temperature [K]. Defaults to 298.15.
+            press (float): Pressure [Pa]. Defaults to 101_317.
+            v0 (float): Cutoff frequency for Quasi-RRHO method [cm^-1]. Defaults to 100.
+        """
+        # TO-DO: calculate sigma_r with PointGroupAnalyzer
+        # and/or edit Gaussian and QChem io to parse for sigma_r
+
+        self.temp = temp
+        self.press = press
+        self.v0 = v0
+
+        self.entropy_quasiRRHO = None  # Ha/K
+        self.free_energy_quasiRRHO = None  # Ha
+        self.h_corrected = None  # Ha
+
+        self.entropy_ho = None  # Ha/K
+        self.free_energy_ho = None  # Ha
+
+        self._get_quasirrho_thermo(mol=mol, mult=mult, frequencies=frequencies, elec_energy=energy, sigma_r=sigma_r)
+
+    @classmethod
+    def from_gaussian_output(cls, output: GaussianOutput, **kwargs) -> QuasiRRHO:
+        """
+
+        Args:
+            output (GaussianOutput): Pymatgen GaussianOutput object
+
+        Returns:
+            QuasiRRHO: QuasiRRHO class instantiated from a Gaussian Output
+        """
+        mult = output.spin_multiplicity
+        elec_e = output.final_energy
+        mol = output.final_structure
+        vib_freqs = [f["frequency"] for f in output.frequencies[-1]]
+        return cls(mol=mol, frequencies=vib_freqs, energy=elec_e, mult=mult, **kwargs)
+
+    @classmethod
+    def from_qc_output(cls, output: QCOutput, **kwargs) -> QuasiRRHO:
+        """
+
+        Args:
+            output (QCOutput): Pymatgen QCOutput object
+
+        Returns:
+            QuasiRRHO: QuasiRRHO class instantiated from a QChem Output
+
+        """
+        mult = output.data["multiplicity"]
+        elec_e = output.data["SCF_energy_in_the_final_basis_set"]
+        if output.data["optimization"]:
+            mol = output.data["molecule_from_last_geometry"]
+        else:
+            mol = output.data["initial_molecule"]
+        frequencies = output.data["frequencies"]
+
+        return cls(mol=mol, frequencies=frequencies, energy=elec_e, mult=mult, **kwargs)
+
+    @due.dcite(
+        Doi("10.1002/chem.201200497"),
+        description="Supramolecular Binding Thermodynamics by Dispersion-Corrected Density Functional Theory",
+    )
+    def _get_quasirrho_thermo(
+        self, mol: Molecule, mult: int, sigma_r: int, frequencies: list[float], elec_energy: float
+    ) -> None:
+        """
+        Calculate Quasi-RRHO thermochemistry
+
+        Args:
+            mol (Molecule): Pymatgen molecule
+            mult (int): Spin multiplicity
+            sigma_r (int): Rotational symmetry number
+            frequencies (list): List of frequencies [cm^-1]
+            elec_energy (float): Electronic energy [Ha]
+        """
+        # Calculate mass in kg
+        mass: float = 0
+        for site in mol.sites:
+            mass += site.specie.atomic_mass
+        mass *= amu_to_kg
+
+        # Calculate vibrational temperatures
+        vib_temps = [freq * light_speed * h_plank / kb for freq in frequencies if freq > 0]
+
+        # Translational component of entropy and energy
+        qt = (2 * np.pi * mass * kb * self.temp / (h_plank * h_plank)) ** (3 / 2) * kb * self.temp / self.press
+        st = ideal_gas_const * (np.log(qt) + 5 / 2)
+        et = 3 * ideal_gas_const * self.temp / 2
+
+        # Electronic component of Entropy
+        se = ideal_gas_const * np.log(mult)
+
+        # Get properties related to rotational symmetry. Bav is average moment of inertia
+        Bav, i_eigen = get_avg_mom_inertia(mol)
+
+        # Check if linear
+        coords = mol.cart_coords
+        v0 = coords[1] - coords[0]
+        linear = True
+        for coord in coords[1:]:
+            theta = abs(np.dot(coord - coords[0], v0) / np.linalg.norm(coord - coords[0]) / np.linalg.norm(v0))
+            if not isclose(theta, 1, abs_tol=1e-4):
+                linear = False
+
+        # Rotational component of Entropy and Energy
+        if linear:
+            i = np.amax(i_eigen)
+            qr = 8 * np.pi**2 * i * kb * self.temp / (sigma_r * (h_plank * h_plank))
+            sr = ideal_gas_const * (np.log(qr) + 1)
+            er = ideal_gas_const * self.temp
+        else:
+            rot_temps = [h_plank**2 / (np.pi**2 * kb * 8 * i) for i in i_eigen]
+            qr = np.sqrt(np.pi) / sigma_r * self.temp ** (3 / 2) / np.sqrt(rot_temps[0] * rot_temps[1] * rot_temps[2])
+            sr = ideal_gas_const * (np.log(qr) + 3 / 2)
+            er = 3 * ideal_gas_const * self.temp / 2
+
+        # Vibrational component of Entropy and Energy
+        ev = 0
+        sv_quasiRRHO = 0
+        sv = 0
+
+        for vt in vib_temps:
+            ev += vt * (1 / 2 + 1 / (np.exp(vt / self.temp) - 1))
+            sv_temp = vt / (self.temp * (np.exp(vt / self.temp) - 1)) - np.log(1 - np.exp(-vt / self.temp))
+            sv += sv_temp
