arXiv subjects

Christian F. A. Negre

Publications and source records attributed to Christian F. A. Negre.

36 records · Page 2Linked to original sources

arXiv2022

QUBO-based density matrix electronic structure method

Density matrix electronic structure theory is used in many quantum chemistry methods to "alleviate" the computational cost that arises from directly using wave functions. Although density matrix based methods are computationally more efficient than wave functions based methods, yet significant computational effort is involved. Since the Schrödinger equation needs to be solved as an eigenvalue problem, the time-to-solution scales cubically with the system size, and is solved as many times in order to reach charge or field self-consistency. We hereby propose and study a method to compute the density matrix by using a quadratic unconstrained binary optimization (QUBO) solver. This method could be useful to solve the problem with quantum computers, and more specifically, quantum annealers. The method hereby proposed is based on a direct construction of the density matrix using a QUBO eigensolver. We explore the main parameters of the algorithm focusing on precision and efficiency. We show that, while direct construction of the density matrix using a QUBO formulation is possible, the efficiency and precision have room for improvement. Moreover, calculations performing Quantum Annealing with the D-Wave's new Advantage quantum processing units is compared with classical Simulated annealing, further highlighting some problems of the proposed method. We also show some alternative methods that could lead to a better performance of the density matrix construction.

physics.chem-ph↗

arXiv2021

Quantum-based Molecular Dynamics Simulations Using Tensor Cores

Tensor cores, along with tensor processing units, represent a new form of hardware acceleration specifically designed for deep neural network calculations in artificial intelligence applications. Tensor cores provide extraordinary computational speed and energy efficiency, but with the caveat that they were designed for tensor contractions (matrix-matrix multiplications) using only low-precision floating point operations. In spite of this, we demonstrate how tensor cores can be applied with high efficiency to the challenging and numerically sensitive problem of quantum-based Born-Oppenheimer molecular dynamics, which requires highly accurate electronic structure optimizations and conservative force evaluations. The interatomic forces are calculated on-the-fly from an electronic structure that is obtained from a generalized deep neural network, where the computational structure naturally takes advantage of the exceptional processing power of the tensor cores and allows for high performance in excess of 100 Tflops on the tensor cores of a single Nvidia A100 GPU. Stable molecular dynamics trajectories are generated using the framework of extended Lagrangian Born-Oppenheimer molecular dynamics, which combines computational efficiency with long-term stability, even when using approximate charge relaxations and force evaluations that are limited in accuracy by the numerically noisy conditions caused by the low precision tensor core floating-point operations. A canonical ensemble simulation scheme is also presented, where the additional numerical noise in the calculated forces is absorbed into a Langevin-like dynamics.

physics.comp-ph↗

arXiv2021

Computing molecular excited states on a D-Wave quantum annealer

The possibility of using quantum computers for electronic structure calculations has opened up a promising avenue for computational chemistry. Towards this direction, numerous algorithmic advances have been made in the last five years. The potential of quantum annealers, which are the prototypes of adiabatic quantum computers, is yet to be fully explored. In this work, we demonstrate the use of a D-Wave quantum annealer for the calculation of excited electronic states of molecular systems. These simulations play an important role in a number of areas, such as photovoltaics, semiconductor technology and nanoscience. The excited states are treated using two methods, time-dependent Hartree-Fock (TDHF) and time-dependent density-functional theory (TDDFT), both within a commonly used Tamm-Dancoff approximation (TDA). The resulting TDA eigenvalue equations are solved on a D-Wave quantum annealer using the Quantum Annealer Eigensolver (QAE), developed previously. The method is shown to reproduce a typical basis set convergence on the example H$_2$ molecule and is also applied to several other molecular species. Characteristic properties such as transition dipole moments and oscillator strengths are computed as well. Three potential energy profiles for excited states are computed for NH$_3$ as a function of the molecular geometry. Similar to previous studies, the accuracy of the method is dependent on the accuracy of the intermediate meta-heuristic software called qbsolv.

