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DOE OSTI2011

NWChem: scalable parallel computational chemistry

NWChem is a general purpose computational chemistry code specifically designed to run on distributed memory parallel computers. The core functionality of the code focuses on molecular dynamics, Hartree-Fock and density functional theory methods for both plane-wave basis sets as well as Gaussian basis sets, tensor contraction engine based coupled cluster capabilities and combined quantum mechanics/molecular mechanics descriptions. It was realized from the beginning that scalable implementations of these methods required a programming paradigm inherently different from what message passing approaches could offer. In response a global address space library, the Global Array Toolkit, was developed. The programming model it offers is based on using predominantly one-sided communication. This model underpins most of the functionality in NWChem and the power of it is exemplified by the fact that the code scales to tens of thousands of processors. In this paper the core capabilities of NWChem are described as well as their implementation to achieve an efficient computational chemistry code with high parallel scalability. NWChem is a modern, open source, computational chemistry code1 specifically designed for large scale parallel applications2. To meet the challenges of developing efficient, scalable and portable programs of this nature a particular code design was adopted. This code design involved two main features. First of all, the code is build up in a modular fashion so that a large variety of functionality can be integrated easily. Secondly, to facilitate writing complex parallel algorithms the Global Array toolkit was developed. This toolkit allows one to write parallel applications in a shared memory like approach, but offers additional mechanisms to exploit data locality to lower communication overheads. This framework has proven to be very successful in computational chemistry but is applicable to any engineering domain. Within the context created by the features above NWChem has grown into a general purpose computational chemistry code that supports a wide variety of energy expressions and capabilities to calculate properties based there upon. The main energy expressions are classical mechanics force fields, Hartree-Fock and DFT both for finite systems and condensed phase systems, coupled cluster, as well as QM/MM. For most energy expressions single point calculations, geometry optimizations, excited states, and other properties are available. Below we briefly discuss each of the main energy expressions and the critical points involved in scalable implementations thereof.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2025

Further steps toward the next generation of covariant energy density functionals

The present study aims at further development of covariant energy density functionals (CEDFs) towards more accurate description of binding energies across the nuclear chart. Infinite basis corrections to binding energies in the fermionic and bosonic sectors of the covariant density functional theory are taken into account in the fitting protocol within the covariant density functional theory. In addition, total electron binding energies are used in the conversion of atomic binding energies into nuclear ones. Their dependence on neutron excess is investigated across the nuclear chart within the atomic approach. Furthermore, these factors were disregarded in the previous generation of covariant energy density functionals, but their omission leads to substantial global calculation errors for physical quantities of interest. For example, these errors for binding energies are of the order of 0.8 MeV or higher for the three major classes of covariant energy density functionals.

Binding energy & masses↗

DOE OSTI2022

Grassland ecosystem type drives AM fungal diversity and functional guild distribution in North American grasslands

Nutrient exchange forms the basis of the ancient symbiotic relationship that occurs between most land plants and arbuscular mycorrhizal (AM) fungi. Plants provide carbon (C) to AM fungi and fungi provide the plant with nutrients such as nitrogen (N) and phosphorous (P). Nutrient addition can alter this symbiotic coupling in key ways, such as reducing AM fungal root colonization and changing the AM fungal community composition. However, environmental parameters that differentiate ecosystems and drive plant distribution patterns (e.g., pH, moisture), are also known to impact AM fungal communities. Identifying the relative contribution of environmental factors impacting AM fungal distribution patterns is important for predicting biogeochemical cycling patterns and plant-microbe relationships across ecosystems. Here, to evaluate the relative impacts of local environmental conditions and long-term nutrient addition on AM fungal abundance and composition across grasslands, we studied experimental plots amended for 10 years with N, P, or N and P fertilizer in different grassland ecosystem types, including tallgrass prairie, montane, shortgrass prairie, and desert grasslands. Contrary to our hypothesis, we found ecosystem type, not nutrient treatment, was the main driver of AM fungal root colonization, diversity, and community composition, even when accounting for site-specific nutrient limitations. We identified several important environmental drivers of grassland ecosystem AM fungal distribution patterns, including aridity, mean annual temperature, root moisture, and soil pH. This work provides empirical evidence for niche partitioning strategies of AM fungal functional guilds and emphasizes the importance of long-term, large scale research projects to provide ecologically relevant context to nutrient addition studies.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2015