+
+            mu = h_plank / (8 * np.pi**2 * vt * light_speed)
+            mu_prime = mu * Bav / (mu + Bav)
+            s_rotor = 1 / 2 + np.log(np.sqrt(8 * np.pi**3 * mu_prime * kb * self.temp / h_plank**2))
+            weight = 1 / (1 + (self.v0 / vt) ** 4)
+            sv_quasiRRHO += weight * sv_temp + (1 - weight) * s_rotor
+
+        sv_quasiRRHO *= ideal_gas_const
+        sv *= ideal_gas_const
+        ev *= ideal_gas_const
+        e_tot = (et + er + ev) * kcal_to_hartree / 1000
+        self.h_corrected = e_tot + ideal_gas_const * self.temp * kcal_to_hartree / 1000
+        self.entropy_ho = st + sr + sv + se
+        self.free_energy_ho = elec_energy + self.h_corrected - (self.temp * self.entropy_ho * kcal_to_hartree / 1000)
+        self.entropy_quasiRRHO = st + sr + sv_quasiRRHO + se
+        self.free_energy_quasiRRHO = (
+            elec_energy + self.h_corrected - (self.temp * self.entropy_quasiRRHO * kcal_to_hartree / 1000)
+        )
diff --git a/tests/analysis/test_quasirrho.py b/tests/analysis/test_quasirrho.py
@@ -0,0 +1,84 @@
+from __future__ import annotations
+
+import unittest
+
+import pytest
+
+from pymatgen.analysis.quasirrho import QuasiRRHO, get_avg_mom_inertia
+from pymatgen.io.gaussian import GaussianOutput
+from pymatgen.io.qchem.outputs import QCOutput
+from pymatgen.util.testing import TEST_FILES_DIR
+
+
+class TestQuasiRRHO(unittest.TestCase):
+    """Test class for QuasiRRHO"""
+
+    def setUp(self):
+        test_dir = TEST_FILES_DIR
+        self.gout = GaussianOutput(f"{test_dir}/molecules/quasirrho_gaufreq.log")
+        self.linear_gout = GaussianOutput(f"{test_dir}/molecules/co2.log.gz")
+        self.qout = QCOutput(f"{test_dir}/molecules/new_qchem_files/Frequency_no_equal.qout")
+
+    def test_qrrho_gaussian(self):
+        """
+        Testing from a Gaussian Output file. Correct values are taken from
+        Trevor Seguin's original bash script.
+        """
+        correct_g = -884.776886
+        correct_stot = 141.584080
+        qrrho = QuasiRRHO.from_gaussian_output(self.gout)
+        assert correct_stot == pytest.approx(qrrho.entropy_quasiRRHO, 0.1), "Incorrect total entropy"
+        assert correct_g == pytest.approx(qrrho.free_energy_quasiRRHO), "Incorrect Quasi-RRHO free energy"
+
+    def test_qrrho_qchem(self):
+        """
+        Testing from a QChem output file. "Correct" values are from
+        the version of QuasiRRHO that worked for Gaussian.
+        initial run.
+        """
+        correct_g = -428.60768184222934
+        correct_stot = 103.41012732045324
+        # HO total entropy from QChem = 106.521
+
+        qrrho = QuasiRRHO.from_qc_output(self.qout)
+        assert correct_stot == pytest.approx(qrrho.entropy_quasiRRHO, 0.1), "Incorrect total entropy"
+        assert correct_g == pytest.approx(qrrho.free_energy_quasiRRHO), "Incorrect Quasi-RRHO free energy"
+
+    def test_rrho_manual(self):
+        """
+        Test manual input creation. Values from GaussianOutput
+        """
+        e = self.gout.final_energy
+        mol = self.gout.final_structure
+        vib_freqs = [f["frequency"] for f in self.gout.frequencies[-1]]
+
+        correct_g = -884.776886
+        correct_stot = 141.584080
+        qrrho = QuasiRRHO(mol=mol, energy=e, frequencies=vib_freqs, mult=1)
+        assert correct_stot == pytest.approx(qrrho.entropy_quasiRRHO, 0.1), "Incorrect total entropy"
+        assert correct_g == pytest.approx(qrrho.free_energy_quasiRRHO), "Incorrect Quasi-RRHO free energy"
+
+    def test_rrho_linear(self):
+        """Test on a linear CO2 molecule from Gaussian Output file.
+        Correct free_energy_ho is checked with Gaussian's internal calculation.
+        Correct free_energy_quasirrho is compared internally in the hope of
+        preventing future errors.
+        """
+        correct_g_ho = -187.642070
+        correct_g_qrrho = -187.642725
+        qrrho = QuasiRRHO.from_gaussian_output(self.linear_gout)
+        assert correct_g_ho == pytest.approx(
+            qrrho.free_energy_ho, rel=1e-5
+        ), f"Incorrect harmonic oscillator free energy, {correct_g_ho} != {qrrho.free_energy_ho}"
+        assert correct_g_qrrho == pytest.approx(qrrho.free_energy_quasiRRHO), "Incorrect  Quasi-RRHO free energy"
+
+    def test_extreme_temperature_and_pressure(self):
+        qrrho = QuasiRRHO.from_gaussian_output(self.gout, temp=0.1, press=1e9)
+        assert qrrho.temp == 0.1
+        assert qrrho.press == 1e9
+
+    def test_get_avg_mom_inertia(self):
+        mol = self.gout.final_structure
+        avg_mom_inertia, inertia_eigen_vals = get_avg_mom_inertia(mol)
+        assert avg_mom_inertia == pytest.approx(0)
+        assert inertia_eigen_vals == pytest.approx([0, 0, 0])
diff --git a/tests/files/molecules/co2.log.gz b/tests/files/molecules/co2.log.gz