physics.chem-ph↗

arXiv2021

Variational Quantum Eigensolver with Reduced Circuit Complexity

The variational quantum eigensolver (VQE) is one of the most promising algorithms to find eigenvalues and eigenvectors of a given Hamiltonian on noisy intermediate-scale quantum (NISQ) devices. A particular application is to obtain ground or excited states of molecules. The practical realization is currently limited by the complexity of quantum circuits. Here we present a novel approach to reduce quantum circuit complexity in VQE for electronic structure calculations. Our algorithm, called ClusterVQE, splits the initial qubit space into subspaces (qubit clusters) which are further distributed on individual (shallower) quantum circuits. The clusters are obtained based on quantum mutual information reflecting maximal entanglement between qubits, whereas entanglement between different clusters is taken into account via a new "dressed" Hamiltonian. ClusterVQE therefore allows exact simulation of the problem by using fewer qubits and shallower circuit depth compared to standard VQE at the cost of additional classical resources. In addition, a new gradient measurement method without using an ancillary qubit is also developed in this work. Proof-of-principle demonstrations are presented for several molecular systems based on quantum simulators as well as an IBM quantum device with accompanying error mitigation. The efficiency of the new algorithm is comparable to or even improved over qubit-ADAPT-VQE and iterative Qubit Coupled Cluster (iQCC), state-of-the-art circuit-efficient VQE methods to obtain variational ground state energies of molecules on NISQ hardware. Above all, the new ClusterVQE algorithm simultaneously reduces the number of qubits and circuit depth, making it a potential leader for quantum chemistry simulations on NISQ devices.

quant-ph↗

arXiv2021

A QUBO Algorithm to Compute Eigenvectors of Symmetric Matrices

We describe an algorithm to compute the extremal eigenvalues and corresponding eigenvectors of a symmetric matrix by solving a sequence of Quadratic Binary Optimization problems. This algorithm is robust across many different classes of symmetric matrices, can compute the eigenvector/eigenvalue pair to essentially arbitrary precision, and with minor modifications can also solve the generalized eigenvalue problem. Performance is analyzed on small random matrices and selected larger matrices from practical applications.

cs.ET↗

arXiv2021

Performance Optimizations of Recursive Electronic Structure Solvers targeting Multi-Core Architectures (LA-UR-20-26665)

As we rapidly approach the frontiers of ultra large computing resources, software optimization is becoming of paramount interest to scientific application developers interested in efficiently leveraging all available on-Node computing capabilities and thereby improving a requisite science per watt metric. The scientific application of interest here is the Basic Math Library (BML) that provides a singular interface for linear algebra operation frequently used in the Quantum Molecular Dynamics (QMD) community. The provisioning of a singular interface indicates the presence of an abstraction layer which in-turn suggests commonalities in the code-base and therefore any optimization or tuning introduced in the core of code-base has the ability to positively affect the performance of the aforementioned library as a whole. With that in mind, we proceed with this investigation by performing a survey of the entirety of the BML code-base, and extract, in form of micro-kernels, common snippets of code. We introduce several optimization strategies into these micro-kernels including 1.) Strength Reduction 2.) Memory Alignment for large arrays 3.) Non Uniform Memory Access (NUMA) aware allocations to enforce data locality and 4.) appropriate thread affinity and bindings to enhance the overall multi-threaded performance. After introducing these optimizations, we benchmark the micro-kernels and compare the run-time before and after optimization for several target architectures. Finally we use the results as a guide to propagating the optimization strategies into the BML code-base. As a demonstration, herein, we test the efficacy of these optimization strategies by comparing the benchmark and optimized versions of the code.

cs.PF↗

arXiv2021

Mixed Precision Fermi-Operator Expansion on Tensor Cores From a Machine Learning Perspective

