Quantum chemistry is a discipline which relies heavily on very expensive numerical computations. The scaling of correlated wave function methods lies, in their standard implementation, between and , where N is proportional to the system size. Therefore, performing accurate calculations on chemically meaningful systems requires (i) approximations that can lower the computational scaling and (ii) efficient implementations that take advantage of modern massively parallel architectures. Quantum Package is an open-source programming environment for quantum chemistry specially designed for wave function methods. Its main goal is the development of determinant-driven selected configuration interaction (sCI) methods and multireference second-order perturbation theory (PT2). The determinant-driven framework allows the programmer to include any arbitrary set of determinants in the reference space, hence providing greater methodological freedom. The sCI method implemented in Quantum Package is based on the CIPSI (Configuration Interaction using a Perturbative Selection made Iteratively) algorithm which complements the variational sCI energy with a PT2 correction. Additional external plugins have been recently added to perform calculations with multireference coupled cluster theory and range-separated density-functional theory. All the programs are developed with the IRPF90 code generator, which simplifies collaborative work and the development of new features. Quantum Package strives to allow easy implementation and experimentation of new methods, while making parallel computation as simple and efficient as possible on modern supercomputer architectures. Currently, the code enables, routinely, to realize runs on roughly 2 000 CPU cores, with tens of millions of determinants in the reference space. Moreover, we have been able to push up to 12 288 cores in order to test its parallel efficiency. In the present manuscript, we also introduce some key new developments: (i) a renormalized second-order perturbative correction for efficient extrapolation to the full CI limit and (ii) a stochastic version of the CIPSI selection performed simultaneously to the PT2 calculation at no extra cost.

The present work proposes to use density-functional theory (DFT) to correct for the basis-set error of wavefunction theory (WFT). One of the key ideas developed here is to define a range-separation parameter which automatically adapts to a given basis set. The derivation of the exact equations are based on the Levy-Lieb formulation of DFT, which helps us to define a complementary functional which corrects uniquely for the basis-set error of WFT. The coupling of DFT and WFT is done through the definition of a realspace representation of the electron-electron Coulomb operator projected in a one-particle basis set. Such an effective interaction has the particularity to coincide with the exact electron-electron interaction in the limit of a complete basis set, and to be finite at the electron-electron coalescence point when the basis set is incomplete. The non-diverging character of the effective interaction allows one to define a mapping with the long-range interaction used in the context of range-separated DFT and to design practical approximations for the unknown complementary functional. Here, a local-density approximation is proposed for both fullconfiguration-interaction (FCI) and selected configuration-interaction approaches. Our theory is numerically tested to compute total energies and ionization potentials for a series of atomic systems. The results clearly show that the DFT correction drastically improves the basis-set convergence of both the total energies and the energy differences. For instance, a sub kcal/mol accuracy is obtained from the aug-cc-pVTZ basis set with the method proposed here when an aug-cc-pV5Z basis set barely reaches such a level of accuracy at the near FCI level.

<div> <div> <div> <p> </p><div> <div> <div> <p>Quantum Package is an open-source programming environment for quantum chemistry specially designed for wave function methods. Its main goal is the development of determinant-driven selected configuration interaction (sCI) methods and multi-reference second-order perturbation theory (PT2). The determinant-driven framework allows the programmer to include any arbitrary set of determinants in the reference space, hence providing greater method- ological freedoms. The sCI method implemented in Quantum Package is based on the CIPSI (Configuration Interaction using a Perturbative Selection made Iteratively) algorithm which complements the variational sCI energy with a PT2 correction. Additional external plugins have been recently added to perform calculations with multireference coupled cluster theory and range-separated density-functional theory. All the programs are developed with the IRPF90 code generator, which simplifies collaborative work and the development of new features. Quantum Package strives to allow easy implementation and experimentation of new methods, while making parallel computation as simple and efficient as possible on modern supercomputer architectures. Currently, the code enables, routinely, to realize runs on roughly 2 000 CPU cores, with tens of millions of determinants in the reference space. Moreover, we have been able to push up to 12 288 cores in order to test its parallel efficiency. In the present manuscript, we also introduce some key new developments: i) a renormalized second-order perturbative correction for efficient extrapolation to the full CI limit, and ii) a stochastic version of the CIPSI selection performed simultaneously to the PT2 calculation at no extra cost. </p> </div> </div> </div> </div> </div> </div>

Background: PfHRP2-based rapid diagnostic tests (RDTs), based on the recognition of the Plasmodium falciparum histidine-rich protein 2, are currently the most used tests in malaria detection. Most of the antibodies used in RDTs also detect PfHRP3. However, false-negative results were reported. Significant variation in the pfhrp2 gene could lead to the expression of a modified protein that would no longer be recognized by the antibodies used in PfHRP2-based RDTs. Additionally, parasites lacking the PfHRP2 do not express the protein and are, therefore, not identifiable. Aims: This review aims to assess the pfhrp2 and pfhrp3 genetic variation or the prevalence of gene deletion in areas where malaria is endemic and describe its implications on RDT use. Sources: Publications of interest were identified using PubMed, Google Scholar and Google. Content: More than 18 types of amino acid repeats were identified from the PfHRP2 sequences. Sequencing analysis revealed high-level genetic variation in the pfhrp2 and pfhrp3 genes (>90% of variation in Madagascar, Nigeria or Senegal) both within and between countries. However, genetic variation of PfHRP2 and PfHRP3 does not seem to be a major cause of false-negative results. The countries that showed the highest proportions of pfhrp2-negative parasites were Peru (20%e100%) and Guyana (41%) in South America, Ghana (36%) and Rwanda (23%) in Africa. High prevalence of pfhrp2 deletion causes a high rate of false-negatives results. Implications: Presence of parasites lacking the pfhrp2 gene may pose a major threat to malaria control programmes because P. falciparum-infected individuals are not diagnosed and properly treated.

