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Computational chemistry is a branch of chemistry that uses computer simulation to assist in solving chemical problems. It uses methods of theoretical chemistry, incorporated into computer programs, to calculate the structures and properties of molecules, groups of molecules, and solids. It is necessary because, apart from relatively recent results concerning the hydrogen molecular ion, the quantum many-body problem cannot be solved analytically, much less in closed form. While computational results normally complement the information obtained by chemical experiments, it can in some cases predict hitherto unobserved chemical phenomena. It is widely used in the design of new drugs and materials.
Computational physics is the study and implementation of numerical analysis to solve problems in physics for which a quantitative theory already exists. Historically, computational physics was the first application of modern computers in science, and is now a subset of computational science. It is sometimes regarded as a subdiscipline of theoretical physics, but others consider it an intermediate branch between theoretical and experimental physics - an area of study which supplements both theory and experiment.
Density-functional theory (DFT) is a computational quantum mechanical modelling method used in physics, chemistry and materials science to investigate the electronic structure of many-body systems, in particular atoms, molecules, and the condensed phases. Using this theory, the properties of a many-electron system can be determined by using functionals, i.e. functions of another function. In the case of DFT, these are functionals of the spatially dependent electron density. DFT is among the most popular and versatile methods available in condensed-matter physics, computational physics, and computational chemistry.
NWChem is an ab initio computational chemistry software package which includes quantum chemical and molecular dynamics functionality. It was designed to run on high-performance parallel supercomputers as well as conventional workstation clusters. It aims to be scalable both in its ability to treat large problems efficiently, and in its usage of available parallel computing resources. NWChem has been developed by the Molecular Sciences Software group of the Theory, Modeling & Simulation program of the Environmental Molecular Sciences Laboratory (EMSL) at the Pacific Northwest National Laboratory (PNNL). The early implementation was funded by the EMSL Construction Project.
SIESTA is an original method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids. SIESTA's efficiency stems from the use of strictly localized basis sets and from the implementation of linear-scaling algorithms which can be applied to suitable systems. A very important feature of the code is that its accuracy and cost can be tuned in a wide range, from quick exploratory calculations to highly accurate simulations matching the quality of other approaches, such as plane-wave and all-electron methods.
Jaguar is a computer software package used for ab initio quantum chemistry calculations for both gas and solution phases. It is commercial software marketed by the company Schrödinger. The program was originated in research groups of Richard Friesner and William Goddard and was initially called PS-GVB.
Spartan is a molecular modelling and computational chemistry application from Wavefunction. It contains code for molecular mechanics, semi-empirical methods, ab initio models, density functional models, post-Hartree–Fock models, and thermochemical recipes including G3(MP2) and T1. Quantum chemistry calculations in Spartan are powered by Q-Chem.
Car–Parrinello molecular dynamics or CPMD refers to either a method used in molecular dynamics or the computational chemistry software package used to implement this method.
Hybrid functionals are a class of approximations to the exchange–correlation energy functional in density functional theory (DFT) that incorporate a portion of exact exchange from Hartree–Fock theory with the rest of the exchange–correlation energy from other sources. The exact exchange energy functional is expressed in terms of the Kohn–Sham orbitals rather than the density, so is termed an implicit density functional. One of the most commonly used versions is B3LYP, which stands for "Becke, 3-parameter, Lee–Yang–Parr".
The WIEN2k package is a computer program written in Fortran which performs quantum mechanical calculations on periodic solids. It uses the full-potential (linearized) augmented plane-wave and local-orbitals [FP-(L)APW+lo] basis set to solve the Kohn–Sham equations of density functional theory.
CP2K is a freely available (GPL) quantum chemistry and solid state physics program package, written in Fortran 2008, to perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems. It provides a general framework for different methods: density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW) via LDA, GGA, MP2, or RPA levels of theory, classical pair and many-body potentials, semi-empirical and tight-binding Hamiltonians, as well as Quantum Mechanics/Molecular Mechanics (QM/MM) hybrid schemes relying on the Gaussian Expansion of the Electrostatic Potential (GEEP). The Gaussian and Augmented Plane Waves method (GAPW) as an extension of the GPW method allows for all-electron calculations. CP2K can do simulations of molecular dynamics, metadynamics, Monte Carlo, Ehrenfest dynamics, vibrational analysis, core level spectroscopy, energy minimization, and transition state optimization using NEB or dimer method.
Minnesota Functionals (Myz) are a group of highly parameterized approximate exchange-correlation energy functionals in density functional theory (DFT). They are developed by the group of Prof. Donald Truhlar at the University of Minnesota. These functionals are based on the meta-GGA approximation, i.e. they include terms that depend on the kinetic energy density, and are all based on complicated functional forms parametrized on high-quality benchmark databases. These functionals can be used for traditional quantum chemistry and solid-state physics calculations. The Myz functionals are widely used and tested in the quantum chemistry community.
