The dynamic rearrangement of a molecule at finite temperature is not captured by a single static input geometry to a quantum chemical calculation. Multilevel workflows have established themselves as standard procedures to capture the dependence of the molecule’s configuration on computed properties. Each step within this workflow uses an electronic structure theory method that features the optimal computational time to accuracy ratio. For exploratory steps the computational expense of a method needs to be minimal as several thousand energy and nuclear gradient evaluations are needed. Semiempirical tight binding methods, such as GFN2-xTB are often used for such purposes. However, these methods usually lack the accuracy to rank conformers relative to each other within chemical accuracy (2 kcal/mol). Therefore, so-called “low-cost” DFT methods are commonly used for geometry optimizations and conformer ranking. The combination of (semi)empirical correction models with small basis sets leads to good accuracy at moderate computational cost. However, even these highly efficient methods reach the limits of feasibility for very large systems (> 200 atoms). This work proposes solutions to partially alleviate those restrictions and allow routine calculations of these system sizes outside of large high-performance computing facilities. The key to unlock those calculations is to combine tailored algorithmic developments with consumer-grade GPUs. A GPU-enabled linear algebra library is developed to accelerate further development and make the entry to GPU-accelerated software development easier. To demonstrate the ease of implementation, the addition of Mulliken-approximated exchange to GFN2-xTB will be shown. In most semiempirical methods, the general eigenvalue solver algorithm becomes the computational bottleneck, dominating the walltime with increasing system size. A density matrix purification algorithm is tailored to give up to six-fold acceleration of GFN2-xTB calculations using a mixed-precision approach. Lastly, 3c-methods are added to the GPU-accelerated TeraChem software package. In combination with the “mixed-precision” scheme for computing the electron repulsion integrals, this addition decreases the runtime of DFT calculations by up to an order of magnitude on mid-level consumer hardware. The overall goal of these projects is to make GPU-accelerated calculations in quantum chemistry more available. This achieve by exposing algorithmic developments that are performant on reasonably priced hardware and making GPU computing more accessible to non-experts.
The dynamic rearrangement of a molecule at finite temperature is not captured by a single static input geometry to a quantum chemical calculation. Multilevel workflows have established themselves as standard procedures to capture the dependence of the molecule’s configuration on computed properties. Each step within this workflow uses an electronic structure theory method that features the optimal computational time to accuracy ratio. For exploratory steps the computational expense of a method needs to be minimal as several thousand energy and nuclear gradient evaluations are needed. Semiempirical tight binding methods, such as GFN2-xTB are often used for such purposes. However, these methods usually lack the accuracy to rank conformers relative to each other within chemical accuracy (2 kcal/mol). Therefore, so-called “low-cost” DFT methods are commonly used for geometry optimizations and conformer ranking. The combination of (semi)empirical correction models with small basis sets leads to good accuracy at moderate computational cost. However, even these highly efficient methods reach the limits of feasibility for very large systems (> 200 atoms). This work proposes solutions to partially alleviate those restrictions and allow routine calculations of these system sizes outside of large high-performance computing facilities. The key to unlock those calculations is to combine tailored algorithmic developments with consumer-grade GPUs. A GPU-enabled linear algebra library is developed to accelerate further development and make the entry to GPU-accelerated software development easier. To demonstrate the ease of implementation, the addition of Mulliken-approximated exchange to GFN2-xTB will be shown. In most semiempirical methods, the general eigenvalue solver algorithm becomes the computational bottleneck, dominating the walltime with increasing system size. A density matrix purification algorithm is tailored to give up to six-fold acceleration of GFN2-xTB calculations using a mixed-precision approach. Lastly, 3c-methods are added to the GPU-accelerated TeraChem software package. In combination with the “mixed-precision” scheme for computing the electron repulsion integrals, this addition decreases the runtime of DFT calculations by up to an order of magnitude on mid-level consumer hardware. The overall goal of these projects is to make GPU-accelerated calculations in quantum chemistry more available. This achieve by exposing algorithmic developments that are performant on reasonably priced hardware and making GPU computing more accessible to non-experts.
