Subsystem Density Functional Theory Research Articles

Massively parallel fragment-based quantum chemistry for large molecular systems: the serestipy software

We present the Serestipy software as an add-on to the quantum-chemistry program Serenity. Serestipy is a representational-state transfer-oriented application programming interface written in the Python programming language enabling parallel subsystem density-functional theory calculations. We introduce approximate strategies in the context of frozen-density embedding time-dependent density-functional theory to make parallel large-scale excited-state calculations feasible. Their accuracy is carefully benchmarked with calculations for a model system consisting of porphine rings. We apply this framework to a nanotube made up of those porphine rings consisting of 12 160 atoms (or 264 960 basis functions) and obtain its electronic structure and absorption spectrum in less than a day of computational time.

Symmetrized non-decomposable approximations of the non-additive kinetic energy functional.

In subsystem density functional theory (DFT), the bottom-up strategy to approximate the multivariable functional of the non-additive kinetic energy (NAKE) makes it possible to impose exact properties on the corresponding NAKE potential (NAKEP). Such a construction might lead to a non-symmetric and non-homogeneous functional, which excludes the use of such approximations for the evaluation of the total energy. We propose a general formalism to construct a symmetric version based on a perturbation theory approach of the energy expression for the asymmetric part. This strategy is then applied to construct a symmetrized NAKE corresponding to the NAKEP developed recently [Polak et al., J. Chem. Phys. 156, 044103 (2022)], making it possible to evaluate consistently the energy. These functionals were used to evaluate the interaction energy in several model intermolecular complexes using the formal framework of subsystem DFT. The new symmetrized energy expression shows a superior qualitative performance over common decomposable models.

A variational formulation of the Harris functional as a correction to approximate Kohn-Sham density functional theory.

Accurate descriptions of intermolecular interactions are of great importance in simulations of molecular liquids. We present an electronic structure method that combines the accuracy of the Harris functional approach with the computational efficiency of approximately linear-scaling density functional theory (DFT). The non-variational nature of the Harris functional has been addressed by constructing a Lagrangian energy functional, which restores the variational condition by imposing stationarity with respect to the reference density. The associated linear response equations may be treated with linear-scaling efficiency in an atomic orbital based scheme. Key ingredients to describe the structural and dynamical properties of molecular systems are the forces acting on the atoms and the stress tensor. These first-order derivatives of the Harris Lagrangian have been derived and implemented in consistence with the energy correction. The proposed method allows for simulations with accuracies close to the Kohn-Sham DFT reference. Embedded in the CP2K program package, the method is designed to enable ab initio molecular dynamics simulations of molecular solutions for system sizes of several thousand atoms. Available subsystem DFT methods may be used to provide the reference density required for the energy correction at near linear-scaling efficiency. As an example of production applications, we applied the method to molecular dynamics simulations of the binary mixtures cyclohexane-methanol and toluene-methanol, performed within the isobaric-isothermal ensemble, to investigate the hydrogen bonding network in these non-ideal mixtures.

The subsystem quantum chemistry program Serenity

AbstractSERENITY [J Comput Chem. 2018;39:788–798] is an open‐source quantum chemistry software that provides an extensive development platform focused on quantum‐mechanical multilevel and embedding approaches. In this study, we give an overview over the developments done in Serenity since its original publication in 2018. This includes efficient electronic‐structure methods for ground states such as multilevel domain‐based local pair natural orbital coupled cluster and Møller–Plesset perturbation theory as well as the multistate frozen‐density embedding quasi‐diabatization method. For the description of excited states, SERENITY features various subsystem‐based methods such as embedding variants of coupled time‐dependent density‐functional theory, approximate second‐order coupled cluster theory and the second‐order algebraic diagrammatic construction technique as well as GW/Bethe–Salpeter equation approaches. SERENITY's modular structure allows combining these methods with density‐functional theory (DFT)‐based embedding through various practical realizations and variants of subsystem DFT including frozen‐density embedding, potential‐reconstruction techniques and projection‐based embedding.This article is categorized under: Electronic Structure Theory > Density Functional Theory Electronic Structure Theory > Ab Initio Electronic Structure Methods Software > Quantum Chemistry

Subsystem density-functional theory: A reliable tool for spin-density based properties.

