Thermodynamic integration with harmonic reference

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The Helmholtz free energy (Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): A ) of a fully interacting system (1) can be expressed in terms of that of system harmonic in Cartesian coordinates (0,Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle \mathbf{x}} ) as follows

Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle A_{1} = A_{0,\mathbf{x}} + \Delta A_{0,\mathbf{x}\rightarrow 1} }

where Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle \Delta A_{0,\mathbf{x}\rightarrow 1}} is anharmonic free energy. The latter term can be determined by means of thermodynamic integration[1] (TI)

Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle \Delta A_{0,\mathbf{x}\rightarrow 1} = \int_0^1 d\lambda \langle V_1 -V_{0,\mathbf{x}} \rangle_\lambda }

with Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle V_i} being the potential energy of system Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): i , Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle \lambda } is a coupling constant and Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle \langle\cdots\rangle_\lambda} is the NVT ensemble average of the system driven by the Hamiltonian

Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle \mathcal{H}_\lambda = \lambda \mathcal{H}_1 + (1-\lambda)\mathcal{H}_{0,\mathbf{x}} }

Free energy of harmonic reference system within the quasi-classical theory writes

Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle A_{0,\mathbf{x}} = A_\mathrm{el}(\mathbf{x}_0) - k_\mathrm{B} T \sum_{i = 1}^{N_\mathrm{vib}} \ln \frac{k_\mathrm{B} T}{\hbar \omega_i} }

with the electronic free energy Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle A_\mathrm{el}(\mathbf{x}_0)} for the configuration corresponding to the potential energy minimum with the atomic position vector Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle \mathbf{x}_0} , the number of vibrational degrees of freedom Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle N_\mathrm{vib}} , and the angular frequency Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle \omega_i} of vibrational mode Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): i obtained using the Hesse matrix Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle \underline{\mathbf{H}}^\mathbf{x}} . Finally, the harmonic potential energy is expressed as

Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle V_{0,\mathbf{x}}(\mathbf{x}) = V_{0,\mathbf{x}}(\mathbf{x}_0) + \frac{1}{2} (\mathbf{x} - \mathbf{x}_0)^T \underline{\mathbf{H}}^\mathbf{x} (\mathbf{x} - \mathbf{x}_0) }

Thus, a conventional TI calculation consists of the following steps:

  1. determine Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle \mathbf{x}_0} and Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle V_{0,\mathbf{x}}(\mathbf{x}_0)} in structural relaxation
  2. compute Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle \omega_i} in vibrational analysis
  3. use the data obtained in the point 2 to determine Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle \underline{\mathbf{H}}^\mathbf{x}} that defines the harmonic forcefield
  4. perform NVT MD simulations for several values of Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle \lambda \in \langle0,1\rangle} and determine Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle \langle V_1 -V_{0,\mathbf{x}} \rangle}
  5. integrate Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle \langle V_1 -V_{0,\mathbf{x}} \rangle} over the Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle \lambda } grid and compute Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle \Delta A_{0,\mathbf{x}\rightarrow 1}}

Unfortunately, there are several problems linked with such a straightforward approach. First, the systems with rotational and/or translational degrees of freedom cannot be treated in a straightforward manner because Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle V_{0,\mathbf{x}}(\mathbf{x})} is not invariant under rotations and translations. Conventional TI is thus unsuitable for simulations of gas phase molecules or adsorbate-substrate systems. and this problem also imposes restrictions on the choice of thermostat used in NVT simulation (Langevin thermostat, for instance, does not conserve position of the center of mass and is therefore unsuitable for the use in conventional TI). Furthermore, if the Hesse matrix of the harmonic system has one or more eigenvalues that nearly vanish, the simulations with Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle \lambda \rightarrow } 0 is likely to generate unphysical configurations causing serious convergence issues. These problems have been addressed in series of works by Amsler et al.[2]

First, the method was formulated in terms of rotationally and translationally invariant internal coordinates Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle \mathbf{q}=\mathbf{q}(\mathbf{x})} , whereby the free energy of interacting system is repartitioned as follows:

Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle A_1 = A_{0,\mathbf{x}} + \Delta A_{0,\mathbf{x} \rightarrow 0,\mathbf{q}} + \Delta A_{0,\mathbf{q} \rightarrow 1} }

where Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle \Delta A_{0,\mathbf{x} \rightarrow 0,\mathbf{q}}} is the free energy change due to transformation from the system harmonic in Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle \mathbf{x}} into the system harmonic in Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle \mathbf{q}} and Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle \Delta A_{0,\mathbf{q} \rightarrow 1} } is that for the transformation of the latter into a fully interacting system. The force field for the system harmonic in Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle \mathbf{q}} is defined as:

Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle V_{0,\mathbf{q}}(\mathbf{q}) = V_{0,\mathbf{q}}(\mathbf{q}_0) + \frac{1}{2} (\mathbf{q} - \mathbf{q}_0)^T \mathbf{\underline{H}^q} (\mathbf{q} - \mathbf{q}_0) }

where Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle \mathbf{q}_0=\mathbf{q}(\mathbf{x}_0)} and the Hesse matrix Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle \mathbf{\underline{H}}^\mathbf{q}} defined for a potential energy minimum is related to via Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle \mathbf{\underline{H}}^\mathbf{x} = \mathbf{\underline{B}}^T \mathbf{\underline{H}}^\mathbf{q} \mathbf{\underline{B}} } with Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle \mathbf{\underline{B}}_{i,j} = \frac{\partial q_i}{\partial x_j} } being the Wilson matrix. Note that the calculation of the term Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle \Delta A_{0,\mathbf{x} \rightarrow 0,\mathbf{q}}} is inexpensive as it corresponds to a force field to force field transformation. Furthermore, this term vanishes in the case of phase volume conserving coordinates, such as interatomic distances.

The TI calculations in internal coordinates are performed in NVT ensemble using any thermostat available in VASP. The coupling parameter Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle \lambda } is defined by setting the parameter TI_LAMBDA in the INCAR file. The set of internal coordinates used in the TI calculation are defined via the ICONST file by setting the status to 3. The Hesse matrix Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle \mathbf{\underline{H}}^\mathbf{x}} is provided in the file HESSEMAT and its transformation into Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle \mathbf{\underline{H}}^\mathbf{q}} is performed by VASP. The potential energies of the system 1 and 0,Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle \mathbf{q}} , needed to compute Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle \langle V_1 -V_{0,\mathbf{q}} \rangle} used as integrant in the TI expression for Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle \Delta A_{0,\mathbf{q} \rightarrow 1} } , are written in the file REPORT in lines introduce by a string "e_ti>"

  1. ↑ J. G. Kirkwood, J. Chem. Phys. 3, 300–313 (1935)
  2. ↑ J Amsler, PN Plessow, F Studt, T Bucko, J. Chem. Theory Comput. 17, 1155-1169 (2021)
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