Octopus (software)
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Octopus (software)
Octopus is a software package for performing KohnSham density functional theory (DFT) and time-dependent density functional theory (TDDFT) calculations. Octopus employs pseudopotentials and real-space numerical grids to propagate the KohnSham orbitals in real time under the influence of time-varying electromagnetic fields. Specific functionality is provided for simulating one-, two-, and three-dimensional systems. Octopus can calculate static and dynamic polarizabilities and first hyperpolarizabilities, static magnetic susceptibilities, absorption spectra, and perform molecular dynamics simulations with Ehrenfest and Car–Parrinello methods. The code is written predominantly in Fortran, with some C and Perl. It is released under the GPL. The latest version 12.0 was released September 19, 2022. Target problems * Linear optical (i.e. electronic) response of molecules or clusters, also second-order nonlinear response. * Non-linear response to classical high-intensity electr ...
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GNU General Public License
The GNU General Public License (GNU GPL or simply GPL) is a series of widely used free software licenses that guarantee end users the Four Freedoms (Free software), four freedoms to run, study, share, and modify the software. The license was the first copyleft for general use and was originally written by the founder of the Free Software Foundation (FSF), Richard Stallman, for the GNU Project. The license grants the recipients of a computer program the rights of the Free Software Definition. These GPL series are all copyleft licenses, which means that any derivative work must be distributed under the same or equivalent license terms. It is more restrictive than the GNU Lesser General Public License, Lesser General Public License and even further distinct from the more widely used permissive software licenses BSD licenses, BSD, MIT License, MIT, and Apache License, Apache. Historically, the GPL license family has been one of the most popular software licenses in the free and open ...
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Computational Chemistry Software
Computation is any type of arithmetic or non-arithmetic calculation that follows a well-defined model (e.g., an algorithm). Mechanical or electronic devices (or, historically, people) that perform computations are known as ''computers''. An especially well-known discipline of the study of computation is computer science. Physical process of Computation Computation can be seen as a purely physical process occurring inside a closed physical system called a computer. Examples of such physical systems are digital computers, mechanical computers, quantum computers, DNA computers, molecular computers, microfluidics-based computers, analog computers, and wetware computers. This point of view has been adopted by the physics of computation, a branch of theoretical physics, as well as the field of natural computing. An even more radical point of view, pancomputationalism (inaudible word), is the postulate of digital physics that argues that the evolution of the universe is itself a ...
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Quantum Chemistry Computer Programs
Quantum chemistry computer programs are used in computational chemistry to implement the methods of quantum chemistry. Most include the Hartree–Fock (HF) and some post-Hartree–Fock methods. They may also include density functional theory (DFT), molecular mechanics or semi-empirical quantum chemistry methods. The programs include both open source Open source is source code that is made freely available for possible modification and redistribution. Products include permission to use the source code, design documents, or content of the product. The open-source model is a decentralized sof ... and commercial software. Most of them are large, often containing several separate programs, and have been developed over many years. Overview The following tables illustrates some of the main capabilities of notable packages: Numerical details Quantum chemistry and solid-state physics characteristics Post processing packages in quantum chemistry and solid-state physics ...
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OpenMP
OpenMP (Open Multi-Processing) is an application programming interface (API) that supports multi-platform shared-memory multiprocessing programming in C, C++, and Fortran, on many platforms, instruction-set architectures and operating systems, including Solaris, AIX, FreeBSD, HP-UX, Linux, macOS, and Windows. It consists of a set of compiler directives, library routines, and environment variables that influence run-time behavior. OpenMP is managed by the nonprofit technology consortium ''OpenMP Architecture Review Board'' (or ''OpenMP ARB''), jointly defined by a broad swath of leading computer hardware and software vendors, including Arm, AMD, IBM, Intel, Cray, HP, Fujitsu, Nvidia, NEC, Red Hat, Texas Instruments, and Oracle Corporation. OpenMP uses a portable, scalable model that gives programmers a simple and flexible interface for developing parallel applications for platforms ranging from the standard desktop computer to the supercomputer. An application built wi ...
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Atomic Orbital
In atomic theory and quantum mechanics, an atomic orbital is a function describing the location and wave-like behavior of an electron in an atom. This function can be used to calculate the probability of finding any electron of an atom in any specific region around the atom's nucleus. The term ''atomic orbital'' may also refer to the physical region or space where the electron can be calculated to be present, as predicted by the particular mathematical form of the orbital. Each orbital in an atom is characterized by a set of values of the three quantum numbers , , and , which respectively correspond to the electron's energy, angular momentum, and an angular momentum vector component (magnetic quantum number). Alternative to the magnetic quantum number, the orbitals are often labeled by the associated harmonic polynomials (e.g., ''xy'', ). Each such orbital can be occupied by a maximum of two electrons, each with its own projection of spin m_s. The simple names s orbital, p orb ...