Subsystem density-functional theory compiles a set of features that allow for efficiently calculating properties of very large open-shell radical systems such as organic radical crystals, proteins, or deoxyribonucleic acid stacks. It is computationally less costly than correlated ab initio wave function approaches and can pragmatically avoid the overdelocalization problem of Kohn-Sham density-functional theory without employing hard constraints on the electron-density. Additionally, subsystem density-functional theory calculations commonly start from isolated fragment electron densities, pragmatically preserving a priori specified subsystem spin-patterns throughout the calculation. Methods based on subsystem density-functional theory have seen a rapid development over the past years and have become important tools for describing open-shell properties. In this Perspective, we address open questions and possible developments toward challenging future applications in connection with subsystem density-functional theory for spin-dependent properties.

Adaptive Subsystem Density Functional Theory.

Subsystem density functional theory (DFT) is emerging as a powerful electronic structure method for large-scale simulations of molecular condensed phases and interfaces. Key to its computational efficiency is the use of approximate nonadditive noninteracting kinetic energy functionals. Unfortunately, currently available nonadditive functionals lead to inaccurate results when the subsystems interact strongly such as when they engage in chemical reactions. This work disrupts the status quo by devising a workflow that extends subsystem DFT's applicability also to strongly interacting subsystems. This is achieved by implementing a fully automated adaptive definition of subsystems which is realized during geometry optimizations or ab initio molecular dynamics simulations. The new method prescribes subsystem merging and splitting events redistributing the resources (both for work and data) in an efficient way making use of modern parallelization strategies and object-oriented programming. We showcase the method with examples probing from moderate-to-strong inter-subsystem interactions, opening the door to using subsystem DFT for modeling chemical reactions in molecular condensed phases with a black box computational tool.

Towards the description of charge transfer states in solubilised LHCII using subsystem DFT

Light harvesting complex II (LHCII) in plants and green algae have been shown to adapt their absorption properties, depending on the concentration of sunlight, switching between a light harvesting and a non-harvesting or quenched state. In a recent work, combining classical molecular dynamics (MD) simulations with quantum chemical calculations (Liguori et al. in Sci Rep 5:15661, 2015) on LHCII, it was shown that the Chl611–Chl612 cluster of the terminal emitter domain can play an important role in modifying the spectral properties of the complex. In that work the importance of charge transfer (CT) effects was highlighted, in re-shaping the absorption intensity of the chlorophyll dimer. Here in this work, we investigate the combined effect of the local excited (LE) and CT states in shaping the energy landscape of the chlorophyll dimer. Using subsystem Density Functional Theory over the classical mus MD trajectory we look explicitly into the excitation energies of the LE and the CT states of the dimer and their corresponding couplings. Upon doing so, we observe a drop in the excitation energies of the CT states, accompanied by an increase in the couplings between the LE/LE and the LE/CT states facilitated by a shorter interchromophoric distance upon equilibration. Both these changes in conjunction, effectively produces a red-shift of the low-lying mixed exciton/CT states of the supramolecular chromophore pair.

Solvation Free Energies in Subsystem Density Functional Theory.

For many chemical processes the accurate description of solvent effects are vitally important. Here, we describe a hybrid ansatz for the explicit quantum mechanical description of solute-solvent and solvent-solvent interactions based on subsystem density functional theory and continuum solvation schemes. Since explicit solvent molecules may compromise the scalability of the model and transferability of the predicted solvent effect, we aim to retain both, for different solutes as well as for different solvents. The key for the transferability is the consistent subsystem decomposition of solute and solvent. The key for the scalability is the performance of subsystem DFT for increasing numbers of subsystems. We investigate molecular dynamics and stationary point sampling of solvent configurations and compare the resulting (Gibbs) free energies to experiment and theoretical methods. We can show that with our hybrid model reaction barriers and reaction energies are accurately reproduced compared to experimental data.

Local approaches for electric dipole moments in periodic systems and their application to real-time time-dependent density functional theory.

