Fragment-based linear scaling quantum chemistry methods are a promising tool for the accurate simulation of chemical and biomolecular systems. Because of the coupled inter-fragment electrostatic interactions, a dual-layer iterative scheme is often employed to compute the fragment electronic structure and the total energy. In the dual-layer scheme, the self-consistent field (SCF) of the electronic structure of a fragment must be solved first, then followed by the updating of the inter-fragment electrostatic interactions. The two steps are sequentially carried out and repeated; as such a significant total number of fragment SCF iterations is required to converge the total energy and becomes the computational bottleneck in many fragment quantum chemistry methods. To reduce the number of fragment SCF iterations and speed up the convergence of the total energy, we develop here a new SCF scheme in which the inter-fragment interactions can be updated concurrently without converging the fragment electronic structure. By constructing the global, block-wise Fock matrix and density matrix, we prove that the commutation between the two global matrices guarantees the commutation of the corresponding matrices in each fragment. Therefore, many highly efficient numerical techniques such as the direct inversion of the iterative subspace method can be employed to converge simultaneously the electronic structure of all fragments, reducing significantly the computational cost. Numerical examples for water clusters of different sizes suggest that the method shall be very useful in improving the scalability of fragment quantum chemistry methods.
Fragment-based linear scaling quantum chemistry methods are a promising tool for the accurate simulation of chemical and biomolecular systems. Because of the coupled inter-fragment electrostatic interactions, a dual-layer iterative scheme is often employed to compute the fragment electronic structure and the total energy. In the dual-layer scheme, the self-consistent field (SCF) of the electronic structure of a fragment must be solved first, then followed by the updating of the inter-fragment electrostatic interactions. The two steps are sequentially carried out and repeated; as such a significant total number of fragment SCF iterations is required to converge the total energy and becomes the computational bottleneck in many fragment quantum chemistry methods. To reduce the number of fragment SCF iterations and speed up the convergence of the total energy, we develop here a new SCF scheme in which the inter-fragment interactions can be updated concurrently without converging the fragment electronic structure. By constructing the global, block-wise Fock matrix and density matrix, we prove that the commutation between the two global matrices guarantees the commutation of the corresponding matrices in each fragment. Therefore, many highly efficient numerical techniques such as the direct inversion of the iterative subspace method can be employed to converge simultaneously the electronic structure of all fragments, reducing significantly the computational cost. Numerical examples for water clusters of different sizes suggest that the method shall be very useful in improving the scalability of fragment quantum chemistry methods.
Predicting the chemico-physical properties of large molecular systems is a formidable challenge in chemistry and materials science. Traditional quantum mechanical methods, while accurate, have impractical scaling for large molecules with thousands of atoms, which are crucial in the development of novel therapeutics, catalysts, and nanomaterials. To address this, molecular fragmentation algorithms have been proposed to improve scalability and enable extensive parallelism. In this article, we introduce a significant enhancement to the Fragment Molecular Orbital (FMO) method, termed the Coulomb-Perturbed Fragmentation (CPF) method. CPF incorporates algorithmic improvements and implementation enhancements to optimize performance on heterogeneous computing systems equipped with a large number of GPUs. Key developments include a significant simplification of iteratitve self-consistent field (SCF) algorithm, advanced data management through a one-sided communication model, topology-aware optimizations, and a hybrid communication strategy for intra-group exchanges. Moreover, CPF integrates a distributed dynamic multi-layer load balancing scheme to optimise fragment distribution and workload management across nodes and GPUs. Performance evaluations on a 420-atom benzene molecule system comprising 35 fragments reveal that CPF outperforms existing GPU/CPU-based FMO algorithms in both efficiency and accuracy. When deployed on the Gadi supercomputer, CPF achieves over 97% parallel efficiency on 20 nodes, with scalability maintaining above 98% and 90% efficiency in weak-scaling tests for smaller and larger systems, respectively. Notably, CPF matches or exceeds the computational accuracy of conventional FMO methods, marking a substantial progress in the field of computational chemistry for fragmentation-based large-scale molecular modelling.
The inherently high computational cost of iterative self-consistent field (SCF) methods proves to be a critical issue delaying visual and haptic feedback in real-time quantum chemistry. In this work, we introduce two schemes for SCF acceleration. They provide a guess for the initial density matrix of the SCF procedure generated by extrapolation techniques. SCF optimizations then converge in fewer iterations, which decreases the execution time of the SCF optimization procedure. To benchmark the proposed propagation schemes, we developed a test bed for performing quantum chemical calculations on sequences of molecular structures mimicking real-time quantum chemical explorations. Explorations of a set of six model reactions employing the semi-empirical methods PM6 and DFTB3 in this testing environment showed that the proposed propagation schemes achieved speedups of up to 30% as a consequence of a reduced number of SCF iterations.