Graphical Processing Units (GPUs) are highly parallel, programmable accelerators boasting high peak floating point performance. Over the last couple of years the use of GPUs for general purpose computing have revolutionized quantum chemistry. The computational bottleneck in an ab-initio quantum method is the calculation of a large number of twoelectron integrals. To date, a number of GPU accelerated two-electron integral implementations have been developed significantly improving the performance of a static quantum mechanical (QM) calculation. However, when performing an ab-initio QM gradient calculation, optimization, QM or Hybrid Quantum Mechanical/Molecular Mechanical (QM/MM) dynamics simulation the twoelectron integral derivatives arise as an additional bottleneck. Hybrid QM/MM methods particularly dynamics methods are commonly used to study large chemical/biological systems. These methods are a popular choice used for studying reaction mechanisms, conformational and configurational structures important in glycobiology. Usually a semiempirical QM method is used however, these have shown variable accuracy for the study of carbohydrate conformation and prevents an analytical investigation of electronic structure. The use of a higher level of theory, such as an ab initio method, is desirable however this comes at a much greater computational cost. Together with the bottlenecks above this cost results from the polarization of the QM region within an electrostatic embedding scheme, which requires the calculation of a large number of one-electron integral derivatives. Thus for QM/MM calculations the one-electron integral derivatives becomes a third bottleneck together with the two mentioned above. Recently, the above bottlenecks have become popular GPU acceleration targets. This thesis describes an extension of the GPU based Quantum Supercharger Library (QSL) to perform the above calculations/simulations. In contrast to GPU packages developed from the ground up, the QSL is a library of routines aimed at accelerating legacy codes, such as GAMESS-UK, GAMESS-US and NWChem, used in electronic structure calculations. Algorithms are presented for accelerating the one- and two-electron integral derivatives on a GPU. In addition to the derivatives, the one-electron integral calculation was ported to the GPU in order to remove a small additional cost arising for large QM/MM systems. Furthermore, the use of automatic code generation for generating GPU kernels was explored and compared to the original approach. Using the QSL library implemented in GAMESS-UK several benchmark calculations and simulations were performed. These were performed in double precision on a single GPU (Kepler K20) and compared to a single CPU using the 6-31G basis set. A speedup of up to 9.3X is achieved for an ab initio gradient calculation compared to the CPU running an optimized serial version of GAMESS-UK using the Schlegel method. For a single point QM/MM calculation of cellobiose in different sized water spheres (3267-24843 point charges) speedups of between 13X and 34X is achieved. QSL/GAMESS-UK coupled to the CHARMM molecular dynamics package was then used in order to perform accelerated molecular dynamics simulations. Benchmark QM and QM/MM molecular dynamics simulations were performed on cellobiose in vacuo and in a water sphere (45 QM atoms and 24843 point charges respectively). The QSL is able to perform 9.7 ps/day of ab initio QM dynamics and 6.4 ps/day of QM/MM dynamics. Testing of the auto-generated version of the QSL showed better performance for lower angular momentum classes but reduced performance for higher angular momentum classes. The efficiency of the integral and derivative routines within the QSL library was tested on a computationally intense realistic glycobiological condensed phase free energy computation. Ab-initio pucker free energy surfaces/volumes of !-Ribofuranose and !-Glucopyranose in vacuum and in water were computed. These are the first converged Hartree-Fock/MM free energy simulations for these carbohydrates performed in solution. The value of the ab initio Free energy surfaces/volumes was demonstrated through an analysis of solvent polarization effects that are evident through a comparison of the vacuum and solution minimum free energy pathways. In particular the water structure around the pucker conformers, analysis of the primary alcohol distribution as well as analysis of the electronic structure of these conformers reveals that water significantly affects the free energy pathways, primary alcohol distribution and the barriers for inter-conversion between pucker conformers.
