Qbox is an

open-source software Open-source software (OSS) is computer software that is released under a license in which the copyright holder grants users the rights to use, study, change, and distribute the software and its source code to anyone and for any purpose. Op ...

package for atomic-scale simulations of

molecule A molecule is a group of two or more atoms held together by attractive forces known as chemical bonds; depending on context, the term may or may not include ions which satisfy this criterion. In quantum physics, organic chemistry, and bioche ...

s, liquids and

solid Solid is one of the four fundamental states of matter (the others being liquid, gas, and plasma). The molecules in a solid are closely packed together and contain the least amount of kinetic energy. A solid is characterized by structural ...

s. It implements

first principle In philosophy and science, a first principle is a basic proposition or assumption that cannot be deduced from any other proposition or assumption. First principles in philosophy are from First Cause attitudes and taught by Aristotelians, and nua ...

s (or ab initio ''Ab initio'' ( ) is a Latin term meaning "from the beginning" and is derived from the Latin ''ab'' ("from") + ''initio'', ablative singular of ''initium'' ("beginning"). Etymology Circa 1600, from Latin, literally "from the beginning", from ab ...
)

molecular dynamics Molecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of t ...

, a

simulation A simulation is the imitation of the operation of a real-world process or system over time. Simulations require the use of models; the model represents the key characteristics or behaviors of the selected system or process, whereas the s ...

method in which inter-atomic forces are derived from

quantum mechanics Quantum mechanics is a fundamental theory in physics that provides a description of the physical properties of nature at the scale of atoms and subatomic particles. It is the foundation of all quantum physics including quantum chemistr ...

. Qbox is released under a

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 to run, study, share, and modify the software. The license was the first copyleft for general ...

(GPL) with documentation provided a
http://qboxcode.org
It is available as a FreeBSD port.

Main features

* Born-Oppenheimer molecular dynamics in the microcanonical(NVE) or

canonical ensemble In statistical mechanics, a canonical ensemble is the statistical ensemble that represents the possible states of a mechanical system in thermal equilibrium with a heat bath at a fixed temperature. The system can exchange energy with the heat ...

(NVT) * Car-Parrinello molecular dynamics *Constrained molecular dynamics for thermodynamic integration *Efficient computation of maximally localized

Wannier function The Wannier functions are a complete set of orthogonal functions used in solid-state physics. They were introduced by Gregory Wannier in 1937. Wannier functions are the localized molecular orbitals of crystalline systems. The Wannier functions fo ...

s *GGA and hybrid density functional approximations (LDA, PBE, SCAN, PBE0, B3LYP, HSE06, ...) *Electronic structure in the presence of a constant electric field *Computation of the electronic

polarizability Polarizability usually refers to the tendency of matter, when subjected to an electric field, to acquire an electric dipole moment in proportion to that applied field. It is a property of all matter, considering that matter is made up of elementar ...

*Electronic response to arbitrary external potentials *

Infrared Infrared (IR), sometimes called infrared light, is electromagnetic radiation (EMR) with wavelengths longer than those of visible light. It is therefore invisible to the human eye. IR is generally understood to encompass wavelengths from around ...

and Raman spectroscopy

Methods and approximations

Qbox computes molecular dynamics trajectories of atoms using Newton's equations of motion, with forces derived from

electronic structure In quantum chemistry, electronic structure is the state of motion of electrons in an electrostatic field created by stationary nuclei. The term encompasses both the wave functions of the electrons and the energies associated with them. Electr ...

calculations performed using

Density Functional Theory Density-functional theory (DFT) is a computational quantum mechanical modelling method used in physics, chemistry and materials science to investigate the electronic structure (or nuclear structure) (principally the ground state) of many-body ...

. Simulations can be performed either within the Born-Oppenheimer approximation or using Car-Parrinello molecular dynamics. The electronic ground state is computed at each time step by solving the Kohn-Sham equations. Various levels of

approximations can be used, including the

local-density approximation Local-density approximations (LDA) are a class of approximations to the exchange–correlation (XC) energy functional in density functional theory (DFT) that depend solely upon the value of the electronic density at each point in space (and no ...