Quantum entanglement for helium atom in the Debye plasmas

In the present work, we present an investigation on quantum entanglement of the two-electron helium atom immersed in weakly coupled Debye plasmas, modeled by the Debye-Hückel, or screened Coulomb, potential to mimic the interaction between two charged particles inside the plasma. Quantum entanglement is related to correlation effects in a multi-particle system. In a bipartite system, a measurement made on one of the two entangled particles affects the outcome of the other particle, even if such two particles are far apart. Employing wave functions constructed with configuration interaction B-spline basis, we have quantified von Neumann entropy and linear entropy for a series of He {sup 1,3}S{sup e} and {sup 1,3}P{sup o} states in plasma-embedded helium atom.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2018

Drought adaptation in Arabidopsis thaliana by extensive genetic loss-of-function

Interdisciplinary syntheses are needed to scale up discovery of the environmental drivers and molecular basis of adaptation in nature. Here we integrated novel approaches using whole genome sequences, satellite remote sensing, and transgenic experiments to study natural loss-of-function alleles associated with drought histories in wild Arabidopsis thaliana. The genes we identified exhibit population genetic signatures of parallel molecular evolution, selection for loss-of-function, and shared associations with flowering time phenotypes in directions consistent with longstanding adaptive hypotheses seven times more often than expected by chance. We then confirmed predicted phenotypes experimentally in transgenic knockout lines. These findings reveal the importance of drought timing to explain the evolution of alternative drought tolerance strategies and further challenge popular assumptions about the adaptive value of genetic loss-of-function in nature. These results also motivate improved species-wide sequencing efforts to better identify loss-of-function variants and inspire new opportunities for engineering climate resilience in crops.

Life Sciences & Biomedicine - Other Topics↗

DOE OSTI2015

Nanoplasmonics simulations at the basis set limit through completeness-optimized, local numerical basis sets

We present an approach for generating local numerical basis sets of improving accuracy for first-principles nanoplasmonics simulations within time-dependent density functional theory. The method is demonstrated for copper, silver, and gold nanoparticles that are of experimental interest but computationally demanding due to the semi-core d-electrons that affect their plasmonic response. The basis sets are constructed by augmenting numerical atomic orbital basis sets by truncated Gaussian-type orbitals generated by the completeness-optimization scheme, which is applied to the photoabsorption spectra of homoatomic metal atom dimers. We obtain basis sets of improving accuracy up to the complete basis set limit and demonstrate that the performance of the basis sets transfers to simulations of larger nanoparticles and nanoalloys as well as to calculations with various exchange-correlation functionals. This work promotes the use of the local basis set approach of controllable accuracy in first-principles nanoplasmonics simulations and beyond.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Improving Predictions of Spin-Crossover Complex Properties through DFT Calculations with a Local Hybrid Functional

We conducted a study on the performance of the local hybrid exchange-correlation functional PBE0r for a set of 95 experimentally-characterized iron spin crossover (SCO) complexes. The PBE0r functional is a variant of PBE0 where the exchange correction is restricted to on-site terms formulated within the basis of local orbitals. We determine the free parameters of the PBE0r functional against experimental data and other hybrid functionals. With a Hartree-Fock (HF) exchange factor of 4%, the PBE0r functional accurately reproduces the electronic and free energy trends predicted in prior DFT studies for these 95 complexes using the B3LYP functional. Larger values of HF exchange stabilize high-spin states. The PBE0r-predicted bond lengths tend to exceed the experimental bond lengths, and bond lengths are less sensitive to HF exchange. The predicted SCO transition temperatures T 1/2 from PBE0r correlate moderately with the experimental transition temperatures, showing a slight improvement compared to the previous modB3LYP-predicted T 1/2 . Furthermore, this study suggests the PBE0r functional as computationally cost-effective and offers the possibility of simulating larger complexes with accuracy comparable to other global hybrid functionals, provided the HF exchange parameter is carefully optimized.

