| Original author(s) | Francois Gygi |
|---|---|
| Developer(s) | Francois Gygi, Ivan Duchemin, Jun Wu, Quan Wan, William Dawson, Martin Schlipf, He Ma, Michael LaCount |
| Initial release | 2003 |
| Stable release | 1.73.3
/ 20 August 2021 |
| Repository |
github |
| Written in | C++ |
| Operating system | Unix, Unix-like, FreeBSD |
| License | GPL |
| Website |
qboxcode |
Qbox is an open-source software package for atomic-scale simulations of molecules, liquids and solids. It implements first principles (or ab initio) molecular dynamics, a simulation method in which inter-atomic forces are derived from quantum mechanics. Qbox is released under a GNU General Public License (GPL) with documentation provided at http://qboxcode.org. It is available as a FreeBSD port. [1]
Main features
- Born-Oppenheimer molecular dynamics in the microcanonical(NVE) or canonical ensemble (NVT)
- Car-Parrinello molecular dynamics
- Constrained molecular dynamics for thermodynamic integration
- 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 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 calculations performed using Density Functional Theory. 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 Density Functional Theory approximations can be used, including the local-density approximation (LDA), the generalized gradient approximation (GGA), or hybrid functionals that incorporate a fraction of Hartree-Fock exchange energy. Electronic wave functions are expanded using the plane wave basis set. The electron-ion interaction is represented by pseudopotentials.
Examples of use
- Electronic properties of nanoparticles [2]
- Electronic properties of aqueous solutions [3]
- Free energy landscape of molecules [4]
- Infrared and Raman spectra of hydrogen at high pressure [5]
- Properties of solid-liquid interfaces [6]
Code architecture and implementation
Qbox is written in C++ and implements parallelism using both the message passing interface (MPI) and the OpenMP application programming interface. It makes use of the BLAS, LAPACK, ScaLAPACK, FFTW and Apache Xerces libraries. Qbox was designed [7] for operation on massively parallel computers such as the IBM Blue Gene supercomputer, or the Cray XC40 supercomputer. In 2006 it was used to establish a performance record [8] 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 energy computations: Coupled with the WEST many-body perturbation software package.
- Path integral quantum simulations: Coupled with the i-PI universal force engine.
See also
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. S2CID 125608611.
- ^ 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. S2CID 103934369.
- ^ 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".
External links
| Original author(s) | Francois Gygi |
|---|---|
| Developer(s) | Francois Gygi, Ivan Duchemin, Jun Wu, Quan Wan, William Dawson, Martin Schlipf, He Ma, Michael LaCount |
| Initial release | 2003 |
| Stable release | 1.73.3
/ 20 August 2021 |
| Repository |
github |
| Written in | C++ |
| Operating system | Unix, Unix-like, FreeBSD |
| License | GPL |
| Website |
qboxcode |
Qbox is an open-source software package for atomic-scale simulations of molecules, liquids and solids. It implements first principles (or ab initio) molecular dynamics, a simulation method in which inter-atomic forces are derived from quantum mechanics. Qbox is released under a GNU General Public License (GPL) with documentation provided at http://qboxcode.org. It is available as a FreeBSD port. [1]
Main features
- Born-Oppenheimer molecular dynamics in the microcanonical(NVE) or canonical ensemble (NVT)
- Car-Parrinello molecular dynamics
- Constrained molecular dynamics for thermodynamic integration
- 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 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 calculations performed using Density Functional Theory. 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 Density Functional Theory approximations can be used, including the local-density approximation (LDA), the generalized gradient approximation (GGA), or hybrid functionals that incorporate a fraction of Hartree-Fock exchange energy. Electronic wave functions are expanded using the plane wave basis set. The electron-ion interaction is represented by pseudopotentials.
Examples of use
- Electronic properties of nanoparticles [2]
- Electronic properties of aqueous solutions [3]
- Free energy landscape of molecules [4]
- Infrared and Raman spectra of hydrogen at high pressure [5]
- Properties of solid-liquid interfaces [6]
Code architecture and implementation
Qbox is written in C++ and implements parallelism using both the message passing interface (MPI) and the OpenMP application programming interface. It makes use of the BLAS, LAPACK, ScaLAPACK, FFTW and Apache Xerces libraries. Qbox was designed [7] for operation on massively parallel computers such as the IBM Blue Gene supercomputer, or the Cray XC40 supercomputer. In 2006 it was used to establish a performance record [8] 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 energy computations: Coupled with the WEST many-body perturbation software package.
- Path integral quantum simulations: Coupled with the i-PI universal force engine.
See also
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. S2CID 125608611.
- ^ 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. S2CID 103934369.
- ^ 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".