166 research outputs found
Software for the frontiers of quantum chemistry : An overview of developments in the Q-Chem 5 package
This article summarizes technical advances contained in the fifth major release of the Q-Chem quantum chemistry program package, covering developments since 2015. A comprehensive library of exchange–correlation functionals, along with a suite of correlated many-body methods, continues to be a hallmark of the Q-Chem software. The many-body methods include novel variants of both coupled-cluster and configuration-interaction approaches along with methods based on the algebraic diagrammatic construction and variational reduced density-matrix methods. Methods highlighted in Q-Chem 5 include a suite of tools for modeling core-level spectroscopy, methods for describing metastable resonances, methods for computing vibronic spectra, the nuclear–electronic orbital method, and several different energy decomposition analysis techniques. High-performance capabilities including multithreaded parallelism and support for calculations on graphics processing units are described. Q-Chem boasts a community of well over 100 active academic developers, and the continuing evolution of the software is supported by an “open teamware” model and an increasingly modular design.This article summarizes technical advances contained in the fifth major release of the Q-Chem quantum chemistry program package, covering developments since 2015. A comprehensive library of exchange-correlation functionals, along with a suite of correlated many-body methods, continues to be a hallmark of the Q-Chem software. The many-body methods include novel variants of both coupled-cluster and configuration-interaction approaches along with methods based on the algebraic diagrammatic construction and variational reduced density-matrix methods. Methods highlighted in Q-Chem 5 include a suite of tools for modeling core-level spectroscopy, methods for describing metastable resonances, methods for computing vibronic spectra, the nuclear-electronic orbital method, and several different energy decomposition analysis techniques. High-performance capabilities including multithreaded parallelism and support for calculations on graphics processing units are described. Q-Chem boasts a community of well over 100 active academic developers, and the continuing evolution of the software is supported by an "open teamware" model and an increasingly modular design.Peer reviewe
Faster Exact Exchange for Solids via occ-RI-K: Application to Combinatorially Optimized Range-Separated Hybrid Functionals for Simple Solids Near the Basis Set Limit
In this work, we developed and showcased the occ-RI-K algorithm to compute
the exact exchange contribution in density functional calculations of solids
near the basis set limit. Within the gaussian planewave (GPW) density fitting,
our algorithm achieves a 1-2 orders of magnitude speedup compared to
conventional GPW algorithms. Since our algorithm is well-suited for simulations
with large basis sets, we applied it to 12 hybrid density functionals with a
large uncontracted basis set to assess their performance on band gaps of 26
simple solids near the basis set limit. The largest calculation performed in
this work involves 3456 electrons and 75600 basis functions utilizing a
666 k-mesh. With 20-27% exact exchange, global hybrid
functionals (B3LYP, PBE0, revPBE0, B97-3, SCAN0) perform similarly with a
root-mean-square-deviation (RMSD) of 0.60-0.76 eV while other global hybrid
functionals such as M06-2X (1.98 eV) and MN15 (1.03 eV) show higher RMSD due to
their increased fraction of exact exchange. A short-range hybrid functional,
HSE achieves a similar RMSD (0.74 eV) but shows a noticeable underestimation of
band gaps due to the complete lack of long-range exchange. We found that two
combinatorially optimized range-separated hybrid functionals, B97X-rV
(3.86 eV) and B97M-rV (3.34 eV), and the two other range separated
hybrid functionals, CAM-B3LYP (2.36 eV) and CAM-QTP01 (4.08 eV), significantly
overestimate the band gap because of their high fraction of long-range exact
exchange. Given the failure of B97X-rV and B97M-rV, we have yet
to find a density functional that offers consistent performance for both
molecules and solids. Our algorithm development and density functional
assessment will serve as a stepping stone towards developing more accurate
hybrid functionals and applying them to practical applications
A simplified charge projection scheme for long-range electrostatics in ab initio QM/MM calculations
In a previous work [Pan et al., Molecules 23, 2500 (2018)], a charge projection scheme was reported, where outer molecular mechanical (MM) charges [>10 Ă… from the quantum mechanical (QM) region] were projected onto the electrostatic potential (ESP) grid of the QM region to accurately and efficiently capture long-range electrostatics in ab initio QM/MM calculations. Here, a further simplification to the model is proposed, where the outer MM charges are projected onto inner MM atom positions (instead of ESP grid positions). This enables a representation of the long-range MM electrostatic potential via augmentary charges (AC) on inner MM atoms. Combined with the long-range electrostatic correction function from Cisneros et al. [J. Chem. Phys. 143, 044103 (2015)] to smoothly switch between inner and outer MM regions, this new QM/MM-AC electrostatic model yields accurate and continuous ab initio QM/MM electrostatic energies with a 10 Ă… cutoff between inner and outer MM regions. This model enables efficient QM/MM cluster calculations with a large number of MM atoms as well as QM/MM calculations with periodic boundary conditions