25 ENERGY STORAGE↗

DOE OSTI2024

Impact of tensor couplings with scalar mixing on covariant energy density functionals

The recent pioneering campaigns conducted by the Lead Radius Experiment (PREX) and the Calcium Radius Experiment (CREX) Collaborations have uncovered major deficiencies in the theoretical description of some fundamental properties of atomic nuclei. Following a recent refinement to the isovector sector of covariant energy density functionals we present here additional improvements to the functional by including both tensor couplings and an isoscalar-isovector mixing term in the scalar sector. Motivated by the distinct surface properties of calcium and lead, we expect that the tensor terms that generate derivative couplings will help break the linear correlation between the neutron skin thickness of these two nuclei. Moreover, the addition of these new terms mitigates most of the problems identified by Reed et al. in describing the properties of both finite nuclei and neutron stars. While significant progress has been made in reconciling the PREX-CREX results without compromising other observables, the final resolution awaits the completion of a proper calibration for this new class of functionals. As a result, we expect that powerful reduced basis methods used recently to create efficient emulators will be essential to accomplish this task.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2018

Controlling the State of Machine Tools

Globally, manufacturers make great efforts to maintain the performance of industrial equipment. Developers and researchers are interested in automated approaches to maintaining the performance of equipment, especially at enterprises with high degrees of computerization and comprehensive information systems. In the present work, a new approach is outlined: an autonomous control system for maintaining the condition of metal-cutting machines. This approach is based on prior work in the field and permits maintenance on the basis of autonomous control of the state of machine tools. The structure of a system with the following generalized control functions is presented: decision making; and the issuing of commands on the basis of built-in resources. The formulation of control decisions employs the theory of fuzzy sets and fuzzy logic. By means of the ANFIS fuzzy network system, the autonomy of state control of the machine tool may be assessed. Criticality assessment of the condition of machine tools and their components is important in making decisions as to the setup of systems controlling the condition of equipment at enterprises, with assessment of their efficiency. In the monitoring subsystem, provision is made for assessment of the diagnostic results, prediction, and the generation of control decisions so as to prevent disruptions of machine-tool operation.

42 ENGINEERING↗

DOE OSTI2014

Comment on “Rethinking first-principles electron transport theories with projection operators: The problems caused by partitioning the basis set” [J. Chem. Phys. 139, 114104 (2013)]

In a recent paper Reuter and Harrison [J. Chem. Phys. 139, 114104 (2013)] question the widely used mean-field electron transport theories, which employ nonorthogonal localized basis sets. They claim these can violate an “implicit decoupling assumption,” leading to wrong results for the current, different from what would be obtained by using an orthogonal basis, and dividing surfaces defined in real-space. We argue that this assumption is not required to be fulfilled to get exact results. We show how the current/transmission calculated by the standard Greens function method is independent of whether or not the chosen basis set is nonorthogonal, and that the current for a given basis set is consistent with divisions in real space. The ambiguity known from charge population analysis for nonorthogonal bases does not carry over to calculations of charge flux.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2020

Spin Splitting Energy of Transition Metals: A New, More Affordable Wave Function Benchmark Method and Its Use to Test Density Functional Theory