Within periodic boundary conditions, the traditional quantum mechanical position operator is ill-defined, necessitating the use of alternative methods, most commonly the Berry phase formulation in the modern theory of polarization. Since any information about local properties is lost in this change of framework, the Berry phase formulation can only determine the total electric polarization of a system. Previous approaches toward recovering local electric dipole moments have been based on applying the conventional dipole moment operator to the centers of maximally localized Wannier functions (MLWFs). Recently, another approach to local electric dipole moments has been demonstrated in the field of subsystem density functional theory (DFT) embedding. We demonstrate in this work that this approach, aside from its use in ground state DFT-based molecular dynamics, can also be applied to obtain electric dipole moments during real-time propagated time-dependent DFT (RT-TDDFT). Moreover, we present an analogous approach to obtain local electric dipole moments from MLWFs, which enables subsystem analysis in cases where DFT embedding is not applicable. The techniques were implemented in the quantum chemistry software CP2K for the mixed Gaussian and plane wave method and applied to cis-diimide and water in the gas phase, cis-diimide in aqueous solution, and a liquid mixture of dimethyl carbonate and ethylene carbonate to obtain absorption and infrared spectra decomposed into localized subsystem contributions.

Subsystem Density Functional Theory Augmented by a Delta Learning Approach to Achieve Kohn-Sham Accuracy.

Simulations based on electronic structure theory naturally include polarization and have no transferability problems. In particular, Kohn-Sham density functional theory (KS-DFT) has become the method of reference for ab initio molecular dynamics simulations of condensed matter systems. However, the high computational cost often poses strict limits on the affordable system size as well as on the extension of sampling (number of configurations). In this work, we propose an improvement to the subsystem density functional theory approach, known as the Kim-Gordon (KG) scheme, thus enabling the sampling of configurations for condensed molecular systems keeping the KS-DFT level accuracy at a fraction of computer time. Our scheme compensates the known KG shortcomings of the electronic kinetic energy term by adding a simple correction and can match KS-DFT accuracy in energies and forces. The computationally cheap correction is determined by means of a machine learning procedure. The proposed KG scheme is applied within a linear scaling self-consistent field formalism and is assessed by a series of molecular dynamics simulations of liquid water under different conditions. Although system-dependent, the correction is transferable between system sizes and temperatures.

EQE 2.0: Subsystem DFT beyond GGA functionals

By adopting a divide-and-conquer strategy, subsystem-DFT (sDFT) can dramatically reduce the computational cost of large-scale electronic structure calculations. The key ingredients of sDFT are the nonadditive kinetic energy and exchange-correlation functionals which dominate it's accuracy. Even though, available semilocal nonadditive functionals find a broad range of applications, their accuracy is somewhat limited especially for those systems where achieving balance between exchange-correlation interactions on one side and nonadditive kinetic energy on the other is crucial. In eQE 2.0, we improve dramatically the accuracy of sDFT simulations by (1) implementing nonlocal nonadditive kinetic energy functionals based on the LMGP family of functionals; (2) adapting Quantum ESPRESSO's implementation of rVV10 and vdW-DF nonlocal exchange-correlation functionals to be employed in sDFT simulations; (3) implementing “deorbitalized” meta GGA functionals (e.g., SCAN-L). We carefully assess the performance of the newly implemented tools on the S22-5 test set. eQE 2.0 delivers excellent interaction energies compared to conventional Kohn-Sham DFT and CCSD(T). The improved performance does not come at a loss of computational efficiency. We show that eQE 2.0 with nonlocal nonadditive functionals retains the same linear scaling behavior achieved previously in eQE 1.0 with semilocal nonadditive functionals. Program summaryProgram title: eQECPC Library link to program files:https://doi.org/10.17632/g55n9xmnt2.1Developer's repository link:https://gitlab.com/Pavanello/eqeLicensing provisions: GPLv2Programming language: Fortran 90External routines/libraries: BLACS, MPINature of problem: Solving the electronic structure of molecules and materials with subsystem density functional theorySolution method: This version of eQE uses subsystem Density-Functional Theory (DFT) to compute the electronic structure of molecules and materials. Subsystem DFT is a divide-and-conquer version of DFT that can be massively parallelized and is linear scaling in work and data. However, it requires the use of density functionals for kinetic and exchange-correlation energies. eQE can now employ nonlocal functionals as well as meta-GGA functionals for these energy terms.Additional comments: Url of stable release http://eqe.rutgers.edu

Pragmatic Improvement of Magnetic Exchange Couplings from Subsystem Density-Functional Theory through Orthogonalization of Subsystem Orbitals

We explore a pragmatic way of correcting magnetic exchange coupling constants from subsystem density-functional theory (sDFT). Our previous work [ Faraday Discuss. 2020, 224, 201−226] showed that s...

Subsystem-Based GW/Bethe-Salpeter Equation.