Advances in molecular quantum chemistry contained in the Q-Chem 4 program package
A summary of the technical advances that are incorporated in the fourth major release of the Q-CHEM quantum chemistry program is provided, covering approximately the last seven years. These include developments in density functional theory methods and algorithms, nuclear magnetic resonance (NMR) property evaluation, coupled cluster and perturbation theories, methods for electronically excited and open-shell species, tools for treating extended environments, algorithms for walking on potential surfaces, analysis tools, energy and electron transfer modelling, parallel computing capabilities, and graphical user interfaces. In addition, a selection of example case studies that illustrate these capabilities is given. These include extensive benchmarks of the comparative accuracy of modern density functionals for bonded and non-bonded interactions, tests of attenuated second order Møller–Plesset (MP2) methods for intermolecular interactions, a variety of parallel performance benchmarks, and tests of the accuracy of implicit solvation models. Some specific chemical examples include calculations on the strongly correlated Cr2 dimer, exploring zeolite-catalysed ethane dehydrogenation, energy decomposition analysis of a charged ter-molecular complex arising from glycerol photoionisation, and natural transition orbitals for a Frenkel exciton state in a nine-unit model of a self-assembling nanotube
Software for the frontiers of quantum chemistry: An overview of developments in the Q-Chem 5 package
This article summarizes technical advances contained in the fifth major release of the Q-Chem quantum chemistry program package, covering developments since 2015. A comprehensive library of exchange–correlation functionals, along with a suite of correlated many-body methods, continues to be a hallmark of the Q-Chem software. The many-body methods include novel variants of both coupled-cluster and configuration-interaction approaches along with methods based on the algebraic diagrammatic construction and variational reduced density-matrix methods. Methods highlighted in Q-Chem 5 include a suite of tools for modeling core-level spectroscopy, methods for describing metastable resonances, methods for computing vibronic spectra, the nuclear–electronic orbital method, and several different energy decomposition analysis techniques. High-performance capabilities including multithreaded parallelism and support for calculations on graphics processing units are described. Q-Chem boasts a community of well over 100 active academic developers, and the continuing evolution of the software is supported by an “open teamware” model and an increasingly modular design
Cross-scale efficient tensor contractions for coupled cluster computations through multiple programming model backends
Coupled-cluster methods provide highly accurate models of molecular structure through explicit numerical calculation of tensors representing the correlation between electrons. These calculations are dominated by a sequence of tensor contractions, motivating the development of numerical libraries for such operations. While based on matrix–matrix multiplication, these libraries are specialized to exploit symmetries in the molecular structure and in electronic interactions, and thus reduce the size of the tensor representation and the complexity of contractions. The resulting algorithms are irregular and their parallelization has been previously achieved via the use of dynamic scheduling or specialized data decompositions. We introduce our efforts to extend the Libtensor framework to work in the distributed memory environment in a scalable and energy-efficient manner. We achieve up to 240× speedup compared with the optimized shared memory implementation of Libtensor. We attain scalability to hundreds of thousands of compute cores on three distributed-memory architectures (Cray XC30 and XC40, and IBM Blue Gene/Q), and on a heterogeneous GPU-CPU system (Cray XK7). As the bottlenecks shift from being compute-bound DGEMM's to communication-bound collectives as the size of the molecular system scales, we adopt two radically different parallelization approaches for handling load-imbalance, tasking and bulk synchronous models. Nevertheless, we preserve a unified interface to both programming models to maintain the productivity of computational quantum chemists
A Dark Excited State of Fluorescent Protein Chromophores, Considered as Brooker Dyes
The green fluorescent protein (GFP) chromophore is an asymmetric monomethine
dye system. In the resonance color theory of dyes, a strong optical excitation
arises from interactions of two valence-bond structures with a third, higher
structure. We use correlated quantum chemistry to show that the anionic
chromophore is a resonant Brooker dye, and that the third structure corresponds
to a higher stationary electronic state of this species. The excitation energy
of this state should be just below the first excitation energy of the neutral
form. This has implications for excited state mechanism in GFPs, which we
discuss.Comment: This paper has been submitted for publication in Chemical Physics
Letter
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