Accurately predicting the spin splitting energy of chemical species is important for understanding their reactivity and magnetic properties, but it is very challenging, especially for molecules containing transition metals. One impediment to progress is the scarcity of accurate benchmark data. Here we report a set of calculations designed to yield reliable benchmarks for simple transition-metal complexes that can be used to test density functional methods that are affordable for large systems of more practical interest. Various wave function methods are tested against experiment for Fe 2+ , Fe 3+ , and Co 3+ , including CASSCF, CASPT2, CASPT3, MRCISD, MRCISD+Q, ACPF, AQCC, CCSD(T), and CASPT2/CCSD(T) and also a new method called CASPT2.5, which is performed by taking the average of the CASPT2 and CASPT3 energies. Furthermore, we find that MRCISD+Q, ACPF, and AQCC require smaller active spaces for good accuracy than are required by CASPT2 and CASPT3, and this aspect may be important for calculations on larger molecules; here we find that CASPT2.5 extrapolated to a complete basis set is the most suitable method—in terms of computational cost and in terms of accuracy on monatomic systems—and therefore we chose this method for molecular benchmarks. Then Kohn–Sham density functional calculations with 60 exchange-correlation functionals are tested for FeF 2 , FeCl 2 , and CoF 2 . We find that MN15-L, M06-SX, and revM06 have very good agreement with CASPT2.5 benchmarks in terms of both the spin splitting energy and the optimized geometry for each spin state. In addition, we recommend def2-TZVP as the most suitable basis set to perform density functional calculations for molecular spin splitting energies; extra polarization functions in the basis set do not help to increase the accuracy of the spin splitting energy in KS calculations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2015

Mapping the genome of meta-generalized gradient approximation density functionals: The search for B97M-V

A meta-generalized gradient approximation density functional paired with the VV10 nonlocal correlation functional is presented. The functional form is selected from more than 10{sup 10} choices carved out of a functional space of almost 10{sup 40} possibilities. Raw data come from training a vast number of candidate functional forms on a comprehensive training set of 1095 data points and testing the resulting fits on a comprehensive primary test set of 1153 data points. Functional forms are ranked based on their ability to reproduce the data in both the training and primary test sets with minimum empiricism, and filtered based on a set of physical constraints and an often-overlooked condition of satisfactory numerical precision with medium-sized integration grids. The resulting optimal functional form has 4 linear exchange parameters, 4 linear same-spin correlation parameters, and 4 linear opposite-spin correlation parameters, for a total of 12 fitted parameters. The final density functional, B97M-V, is further assessed on a secondary test set of 212 data points, applied to several large systems including the coronene dimer and water clusters, tested for the accurate prediction of intramolecular and intermolecular geometries, verified to have a readily attainable basis set limit, and checked for grid sensitivity. Compared to existing density functionals, B97M-V is remarkably accurate for non-bonded interactions and very satisfactory for thermochemical quantities such as atomization energies, but inherits the demonstrable limitations of existing local density functionals for barrier heights.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2018

Systematic review of biological effects of exposure to static electric fields. Part II: Invertebrates and plants

Highlights: • Environmental impacts of static EF were assessed in invertebrate and plant studies. • Invertebrates are able to perceive the presence of static EF near HVDC power lines. • No evidence for adverse effects on physiological functions at HVDC field levels. • Corona-action appears to cause adverse biological effects at very high field levels. • Methodological flaws in all reviewed studies lowered credibility in the results. The construction of high-voltage direct current (HVDC) lines for the long-distance transport of energy is becoming increasingly popular. This has raised public concern about potential environmental impacts of the static electric fields (EF) produced under and near HVDC power lines. As the second part of a comprehensive literature analysis, the aim of this systematic review was to assess the effects of static EF exposure on biological functions in invertebrates and plants and to provide the basis for an environmental impact assessment of such exposures.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗

DOE OSTI2015

Leading order nonadiabatic corrections to rovibrational levels of H{sub 2}, D{sub 2}, and T{sub 2}

An efficient computational approach to nonadiabatic effects in the hydrogen molecule (H{sub 2}, D{sub 2}, and T{sub 2}) is presented. The electronic wave function is expanded in the James-Coolidge basis set, which enables obtaining a very high accuracy of nonadiabatic potentials. A single point convergence of the potentials with growing size of the basis set reveals a relative accuracy ranging from 10{sup −8} to 10{sup −13}. An estimated accuracy of the leading nonadiabatic correction to the rovibrational energy levels is of the order of 10{sup −7} cm{sup −1}. After a significant increase in the accuracy of the Born-Oppenheimer and adiabatic calculations, the nonadiabatic results presented in this report constitute another step towards highly accurate theoretical description of the hydrogen molecule.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2014