We present a second-order recursive Fermi-operator expansion scheme using mixed precision floating point operations to perform electronic structure calculations using tensor core units. A performance of over 100 teraFLOPs is achieved for half-precision floating point operations on Nvidia's A100 tensor core units. The second-order recursive Fermi-operator scheme is formulated in terms of a generalized, differentiable deep neural network structure, which solves the quantum mechanical electronic structure problem. We demonstrate how this network can be accelerated by optimizing the weight and bias values to substantially reduce the number of layers required for convergence. We also show how this machine learning approach can be used to optimize the coefficients of the recursive Fermi-operator expansion to accurately represent fractional occupation numbers of the electronic states at finite temperatures.

physics.comp-ph↗

arXiv2020

Downfolding the Molecular Hamiltonian Matrix using Quantum Community Detection

Calculating the ground state energy of a molecule efficiently is of great interest in quantum chemistry. The exact numerical solution of the electronic Schrodinger equation remains unfeasible for most molecules requiring approximate methods at best. In this paper we introduce the use of Quantum Community Detection performed using the D-Wave quantum annealer to reduce the molecular Hamiltonian matrix without chemical knowledge. Given a molecule represented by a matrix of Slater determinants, the connectivity between Slater determinants is viewed as a graph adjacency matrix for determining multiple communities based on modularity maximization. The resulting lowest energy cluster of Slater determinants is used to calculate the ground state energy within chemical accuracy. The details of this method are described along with demonstrating its performance across multiple molecules of interest and a bond dissociation example. This approach is general and can be used as part of electronic structure calculations to reduce the computation required.

physics.chem-ph↗

arXiv2020

Multilevel Combinatorial Optimization Across Quantum Architectures

Emerging quantum processors provide an opportunity to explore new approaches for solving traditional problems in the post Moore's law supercomputing era. However, the limited number of qubits makes it infeasible to tackle massive real-world datasets directly in the near future, leading to new challenges in utilizing these quantum processors for practical purposes. Hybrid quantum-classical algorithms that leverage both quantum and classical types of devices are considered as one of the main strategies to apply quantum computing to large-scale problems. In this paper, we advocate the use of multilevel frameworks for combinatorial optimization as a promising general paradigm for designing hybrid quantum-classical algorithms. In order to demonstrate this approach, we apply this method to two well-known combinatorial optimization problems, namely, the Graph Partitioning Problem, and the Community Detection Problem. We develop hybrid multilevel solvers with quantum local search on D-Wave's quantum annealer and IBM's gate-model based quantum processor. We carry out experiments on graphs that are orders of magnitudes larger than the current quantum hardware size, and we observe results comparable to state-of-the-art solvers in terms of quality of the solution.

quant-ph↗

arXiv2020

Modeling solid-liquid interface reactions with next generation extended Lagrangian quantum-based molecular dynamics

We demonstrate the applicability of extended Lagrangian Born-Oppenheimer quantum-based molecular dynamics (XL-BOMD) to model electron transfer reactions occurring on solid-liquid interfaces. Specifically, we consider the reduction of O$_2$ as catalyzed at the interface of an N-doped graphene sheet and H$_2$O at fuel cell cathodes. This system is a good testbed for next-generation computational chemistry methods since the electrochemical functionalities strongly depend on atomic-scale quantum mechanics. As opposed to prior iterations of first principles molecular dynamics, XL-BOMD only requires a full self-consistent-charge relaxation during the initial time step. The electronic ground state and total energy are stabilized thereafter through nuclear and electronic equations of motion assisted by an inner-product kernel updated with low-rank approximations. A species charge analysis reveals that the kernel-based XL-BOMD simulation can capture an electron transfer between the PGM-free catalyst and a solvated O$_2$ molecule mediated by H$_2$O, which results in the molecular dissociation of O$_2$.

