LibERI-A portable and performant multi-GPU accelerated library for electron repulsion integrals via OpenMP offloading and standard language parallelism.

A portable and performant graphics processing unit (GPU)-accelerated library for electron repulsion integral (ERI) evaluation, named LibERI, has been developed and implemented via directive-based (e.g., OpenMP and OpenACC) and standard language parallelism (e.

NWChem: Recent and Ongoing Developments.

This paper summarizes developments in the NWChem computational chemistry suite since the last major release (NWChem 7.0.0).

Enabling Fortran Standard Parallelism in GAMESS for Accelerated Quantum Chemistry Calculations.

The performance of Fortran 2008 DO CONCURRENT (DC) relative to OpenACC and OpenMP target offloading (OTO) with different compilers is studied for the GAMESS quantum chemistry application. Specifically, DC and OTO are used to offload the Fock build, which is a computational bottleneck in most quantum chemistry codes, to GPUs. The DC Fock build performance is studied on NVIDIA A100 and V100 accelerators and compared with the OTO versions compiled by the NVIDIA HPC, IBM XL, and Cray Fortran compilers.

Coupled Cluster Studies of Ionization Potentials and Electron Affinities of Single-Walled Carbon Nanotubes.

In this paper, we apply equation-of-motion coupled cluster (EOM-CC) methods in the studies of the vertical ionization potentials (IPs) and electron affinities (EAs) for a series of single-walled carbon nanotubes (SWCNT). The EOM-CC formulations for IPs and EAs employing excitation manifolds spanned by single and double excitations (IP/EA-EOM-CCSD) are used to study the IPs and EAs of the SWCNTs as a function of the nanotube length. Several armchair nanotubes corresponding to CH models with n = 2-6 have been used in benchmark calculations.

Effect of intrinsic and extrinsic factors on the simulated D-band length of type I collagen.

A signature feature of collagen is its axial periodicity visible in TEM as alternating dark and light bands. In mature, type I collagen, this repeating unit, D, is 67 nm long. This periodicity reflects an underlying packing of constituent triple-helix polypeptide monomers wherein the dark bands represent gaps between axially adjacent monomers.

Parallel scalability of Hartree-Fock calculations.

Quantum chemistry is increasingly performed using large cluster computers consisting of multiple interconnected nodes. For a fixed molecular problem, the efficiency of a calculation usually decreases as more nodes are used, due to the cost of communication between the nodes. This paper empirically investigates the parallel scalability of Hartree-Fock calculations.

Reconsidering Dispersion Potentials: Reduced Cutoffs in Mesh-Based Ewald Solvers Can Be Faster Than Truncation.

Long-range dispersion interactions have a critical influence on physical quantities in simulations of inhomogeneous systems. However, the perceived computational overhead of long-range solvers has until recently discouraged their implementation in molecular dynamics packages. Here, we demonstrate that reducing the cutoff radius for local interactions in the recently introduced particle-particle particle-mesh (PPPM) method for dispersion [Isele-Holder et al.

Flow-Dependent Unfolding and Refolding of an RNA by Nonequilibrium Umbrella Sampling.

Nonequilibrium experiments of single biomolecules such as force-induced unfolding reveal details about a few degrees of freedom of a complex system. Molecular dynamics simulations can provide complementary information, but exploration of the space of possible configurations is often hindered by large barriers in phase space that separate metastable regions. To solve this problem, enhanced sampling methods have been developed that divide a phase space into regions and integrate trajectory segments in each region.

Coupled Cluster Theory on Graphics Processing Units I. The Coupled Cluster Doubles Method.

The coupled cluster (CC) ansatz is generally recognized as providing one of the best wave function-based descriptions of electronic correlation in small- and medium-sized molecules. The fact that the CC equations with double excitations (CCD) may be expressed as a handful of dense matrix-matrix multiplications makes it an ideal method to be ported to graphics processing units (GPUs). We present our implementation of the spin-free CCD equations in which the entire iterative procedure is evaluated on the GPU.

Computational studies of the thermochemistry for conversion of glucose to levulinic acid.

The thermochemistry of the conversion of glucose to levulinic acid through fructofuranosyl intermediates is investigated using the high-level ab initio methods G4 and G4MP2. The calculated gas phase reaction enthalpies indicate that the first two steps involving water molecule elimination are highly endothermic, while the other steps, including additional water elimination and rehydration to form levulinic acid, are exothermic. The calculated gas phase free energies indicate that inclusion of entropic effects makes the dehydration steps more favorable, although the elimination of the first water is still endothermic.

Active-space completely-renormalized equation-of-motion coupled-cluster formalism: Excited-state studies of green fluorescent protein, free-base porphyrin, and oligoporphyrin dimer.