We report a universal density-based basis-set incompleteness correction that can be applied to any wave function method. e present correction, which appropriately vanishes in the complete basis set (CBS) limit, relies on short-range correlation density functionals (with multideterminant reference) from range-separated density-functional theory (RS-DFT) to estimate the basis-set incompleteness error. Contrary to conventional RS-DFT schemes which require an ad hoc range-separation parameter µ, the key ingredient here is a range-separation function µ(r) that automatically adapts to the spatial non-homogeneity of the basis-set incompleteness error.As illustrative examples, we show how this density-based correction allows us to obtain CCSD(T) atomization and correlation energies near the CBS limit for the G2 set of molecules with compact Gaussian basis sets.Contemporary quantum chemistry has developed in two directions -wave function theory (WFT) 1 and density-functional theory (DFT). 2 Although both spring from the same Schrödinger equation, each of these philosophies has its own pros and cons.WFT is a ractive as it exists a well-de ned path for systematic improvement as well as powerful tools, such as perturbation theory, to guide the development of new WFT ansätze. e coupled cluster (CC) family of methods is a typical example of the WFT philosophy and is well regarded as the gold standard of quantum chemistry for weakly correlated systems. By increasing the excitation degree of the CC expansion, one can systematically converge, for a given basis set, to the exact, full con guration interaction (FCI) limit, although the computational cost associated with such improvement is usually high. One of the most fundamental drawbacks of conventional WFT methods is the slow convergence of energies and properties with respect to the size of the one-electron basis set. is undesirable feature was put into light by Kutzelnigg more than thirty years ago. 3 To palliate this, following Hylleraas' footsteps, 4 Kutzelnigg proposed to introduce explicitly the interelectronic distance r 12 = |r 1 − r 2 | to properly describe the electronic wave function around the coalescence of two electrons. 3,5,6 e resulting F12 methods yield a prominent improvement of the energy convergence, and achieve chemical accuracy for small organic molecules with relatively small Gaussian basis sets. [7][8][9][10][11][12] For example, at the CCSD(T) level, one can obtain quintuple-ζ quality correlation energies with a triple-ζ basis, 13 although computational overheads are introduced by the large auxiliary basis used to resolve three-and four-electron integrals. 14 To reduce further the computational cost and/or ease the transferability of the F12 correction, approximated and/or universal schemes have recently emerged. [15][16][17][18][19][20] Present-day DFT calculations are almost exclusively done within the so-called Kohn-Sham (KS) formalism, which corresponds to an exact dressed one-electron theory. 21 e a ractiveness of DFT originates from its very favor...

Similar to other electron correlation methods, manybody perturbation theory methods based on Green functions, such as the so-called GW approximation, suffer from the usual slow convergence of energetic properties with respect to the size of the one-electron basis set. This displeasing feature is due to the lack of explicit electron-electron terms modeling the infamous Kato electron-electron cusp and the correlation Coulomb hole around it. Here, we propose a computationally efficient density-based basis-set correction based on short-range correlation density functionals which significantly speeds up the convergence of energetics towards the complete basis set limit. The performance of this density-based correction is illustrated by computing the ionization potentials of the twenty smallest atoms and molecules of the GW100 test set at the perturbative GW (or G 0 W 0 ) level using increasingly large basis sets. We also compute the ionization potentials of the five canonical nucleobases (adenine, cytosine, thymine, guanine, and uracil) and show that, here again, a significant improvement is obtained.

No abstract

This work provides a self-consistent extension of the recently proposed density-based basis-set correction method for wave function electronic-structure calculations [E. Giner et al., J. Chem. Phys. 149, 194301 (2018)]. In contrast to the previously used approximation where the basis-set correction density functional was a posteriori added to the energy from a wave-function calculation, here the energy minimization is performed including the basis-set correction. Compared to the non-self-consistent approximation, this allows one to lower the total energy and change the wave function under the effect of the basis-set correction. This work addresses two main questions: (i) What is the change in total energy compared to the non-self-consistent approximation and (ii) can we obtain better properties, namely, dipole moments, with the basis-set corrected wave functions. We implement the present formalism with two different basis-set correction functionals and test it on different molecular systems. The main results of the study are that (i) the total energy lowering obtained by the self-consistent approach is extremely small, which justifies the use of the non-self-consistent approximation, and (ii) the dipole moments obtained from the basis-set corrected wave functions are improved, being already close to their complete basis-set values with triple-zeta basis sets. Thus, the present study further confirms the soundness of the density-based basis-set correction scheme.