Subsystem Density-Functional Theory and its extension to excited states, namely, subsystem Time-Dependent Density-Functional Theory, have been proven to be efficient and accurate fragmentation approaches for ground and excited states. In the present study we extend this approach to the subsystem-based description of total systems by means of GW and the Bethe-Salpeter equation (BSE). For this, we derive the working equations starting from a subsystem-based partitioning of the screened-Coulomb interaction for an arbitrary number of subsystems. Making use of certain approximations, we develop a parameter-free approach in which environmental screening contributions are effectively included for each subsystem. We demonstrate the applicability of these approximations by comparing quasi-particle energies and excitation energies from subsystem-based GW/BSE calculations to the supermolecular reference. Furthermore, we demonstrate the computational efficiency and the usefulness of this method for the description of photoinduced processes in complex chemical environments.

Many‐body response of benzene at monolayer MoS2: Van der Waals interactions and spectral broadening

AbstractModels of surface enhancement of molecular electronic response properties are challenging for two reasons: (a) molecule‐surface interactions require a simultaneous solution of the molecular and the surface dynamic response (a daunting task), and (b) when solving for the electronic structure of the combined molecule + surface system, it is not trivial to single out the particular physical effects responsible for enhancement. To tackle this problem, in this work, we apply a formally exact decomposition of the system's response function into subsystem contributions by using subsystem density functional theory (DFT), which grants access to dynamic polarizabilities and optical spectra. In order to access information about the interactions between the subsystems, we extend a previously developed subsystem‐based adiabatic connection fluctuation‐dissipation theorem of DFT to separate the additive from the nonadditive correlation energy and identify the nonadditive correlation as the van der Waals interactions. As an example, we choose benzene adsorbed on monolayer MoS2. We isolate the contributions to benzene's dynamic response arising from the interaction with the surface, and for the first time, we evaluate the enhancements to the effectiveness of C6 coefficients as a function of benzene‐MoS2 distance and adsorption site. We also quantify the spectral broadening of the benzene's electronic excited states due to their interaction with the surface. We find that the broadening has a similar decay law with the molecule‐surface distance as the leading van der Waals interactions (ie, R−6) and that the surface enhancement of dispersion interactions between benzene molecules is less than 5% but is still large enough (0.5 kcal/mol) to likely play a role in the prediction of interface morphologies.

Frozen‐density embedding‐based many‐body expansions

AbstractFragmentation methods allow for the accurate quantum chemical (QC) treatment of large molecular clusters and materials. Here we explore the combination of two complementary approaches to the development of such fragmentation methods: the many‐body expansion (MBE) on the one hand, and subsystem density‐functional theory (DFT) or frozen‐density embedding (FDE) theory on the other hand. First, we assess potential benefits of using FDE to account for the environment in the subsystem calculations performed within the MBE. Second, we use subsystem DFT to derive a density‐based MBE, in which a many‐body expansion of the electron density is used to calculate the system's total energy. This provides a correction to the energies calculated with a conventional energy‐based MBE that depends only on the subsystem's electron densities. For the test case of clusters of water and of aspirin, we show that such a density‐based MBE converges faster than the conventional energy‐based MBE. For our test cases, truncation errors in the interaction energies are below chemical accuracy already with a two‐body expansion. The density‐based MBE thus provides a promising avenue for accurate QC calculation of molecular clusters and materials.

Subsystem density-functional theory for interacting open-shell systems: spin densities and magnetic exchange couplings.

We investigate the possibility of describing interacting open-shell systems in high-spin and broken-symmetry (BS) states with subsystem density-functional theory (sDFT). This subsystem method typically starts from the electronic-structure results obtained for individual systems, for which the spin states can be individually defined. Through the confining effect of the embedding potential and/or the use of monomer basis sets, these individual spin states can be preserved in sDFT calculations. This offers the possibility of easy convergence to broken-symmetry states with arbitrary local spin patterns. We show that the resulting spin densities are in very good agreement with successfully converged broken-symmetry Kohn-Sham density-functional theory (KS-DFT) calculations. Yet sDFT can even cure those BS cases where KS-DFT suffers from convergence problems or convergence to undesired spin states. In contrast to KS-DFT, the sDFT-results only show a mild exchange-correlation functional dependence. We also show that magnetic coupling constants from sDFT are not satisfactory with standard approximations for the non-additive kinetic energy. When this component is evaluated "exactly", i.e. based on potential reconstruction, however, the magnetic coupling constants derived from spin-state energy differences are greatly improved. Hence, the interacting radicals studied here represent cases where even (semi-)local approximations for the non-additive kinetic-energy potential work well, while the parent energy functionals do not yield satisfactory results for spin-state energy differences.

