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. Ope ...

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 bio ...

liquid A liquid is a nearly incompressible fluid that conforms to the shape of its container but retains a (nearly) constant volume independent of pressure. As such, it is one of the four fundamental states of matter (the others being solid, gas, an ...

s 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 structura ...

s. It implements first principles (or ab initio)

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 th ...

, 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 ...

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 chemistry, q ...

. 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 user In product development, an end user (sometimes end-user) is a person who ultimately uses or is intended to ulti ...

(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 (NVT) * Car-Parrinello molecular dynamics *Constrained molecular dynamics for

thermodynamic integration Thermodynamic integration is a method used to compare the difference in free energy between two given states (e.g., A and B) whose potential energies U_A and U_B have different dependences on the spatial coordinates. Because the free energy of a ...

*Efficient computation of maximally localized Wannier functions *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 *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 aroun ...

and

Raman spectroscopy Raman spectroscopy () (named after Indian physicist C. V. Raman) is a spectroscopic technique typically used to determine vibrational modes of molecules, although rotational and other low-frequency modes of systems may also be observed. Raman s ...

Methods and approximations

Qbox computes molecular dynamics trajectories of atoms using Newton's equations of motion, with forces derived from electronic structure 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-bo ...

. 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 (LDA), the generalized gradient approximation (GGA), or

hybrid functional 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–correl ...

s 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 m ...

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, t ...

basis set. The electron-ion interaction is represented by pseudopotentials.

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++ 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 sy ...

application programming interface. It makes use of the BLAS, LAPACK, ScaLAPACK, FFTW and

Apache Xerces In computing, Xerces is Apache Software Foundation, Apache's collection of software library, software libraries for parsing, validating, serializing and manipulating XML. The library implements a number of standard Application programming interface ...

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 supercomputer, or the

Cray XC40 The Cray XC40 is a massively parallel multiprocessor supercomputer manufactured by Cray. It consists of Intel Haswell Xeon processors, with optional Nvidia Tesla or Intel Xeon Phi accelerators, connected together by Cray's proprietary "A ...

supercomputer. In 2006 it was used to establish a performance record on the BlueGene/L computer installed at the

Lawrence Livermore National Laboratory Lawrence Livermore National Laboratory (LLNL) is a federal research facility in Livermore, California, United States. The lab was originally established as the University of California Radiation Laboratory, Livermore Branch in 1952 in response ...

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 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