The accuracy of large-scale ab initio calculations is always desired, but they are unfortunately not usually practical in many fields, such as studies of heterogeneous catalysis, photosynthesis, and functional mechanisms of biomolecules. DFT serves as a prevailing method for large calculations due to its compromise between cost and accuracy, but it has a number of failure cases, like bond breaking. On the other hand, the simple theoretical nature of force-field simulations, which often work well, reminds us that large systems are not necessarily exponentially complicated. A recurring theme in the electronic structure of large systems is therefore the use of fragment-based approaches. Existing fragment approaches typically treat the most powerful electron correlations perturbatively, on the same footing with dispersion forces (if at all). In our approach, electrons are not treated individually in the global calculation, but subunits will be chosen. (e.g., amino acid residues or individual water molecules). The most important local states are selected to account for inter-subunit interactions. Most familiar wavefunction methods (SCF, PT, coupled-cluster) can be applied directly to this internally correlated Hamiltonian, and the Hamiltonian itself is systematically improvable to exactitude. Furthermore, different parts of a system can be treated at different accuracy. Our initial investigations focus on the correlation structure of groups of harmonic oscillators, where the coupling inside of groups is stronger than between groups. This mimics discrete molecules while providing us with exact analytical solutions for comparison. Correlations between grouped oscillators will be characterized by both numerical and analytical methods, in order to shed light on building an algorithm for real molecules and systems.
Determining the exponentially scaled ground state wavefunction and the associated molecular properties remains one of the central challenges in quantum chemistry. Hybrid quantum-classical algorithms implemented on quantum computers offer a promising route toward addressing this problem. However, despite several successful demonstrations on small molecular systems, accurate simulations of large and chemically realistic molecules remain difficult due to the limited capability of noisy intermediate scale quantum (NISQ) hardware. To bypass the limitations of NISQ devices, while simultaneously retaining the accuracy of the ground state energy estimations, we propose a dynamic ansatz construction strategy based on operator commutativity and energy driven screening within density matrix embedding theory (DMET) framework. The partitioning of the full system allows us to dynamically construct the ansatz over individual embedded subsystems, allowing each embedding problem be solved individually to a desired accuracy. The embedding Hamiltonian is updated in a self-consistent manner with dynamically formulated wavefunction, and their coupled optimization leads to accurate and efficient description of the overall system. To assess the performance of this approach, we apply it to several molecular systems and chemical processes with up to 144 qubits. These simulations require at most 20 qubits at a time and demonstrate improved accuracy and significantly reduced quantum gate requirements compared with conventional ansatze. We further investigate the impact of various fragmentation strategies and demonstrate the adaptability of our approach at each step of the DMET self-consistency cycle that leads to significantly improved accuracy for strongly correlated system.
Fragmentation and embedding schemes are of great importance when applying quantum-chemical calculations to more complex and attractive targets. The divide-and-conquer (DC)-based quantum-chemical model is a fragmentation scheme that can be connected to embedding schemes. This feature article explains several DC-based schemes developed by the authors over the last two decades, which was inspired by the pioneering study of DC self-consistent field (SCF) method by Yang and Lee ( J. Chem. Phys . 1995, 103, 5674–5678). First, the theoretical aspects of the DC-based SCF, electron correlation, excited-state, and nuclear orbital methods are described, followed by the two-component relativistic theory, quantum-mechanical molecular dynamics simulation, and the introduction of three programs, including DC-based schemes. Illustrative applications confirmed the accuracy and feasibility of the DC-based schemes.
We present interactive quantum chemistry simulation at the atom superposition and electron delocalization molecular orbital (ASED-MO) level of theory. Our method is based on the divide-and-conquer (D&C) approach, which we show is accurate and efficient for this non-self-consistent semiempirical theory. The method has a linear complexity in the number of atoms, scales well with the number of cores, and has a small prefactor. The time cost is completely controllable, as all steps are performed with direct algorithms, i.e., no iterative schemes are used. We discuss the errors induced by the D&C approach, first empirically on a few examples, and then via a theoretical study of two toy models that can be analytically solved for any number of atoms. Thanks to the precision and speed of the D&C approach, we are able to demonstrate interactive quantum chemistry simulations for systems up to a few hundred atoms on a current multicore desktop computer. When drawing and editing molecular systems, interactive simulations provide immediate, intuitive feedback on chemical structures. As the number of cores on personal computers increases, and larger and larger systems can be dealt with, we believe such interactive simulations-even at lower levels of theory-should thus prove most useful to effectively understand, design and prototype molecules, devices and materials.