Is it worthwhile to go beyond the local‐density approximation in subsystem density functional theory?

AbstractFrozen density embedding (FDE) theory is one of the major techniques aiming to bring modeling of extended chemical systems into the realm of high accuracy calculations. To improve its accuracy it is of interest to develop kinetic energy density functional approximations specifically for FDE applications. In the study reported here we focused on optimizing parameters of a generalized gradient approximation‐like kinetic energy functional with the purpose of better describing electron excitation energies. We found that our optimized parametrizations, named excPBE and excPBE‐3 (as these are derived from a Perdew‐Burke‐Ernzerhof‐like parametrization), could not yield improvements over available functionals when applied on a test set of systems designed to probe solvatochromic shifts. Moreover, as several different functionals yielded very similar errors to the simple local‐density approximation (LDA), it is questionable whether it is worthwhile to go beyond the LDA in this context.

Ab Initio Structure and Dynamics of CO2 at Supercritical Conditions.

Green technologies rely on green solvents and fluids. Among them, supercritical CO2 already finds many important applications. The molecular-level understanding of the dynamics and structure of this supercritical fluid is a prerequisite for rational design of future green technologies. Unfortunately, the commonly employed Kohn-Sham density functional theory (DFT) is too computationally demanding to produce meaningfully converged dynamics within a reasonable time and with a reasonable computational effort. Thanks to subsystem DFT, we analyze finite-size effects by considering simulation cells of varying sizes (up to 256 independent molecules in the cell) and finite-time effects by running 100 ps trajectories. We find that the simulations are in reasonable and semiquantitative agreement with the available neutron diffraction experiments and that, as opposed to the gas phase, the CO2 molecules in the fluid are bent with an average OCO angle of 175.8°. Our simulations also confirm that the dimer T-shape is the most prevalent configuration. Our results further strengthen the experiment-simulation agreement for this fluid when comparing radial distribution functions and diffusion coefficient, confirming subsystem DFT as a viable tool for modeling structure and dynamics of condensed-phase systems.

Inter-subsystem charge-transfer excitations in exact subsystem time-dependent density-functional theory.

We investigate the ability of projection-based embedding (PbE)/subsystem density-functional theory to describe intersubsystem charge-transfer (CT) excitations. To this end, we derive the corresponding subsystem time-dependent density-functional theory (sTDDFT) working equations including the response kernel contributions for three different popular projection operators currently in use in connection with PbE. We demonstrate that supermolecular electronic excitation spectra can be fully restored with this "exact" sTDDFT. Both intra- and intersubsystem CT excitations can be described correctly, provided that suitable long-range corrected functionals and basis sets of sufficient flexibility are used. In particular, we show that outgoing CT excitations can be described in individual subsystem calculations without intersubsystem response coupling. We introduce efficient techniques to restrict the virtual-orbital space to obtain reasonable CT excitation energies with heavily reduced computational cost. Finally, we demonstrate the ability to extract electronic couplings between CT and local excitations with this new formulation of exact sTDDFT.

Polarizable Frozen Density Embedding with External Orthogonalization.

We report a polarizable subsystem density functional theory to describe electronic properties of molecules embedded on a metal cluster. Interaction between the molecule and metal cluster is described using frozen density embedding (FDE). Substituting the nonadditive kinetic potential (NAKP) by approximate functionals is circumvented by enforcing external orthogonality (EO) through a projection operator. The computationally expensive freeze/thaw (FT) cycles are bypassed by including a polarization term in the embedding operator. Furthermore, the combination of polarization and EO permits supermolecular basis set calculations, which was not possible for strongly interacting systems with existing kinetic energy functionals. To test the method, we described the ground state density of pyridine, water, and benzene on a silver cluster. Performing FT on top of EO results in exact density embedding for this category of systems and is thus used for benchmarking the method. We find that the density is reproduced to within 0.15e, and the dipole and quadrupole moments are within 18% of the reference points for subsystem separations ranging from bonding to noninteracting distances. Additionally, our formalism allows the flexibility of incorporating different density functionals to the molecular and the metallic subsystems reducing the overall computational cost.