(LDA), the

generalized gradient approximation Density-functional theory (DFT) is a computational quantum mechanical modelling method used in physics, chemistry and materials science to investigate the electronic structure (or nuclear structure) (principally the ground state) of many-body ...

(GGA), or hybrid functionals that incorporate a fraction of Hartree-Fock exchange energy. Electronic

wave function A wave function in quantum physics is a mathematical description of the quantum state of an isolated quantum system. The wave function is a complex-valued probability amplitude, and the probabilities for the possible results of measurements ...

s are expanded using the

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, ...

basis set. The electron-ion interaction is represented by

pseudopotential In physics, a pseudopotential or effective potential is used as an approximation for the simplified description of complex systems. Applications include atomic physics and neutron scattering. The pseudopotential approximation was first introduced ...

Examples of use

*Electronic properties of nanoparticles *Electronic properties of aqueous solutions *Free energy landscape of molecules *Infrared and Raman spectra of hydrogen at high pressure *Properties of solid-liquid interfaces

Code architecture and implementation

Qbox is written in

C++ C++ (pronounced "C plus plus") is a high-level general-purpose programming language created by Danish computer scientist Bjarne Stroustrup as an extension of the C programming language, or "C with Classes". The language has expanded significan ...

and implements parallelism using both the message passing interface (MPI) and the

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 syst ...

application programming interface. It makes use of the

BLAS Basic Linear Algebra Subprograms (BLAS) is a specification that prescribes a set of low-level routines for performing common linear algebra operations such as vector addition, scalar multiplication, dot products, linear combinations, and matrix ...

LAPACK LAPACK ("Linear Algebra Package") is a standard software library for numerical linear algebra. It provides routines for solving systems of linear equations and linear least squares, eigenvalue problems, and singular value decomposition. It als ...

ScaLAPACK The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers. It is currently written in a Single-Program-Multiple-Data style using explicit message passing for interproc ...

FFTW The Fastest Fourier Transform in the West (FFTW) is a software library for computing discrete Fourier transforms (DFTs) developed by Matteo Frigo and Steven G. Johnson at the Massachusetts Institute of Technology. FFTW is one of the fastest fre ...

and

Apache Xerces In computing, Xerces is Apache's collection of software libraries for parsing, validating, serializing and manipulating XML. The library implements a number of standard APIs for XML parsing, including DOM, SAX and SAX2. The implementation is av ...

libraries. Qbox was designed for operation on

massively parallel Massively parallel is the term for using a large number of computer processors (or separate computers) to simultaneously perform a set of coordinated computations in parallel. GPUs are massively parallel architecture with tens of thousands of t ...

computers such as the

IBM Blue Gene Blue Gene is an IBM project aimed at designing supercomputers that can reach operating speeds in the petaFLOPS (PFLOPS) range, with low power consumption. The project created three generations of supercomputers, Blue Gene/L, Blue Gene/P, ...

supercomputer, or the Cray XC40 supercomputer. In 2006 it was used to establish a performance record on the BlueGene/L computer installed at the Lawrence Livermore National Laboratory.

Interface with other simulation software

The functionality of Qbox can be enhanced by coupling it with other simulation software using a client-server paradigm. Examples of Qbox coupled operation include: * Free energy computations: Coupled with the Software Suite for Advanced Ensemble Simulations (SSAGES). *

Quasiparticle In physics, quasiparticles and collective excitations are closely related emergent phenomena arising when a microscopically complicated system such as a solid behaves as if it contained different weakly interacting particles in vacuum. For exa ...

energy computations: Coupled with the WEST many-body perturbation software package. * Path integral quantum simulations: Coupled with the i-PI universal force engine.

References

External links

* * Computational chemistry software Physics software Free physics software