Ultrafast dynamics of the dielectric functions of ZnO and BaTiO{sub 3} thin films after intense femtosecond laser excitation

The ultrafast carrier dynamics of epitaxial ZnO and BaTiO{sub 3} thin films after intense excitation at 3.10 eV and 4.66 eV photon energy has been studied by femtosecond absorption spectroscopy. Modelling the transient transmission changes on the basis of spectroscopic ellipsometry data and pertinent equilibrium model dielectric functions extended by additional terms for the effects at high carrier density (P-band luminescence and stimulated emission from electron-hole-plasma), a self-consistent parameterized description was obtained for both materials. Excited carrier lifetimes in the range of ≈2 to ≈60 ps and long-lived thermal effects after several hundred ps have been identified in both materials. These findings form a reliable basis to quantitatively describe future femtosecond studies on ZnO/BaTiO{sub 3} heterolayer systems.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2013

Comparison between Gaussian-type orbitals and plane wave ab initio density functional theory modeling of layer silicates: Talc [Mg{sub 3}Si{sub 4}O{sub 10}(OH){sub 2}] as model system

The quantum chemical characterization of solid state systems is conducted with many different approaches, among which the adoption of periodic boundary conditions to deal with three-dimensional infinite condensed systems. This method, coupled to the Density Functional Theory (DFT), has been proved successful in simulating a huge variety of solids. Only in relatively recent years this ab initio quantum-mechanic approach has been used for the investigation of layer silicate structures and minerals. In the present work, a systematic comparison of different DFT functionals (GGA-PBEsol and hybrid B3LYP) and basis sets (plane waves and all-electron Gaussian-type orbitals) on the geometry, energy, and phonon properties of a model layer silicate, talc [Mg{sub 3}Si{sub 4}O{sub 10}(OH){sub 2}], is presented. Long range dispersion is taken into account by DFT+D method. Results are in agreement with experimental data reported in literature, with minimal deviation given by the GTO/B3LYP-D* method regarding both axial lattice parameters and interaction energy and by PW/PBE-D for the unit-cell volume and angular values. All the considered methods adequately describe the experimental talc infrared spectrum.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Range‐separated density functional theory using multiresolution analysis and quantum computing

Quantum computers are expected to outperform classical computers for specific problems in quantum chemistry. Such calculations remain expensive, but costs can be lowered through the partition of the molecular system. In the present study, partition was achieved with range-separated density functional theory (RS-DFT). The use of RS-DFT reduces both the basis set size and the active space size dependence of the ground state energy in comparison with the use of wave function theory (WFT) alone. The utilization of pair natural orbitals (PNOs) in place of canonical molecular orbitals (MOs) results in more compact qubit Hamiltonians. To test this strategy, a basis-set independent framework, known as multiresolution analysis (MRA), was employed to generate PNOs. Tests were conducted with the variational quantum eigensolver for a number of molecules. The results show that the proposed approach reduces the number of qubits needed to reach a target energy accuracy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2016

Triphenylamine based organic dyes for dye sensitized solar cells: A theoretical approach

The geometry, electronic structure and absorption spectra for newly designed triphenylamine based organic dyes were investigated by density functional theory (DFT) and time dependent density functional theory (TD-DFT) with the Becke 3-Parameter-Lee-Yang-parr(B3LYP) functional, where the 6-31G(d,p) basis set was employed. All calculations were performed using the Gaussian 09 software package. The calculated HOMO and LUMO energies show that charge transfer occurs in the molecule. Ultraviolet–visible (UV–vis) spectrum was simulated by TD-DFT in gas phase. The calculation shows that all of the dyes can potentially be good sensitizers for DSSC. The LUMOs are just above the conduction band of TiO{sub 2} and their HOMOs are under the reduction potential energy of the electrolytes (I{sup −}/I{sub 3}{sup −}) which can facilitate electron transfer from the excited dye to TiO{sub 2} and charge regeneration process after photo oxidation respectively. The simulated absorption spectrum of dyes match with solar spectrum. Frontier molecular orbital results show that among all the three dyes, the “dye 3” can be used as potential sensitizer for DSSC.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