TeraChem is a computational chemistry software program designed for CUDA-enabled Nvidia GPUs. The initial development started at the University of Illinois at Urbana-Champaign and was subsequently commercialized. It is currently distributed by PetaChem, LLC, located in Silicon Valley. As of 2020, the software package is still under active development.
Quantum ESPRESSO is a suite for first-principles electronic-structure calculations and materials modeling, distributed for free and as free software under the GNU General Public License. It is based on density-functional theory, plane wave basis sets, and pseudopotentials. ESPRESSO is an acronym for opEn-Source Package for Research in Electronic Structure, Simulation, and Optimization.
Giulia Galli is a condensed-matter physicist. She is the Liew Family Professor of Electronic Structure and Simulations in the Pritzker School of Molecular Engineering and the Department of Chemistry at the University of Chicago and senior scientist at Argonne National Laboratory. She is also the director of the Midwest Integrated Center for Computational Materials. She is recognized for her contributions to the fields of computational condensed-matter, materials science, and nanoscience, most notably first principles simulations of materials and liquids, in particular materials for energy, properties of water, and excited state phenomena.
Mixed quantum-classical (MQC) dynamics is a class of computational theoretical chemistry methods tailored to simulate nonadiabatic (NA) processes in molecular and supramolecular chemistry. Such methods are characterized by:
- Propagation of nuclear dynamics through classical trajectories;
- Propagation of the electrons through quantum methods;
- A feedback algorithm between the electronic and nuclear subsystems to recover nonadiabatic information.
Computational materials science and engineering uses modeling, simulation, theory, and informatics to understand materials. The main goals include discovering new materials, determining material behavior and mechanisms, explaining experiments, and exploring materials theories. It is analogous to computational chemistry and computational biology as an increasingly important subfield of materials science.
FHI-aims is a shared-source software package for computational molecular and materials science written in Fortran. It uses density functional theory and many-body perturbation theory to simulate chemical and physical properties of atoms, molecules, nanostructures, solids, and surfaces. Originally developed at the Fritz Haber Institute in Berlin the ongoing development of the FHI-aims source code is now driven by a world-wide community of collaborating research institutions.
References
- ↑ "FreeBSD Ports Search".
- ↑ Arin R. Greenwood; Márton Vörös; Federico Giberti; Giulia Galli (2018). "Emergent Electronic and Dielectric Properties of Interacting Nanoparticles at Finite Temperature". Nano Letters . 18 (1): 255–261. Bibcode:2018NanoL..18..255G. doi:10.1021/acs.nanolett.7b04047. OSTI 1421969. PMID 29227689.
- ↑ Tuan Anh Pham; Marco Govoni; Robert Seidel; Stephen E. Bradforth; Eric Schwegler; Giulia Galli (2017). "Electronic structure of aqueous solutions: Bridging the gap between theory and experiments". Science Advances . 3 (6): e1603210. Bibcode:2017SciA....3E3210P. doi:10.1126/sciadv.1603210. PMC 5482551 . PMID 28691091.
- ↑ Emre Sevgen; Federico Giberti; Hythem Sidky; Jonathan K. Whitmer; Giulia Galli; Francois Gygi; Juan J. de Pablo (2018). "Hierarchical Coupling of First-Principles Molecular Dynamics with Advanced Sampling Methods". Journal of Chemical Theory and Computation . 14 (6): 2881−2888. doi:10.1021/acs.jctc.8b00192. PMID 29694787.
- ↑ Chunyi Zhang; Cui Zhang; Mohan Chen; Wei Kang; Zhuowei Gu; Jianheng Zhao; Cangli Liu; Chengwei Sun; Ping Zhang (2018). "Finite-temperature infrared and Raman spectra of high-pressure hydrogen from first-principles molecular dynamics". Physical Review B . 98 (14): 144301. Bibcode:2018PhRvB..98n4301Z. doi:10.1103/PhysRevB.98.144301.
- ↑ Rengin Pekös; Davide Donadio (2017). "Dissociative Adsorption of Water at (211) Stepped Metallic Surfaces by First-Principles Simulations". Journal of Physical Chemistry C . 121 (31): 16783–16791. doi:10.1021/acs.jpcc.7b03226.
- ↑ Francois Gygi (2008). "Architecture of Qbox: A scalable first-principles molecular dynamics code". IBM Journal of Research and Development . 52 (1, 2): 137–144. doi:10.1147/rd.521.0137. ISSN 0018-8646.
- ↑ "Supercomputer Sets New Performance Record".