The completely renormalized equation-of-motion coupled-cluster approach with singles, doubles, and noniterative triples [CR-EOMCCSD(T)] has proven to be a reliable tool in describing vertical excitation energies in small and medium size molecules. In order to reduce the high numerical cost of the genuine CR-EOMCCSD(T) method and make noniterative CR-EOMCCSD(T) approaches applicable to large molecular systems, two active-space variants of this formalism [the CR-EOMCCSd(t)-II and CR-EOMCCSd(t)-III methods], based on two different choices of the subspace of triply excited configurations employed to construct noniterative correction, are introduced. In calculations for green fluorescent protein (GFP) and free-base porphyrin, where the CR-EOMCCSD(T) results are available, we show good agreement between the active-space CR-EOMCCSD(T) (variant II) and full CR-EOMCCSD(T) excitation energies.

Accurate dipole polarizabilities for water clusters n=2-12 at the coupled-cluster level of theory and benchmarking of various density functionals.

The static dipole polarizabilities of water clusters (2 View Article and Find Full Text PDF

Parallel computation of coupled-cluster hyperpolarizabilities.

Static hyperpolarizabilities of molecules (water, acetonitrile, chloroform, and para-nitroaniline) are calculated with large basis sets using coupled-cluster response theory and compared to four common density functional theory methods. These results reveal which methods and basis sets are appropriate for nonlinear optical studies for different types of molecules and provide a means for estimating errors from the quantum chemical approximation when including vibrational contributions or solvent effects at the QM/MM level. The largest calculation reported, which was for 72 electrons in 812 functions at C(2v) symmetry, took only a few hours on 256 nodes demonstrating that even larger calculations are quite feasible using modern supercomputers.

MPW1K Performs Much Better than B3LYP in DFT Calculations on Reactions that Proceed by Proton-Coupled Electron Transfer (PCET).

DFT calculations have been performed with the B3LYP and MPW1K functional on the hydrogen atom abstraction reactions of ethenoxyl with ethenol and of phenoxyl with both phenol and alpha-naphthol. Comparison with the results of G3 calculations shows that B3LYP seriously underestimates the barrier heights for the reaction of ethenoxyl with ethenol by both proton-coupled electron transfer (PCET) and hydrogen atom transfer (HAT) mechanisms. The MPW1K functional also underestimates the barrier heights, but by much less than B3LYP.

Reappraisal of cis effect in 1,2-dihaloethenes: an improved virtual orbital multireference approach.

Computed relative stabilities for isomers of 1,2-difluoroethene and 1,2-dichloroethene isomers are compared with predictions based on chemical hardness (eta) and electrophilicity (omega) using the principles of maximum hardness and minimum electrophilicity. The chemical hardness and electrophilicity deduced either from improved virtual orbital (IVO) energies or from correlated treatments correctly predict that cis 1,2-difluoroethene and 1,2-dichloroethene are energetically more stable than the corresponding trans isomers, and the ground state energies from multireference perturbation theory with IVO orbitals agree with these predictions. However, when the same quantities are computed using Hartree-Fock orbitals, serious inconsistencies between the two approaches emerge in predicting the stability of the isomers of the 1,2-dihaloethenes.

Coupled-cluster dynamic polarizabilities including triple excitations.

Dynamic polarizabilities for open- and closed-shell molecules were obtained by using coupled-cluster (CC) linear response theory with full treatment of singles, doubles, and triples (CCSDT-LR) with large basis sets utilizing the NWChem software suite. By using four approximate CC methods in conjunction with augmented cc-pVNZ basis sets, we are able to evaluate the convergence in both many-electron and one-electron spaces. For systems with primarily dynamic correlation, the results for CC3 and CCSDT are almost indistinguishable.

Linear response coupled cluster singles and doubles approach with modified spectral resolution of the similarity transformed Hamiltonian.

This paper discusses practical scheme for correcting the linear response coupled cluster with singles and doubles (CCSD) equations by shifting the poles corresponding to the equation-of-motion CCSD excitation energies by adding noniterative corrections due to triples. A simple criterion is derived for the excited states to be corrected in the spectral resolution of similarity transformed Hamiltonian on the CCSD level. Benchmark calculations were performed to compare the accuracies of static and dynamic polarizabilities obtained in this way with the CC3 and CCSDT counterparts.

Dynamic polarizabilities of polyaromatic hydrocarbons using coupled-cluster linear response theory.

Coupled-cluster theory with single and double excitations is applied to the calculation of optical properties of large polyaromatic hydrocarbons. Dipole polarizabilities are reported for benzene, pyrene, and the oligoacenes sequence n=2-6. Dynamic polarizabilities were calculated on polyacences as large as pentacene for a single frequency and for benzene and pyrene at many frequencies.