physics.chem-ph↗

arXiv2019

Using Graph Partitioning for Scalable Distributed Quantum Molecular Dynamics

The simulation of the physical movement of multi-body systems at an atomistic level, with forces calculated from a quantum mechanical description of the electrons, motivates a graph partitioning problem studied in this article. Several advanced algorithms relying on evaluations of matrix polynomials have been published in the literature for such simulations. We aim to use a special type of graph partitioning in order to efficiently parallelize these computations. For this, we create a graph representing the zero-nonzero structure of a thresholded density matrix, and partition that graph into several components. Each separate submatrix (corresponding to each subgraph) is then substituted into the matrix polynomial, and the result for the full matrix polynomial is reassembled at the end from the individual polynomials. This paper starts by introducing a rigorous definition as well as a mathematical justification of this partitioning problem. We assess the performance of several methods to compute graph partitions with respect to both the quality of the partitioning and their runtime.

physics.comp-ph↗

arXiv2019

Quantum Isomer Search

Isomer search or molecule enumeration refers to the problem of finding all the isomers for a given molecule. Many classical search methods have been developed in order to tackle this problem. However, the availability of quantum computing architectures has given us the opportunity to address this problem with new (quantum) techniques. This paper describes a quantum isomer search procedure for determining all the structural isomers of alkanes. We first formulate the structural isomer search problem as a quadratic unconstrained binary optimization (QUBO) problem. The QUBO formulation is for general use on either annealing or gate-based quantum computers. We use the D-Wave quantum annealer to enumerate all structural isomers of all alkanes with fewer carbon atoms (n < 10) than Decane (C10H22). The number of isomer solutions increases with the number of carbon atoms. We find that the sampling time needed to identify all solutions scales linearly with the number of carbon atoms in the alkane. We probe the problem further by employing reverse annealing as well as a perturbed QUBO Hamiltonian and find that the combination of these two methods significantly reduces the number of samples required to find all isomers.

quant-ph↗

arXiv2019

Detecting Multiple Communities Using Quantum Annealing on the D-Wave System

A very important problem in combinatorial optimization is partitioning a network into communities of densely connected nodes; where the connectivity between nodes inside a particular community is large compared to the connectivity between nodes belonging to different ones. This problem is known as community detection, and has become very important in various fields of science including chemistry, biology and social sciences. The problem of community detection is a twofold problem that consists of determining the number of communities and, at the same time, finding those communities. This drastically increases the solution space for heuristics to work on, compared to traditional graph partitioning problems. In many of the scientific domains in which graphs are used, there is the need to have the ability to partition a graph into communities with the ``highest quality'' possible since the presence of even small isolated communities can become crucial to explain a particular phenomenon. We have explored community detection using the power of quantum annealers, and in particular the D-Wave 2X and 2000Q machines. It turns out that the problem of detecting at most two communities naturally fits into the architecture of a quantum annealer with almost no need of reformulation. This paper addresses a systematic study of detecting two or more communities in a network using a quantum annealer.

cs.OH↗

arXiv2018

Eigenvector Centrality Distribution for Characterization of Protein Allosteric Pathways

Determining the principal energy pathways for allosteric communication in biomolecules, that occur as a result of thermal motion, remains challenging due to the intrinsic complexity of the systems involved. Graph theory provides an approach for making sense of such complexity, where allosteric proteins can be represented as networks of amino acids. In this work, we establish the eigenvector centrality metric in terms of the mutual information, as a mean of elucidating the allosteric mechanism that regulates the enzymatic activity of proteins. Moreover, we propose a strategy to characterize the range of the physical interactions that underlie the allosteric process. In particular, the well known enzyme, imidazol glycerol phosphate synthase (IGPS), is utilized to test the proposed methodology. The eigenvector centrality measurement successfully describes the allosteric pathways of IGPS, and allows to pinpoint key amino acids in terms of their relevance in the momentum transfer process. The resulting insight can be utilized for refining the control of IGPS activity, widening the scope for its engineering. Furthermore, we propose a new centrality metric quantifying the relevance of the surroundings of each residue. In addition, the proposed technique is validated against experimental solution NMR measurements yielding fully consistent results. Overall, the methodologies proposed in the present work constitute a powerful and cost effective strategy to gain insight on the allosteric mechanism of proteins.