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Plane Wave
In physics, a plane wave is a special case of wave or field: a physical quantity whose value, at any moment, is constant through any plane that is perpendicular to a fixed direction in space. For any position \vec x in space and any time t, the value of such a field can be written as :F(\vec x,t) = G(\vec x \cdot \vec n, t), where \vec n is a unit-length vector, and G(d,t) is a function that gives the field's value as dependent on only two real parameters: the time t, and the scalar-valued displacement d = \vec x \cdot \vec n of the point \vec x along the direction \vec n. The displacement is constant over each plane perpendicular to \vec n. The values of the field F may be scalars, vectors, or any other physical or mathematical quantity. They can be complex numbers, as in a complex exponential plane wave. When the values of F are vectors, the wave is said to be a longitudinal wave if the vectors are always collinear with the vector \vec n, and a transverse wave if they ...
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Basis Set (chemistry)
In theoretical and computational chemistry, a basis set is a set of functions (called basis functions) that is used to represent the electronic wave function in the Hartree–Fock method or density-functional theory in order to turn the partial differential equations of the model into algebraic equations suitable for efficient implementation on a computer. The use of basis sets is equivalent to the use of an approximate resolution of the identity: the orbitals , \psi_i\rangle are expanded within the basis set as a linear combination of the basis functions , \psi_i\rangle \approx \sum_\mu c_ , \mu\rangle, where the expansion coefficients c_ are given by c_ = \sum_\nu \langle \mu, \nu \rangle^ \langle \nu , \psi_i \rangle. The basis set can either be composed of atomic orbitals (yielding the linear combination of atomic orbitals approach), which is the usual choice within the quantum chemistry community; plane waves which are typically used within the solid state community, or ...
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Perturbation Theory
In mathematics and applied mathematics, perturbation theory comprises methods for finding an approximate solution to a problem, by starting from the exact solution of a related, simpler problem. A critical feature of the technique is a middle step that breaks the problem into "solvable" and "perturbative" parts. In perturbation theory, the solution is expressed as a power series in a small parameter The first term is the known solution to the solvable problem. Successive terms in the series at higher powers of \varepsilon usually become smaller. An approximate 'perturbation solution' is obtained by truncating the series, usually by keeping only the first two terms, the solution to the known problem and the 'first order' perturbation correction. Perturbation theory is used in a wide range of fields, and reaches its most sophisticated and advanced forms in quantum field theory. Perturbation theory (quantum mechanics) describes the use of this method in quantum mechanics. The ...
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Carbon Nanotube
A scanning tunneling microscopy image of a single-walled carbon nanotube Rotating single-walled zigzag carbon nanotube A carbon nanotube (CNT) is a tube made of carbon with diameters typically measured in nanometers. ''Single-wall carbon nanotubes'' (''SWCNTs'') are one of the allotropes of carbon, intermediate between fullerene cages and flat graphene, with diameters in the range of a nanometre. Although not made this way, single-wall carbon nanotubes can be idealized as cutouts from a two-dimensional Hexagonal tiling, hexagonal lattice of carbon atoms rolled up along one of the Bravais lattice vectors of the hexagonal lattice to form a hollow cylinder. In this construction, periodic boundary conditions are imposed over the length of this roll-up vector to yield a helical lattice of seamlessly bonded carbon atoms on the cylinder surface. ''Multi-wall carbon nanotubes'' (''MWCNTs'') consisting of nested single-wall carbon nanotubes weakly bound together by van der Waals ...
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Polymer
A polymer (; Greek '' poly-'', "many" + ''-mer'', "part") is a substance or material consisting of very large molecules called macromolecules, composed of many repeating subunits. Due to their broad spectrum of properties, both synthetic and natural polymers play essential and ubiquitous roles in everyday life. Polymers range from familiar synthetic plastics such as polystyrene to natural biopolymers such as DNA and proteins that are fundamental to biological structure and function. Polymers, both natural and synthetic, are created via polymerization of many small molecules, known as monomers. Their consequently large molecular mass, relative to small molecule compounds, produces unique physical properties including toughness, high elasticity, viscoelasticity, and a tendency to form amorphous and semicrystalline structures rather than crystals. The term "polymer" derives from the Greek word πολύς (''polus'', meaning "many, much") and μέρος (''meros'' ...
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