This dissertation is focused around enabling large-scale quantum chemistry calculations by developing novel algorithms on new heterogeneous hardware architectures. Section 2 contains a study on assessing the importance of many-body dispersion phenomena in molecular clusters and understanding the need to incorporate the phenomena into existing quantum chemistry methods to accurately capture long-range interactions. It is known that highly accurate quantum chemistry methods are computationally expensive; therefore, there is a need for new computer algorithms that will be able to vastly improve the time to solution and enable correlated quantum chemistry calculations on large molecular systems. Sections 3 and 4 focus on the development and implementation of various algorithms that enable quantum chemistry calculations on molecules of unprecedent sizes. Specifically, Section 3 describes a novel CUDA-based algorithm that enables GPU-acceleration of the main parts of the Self-Consistent Field (SCF) cycle, resulting in the fastest SCF code to date. Section 4 introduces a novel OpenMP-based implementation of the Fock build formation, which enables GPU-accelerated calculations on all existing GPU and CPU hardware. Section 5 expands upon the OpenMP work and describes a new GPU-accelerated library named LibERI for evaluating molecular integrals – often the main computational bottleneck in many quantum chemistry methods. LibERI is intended to serve as a library for fast quantum chemistry calculations that can be interfaced with any existing quantum chemistry software packages through the MolSSI Driver Interface (MDI). MDI is a standard interface between scientific computational codes. One of LibERI’s objectives is to seamlessly integrate with a Molecular Mechanics (MM) package using MDI to enable fast QM/MM calculations. This integration would allow for efficient GPU-accelerated treatment of large QM regions via LibERI. Lastly, Section 6 concludes this dissertation with a study that applies existing quantum chemistry methods to unravel the mechanism of a Pd-catalyzed carboacylation reaction involving the activation of ester C-O bonds.
The increasing availability of graphics processing units (GPUs) for scientific computing has prompted interest in accelerating quantum chemical calculations through their use. However, the complexity of integral kernels for high angular momentum basis functions often limits the utility of GPU implementations with large basis sets or for metal containing systems. In this work, we report the implementation of f function support in the GPU-accelerated TeraChem software package through the development of efficient kernels for the evaluation of Hamiltonian integrals. The high efficiency of the resulting code is demonstrated through density functional theory (DFT) calculations on increasingly large organic molecules and transition metal complexes, as well as coupled cluster singles and doubles calculations on water clusters. Preliminary investigations into Ni(I) catalysis with DFT and the photochemistry of MnH(CH3) with complete active space self-consistent field are also carried out. Overall, our GPU-accelerated software appears to be well-suited for fast simulation of large transition metal containing systems, as well as organic molecules.
Graph-based electronic structure theory offers a scalable approach to study large, complex atomistic systems using distributed and hybrid computational platforms. We demonstrate the coupling of graph-based linear scaling electronic structure theory, as implemented in the Scalable Ecosystem, Driver, and Analyzer for Complex Chemistry Simulations (SEDACS), with semiempirical quantum chemistry methods as implemented in the PySEQM code, with Graphics Processing Unit (GPU) acceleration. This powerful combination enables efficient, scalable electronic structure calculations over many nodes, significantly reducing computational cost while naturally harnessing parallelism. Detailed analyses of parallelization efficiency, computational accuracy, and communication overheads are provided, highlighting an order-of-magnitude speedup for systems of up to 10,000 atoms.
We present a GPU-accelerated software package for the evaluation of analytic two-electron energy and gradient contributions in Hartree-Fock (HF) and Density Functional theory (DFT) calculations. The implementation is provided as a Python library with a C++ backend, enabling straightforward integration into modern computational chemistry and drug-discovery workflows. The code supports single-point energy and nuclear gradient evaluations on both single- and multi-GPU systems, and employs MPI-based parallelization with dynamic load balancing in multi-node environments. We report comprehensive benchmarks demonstrating favorable scaling with respect to system size, as well as high throughput for batched evaluations relevant to molecular dynamics, geometry optimization, and large-scale virtual screening. Parallel execution of a single system was carried out on up to 24 A100 GPUs. The implementation builds on optimized GPU-enabled variants of the LibintX and GauXC libraries to efficiently compute density-fitted Coulomb, semi-numerical exchange, and exchange--correlation contributions.
We present a GPU-accelerated software package for the evaluation of analytic two-electron energy and gradient contributions in Hartree-Fock (HF) and Density Functional theory (DFT) calculations. The implementation is provided as a Python library with a C++ backend, enabling straightforward integration into modern computational chemistry and drug-discovery workflows. The code supports single-point energy and nuclear gradient evaluations on both single- and multi-GPU systems, and employs MPI-based parallelization with dynamic load balancing in multi-node environments. We report comprehensive benchmarks demonstrating favorable scaling with respect to system size, as well as high throughput for batched evaluations relevant to molecular dynamics, geometry optimization, and large-scale virtual screening. Parallel execution of a single system was carried out on up to 24 A100 GPUs. The implementation builds on optimized GPU-enabled variants of the LibintX and GauXC libraries to efficiently compute density-fitted Coulomb, semi-numerical exchange, and exchange--correlation contributions.