q-bio.BM↗

arXiv2018

Graph Partitioning Methods for Fast Parallel Quantum Molecular Dynamics

We study a graph partitioning problem motivated by the simulation of the physical movement of multi-body systems on an atomistic level, where the forces are calculated from a quantum mechanical description of the electrons. Several advanced algorithms have been published in the literature for such simulations that are based on evaluations of matrix polynomials. We aim at efficiently parallelizing these computations by using a special type of graph partitioning. For this, we represent the zero-nonzero structure of a thresholded matrix as a graph and partition that graph into several components. The matrix polynomial is then evaluated for each separate submatrix corresponding to the subgraphs and the evaluated submatrix polynomials are used to assemble the final result for the full matrix polynomial. The paper provides a rigorous definition as well as a mathematical justification of this partitioning problem. We use several algorithms to compute graph partitions and experimentally evaluate their performance with respect to the quality of the partition obtained with each method and the time needed to produce it.

quant-ph↗

arXiv2018

Task-based Parallel Computation of the Density Matrix in Quantum-based Molecular Dynamics using Graph Partitioning

Quantum-based molecular dynamics (QMD) is a highly accurate and transferable method for material science simulations. However, the time scales and system sizes accessible to QMD are typically limited to picoseconds and a few hundred atoms. These constraints arise due to expensive self-consistent ground-state electronic structure calculations that can often scale cubically with the number of atoms. Linearly scaling methods depend on computing the density matrix P from the Hamiltonian matrix H by exploiting the sparsity in both matrices. The second-order spectral projection (SP2) algorithm is an O(N) algorithm that computes P with a sequence of 40-50 matrix-matrix multiplications. In this paper, we present task-based implementations of a recently developed data-parallel graph-based approach to the SP2 algorithm, G-SP2. We represent the density matrix P as an undirected graph and use graph partitioning techniques to divide the computation into smaller independent tasks. The partitions thus obtained are generally not of equal size and give rise to undesirable load imbalances in standard MPI-based implementations. This load-balancing challenge can be mitigated by dynamically scheduling parallel computations at runtime using task-based programming models. We develop task-based implementations of the data-parallel G-SP2 algorithm using both Intel's Concurrent Collections (CnC) as well as the Charm++ programming model and evaluate these implementations for future use. Scaling and performance results of our implementations are investigated for representative segments of QMD simulations for solvated protein systems containing more than 10,000 atoms.

physics.comp-ph↗

arXiv2017

Graph Partitioning using Quantum Annealing on the D-Wave System

In this work, we explore graph partitioning (GP) using quantum annealing on the D-Wave 2X machine. Motivated by a recently proposed graph-based electronic structure theory applied to quantum molecular dynamics (QMD) simulations, graph partitioning is used for reducing the calculation of the density matrix into smaller subsystems rendering the calculation more computationally efficient. Unconstrained graph partitioning as community clustering based on the modularity metric can be naturally mapped into the Hamiltonian of the quantum annealer. On the other hand, when constraints are imposed for partitioning into equal parts and minimizing the number of cut edges between parts, a quadratic unconstrained binary optimization (QUBO) reformulation is required. This reformulation may employ the graph complement to fit the problem in the Chimera graph of the quantum annealer. Partitioning into 2 parts, 2^N parts recursively, and k parts concurrently are demonstrated with benchmark graphs, random graphs, and small material system density matrix based graphs. Results for graph partitioning using quantum and hybrid classical-quantum approaches are shown to equal or out-perform current "state of the art" methods.

quant-ph↗

arXiv2016

Graph-based linear scaling electronic structure theory

We show how graph theory can be combined with quantum theory to calculate the electronic structure of large complex systems. The graph formalism is general and applicable to a broad range of electronic structure methods and materials, including challenging systems such as biomolecules. The methodology combines well-controlled accuracy, low computational cost, and natural low-communication parallelism. This combination addresses substantial shortcomings of linear scaling electronic structure theory, in particular with respect to quantum-based molecular dynamics simulations.

physics.comp-ph↗