材料科学中的高性能计算
|
摘要
高性能计算是研究材料的成分-结构-性质三者之间关系的有力工具。材料科学中的计算模拟主要使用密度泛函理论研究原子到微米尺度的材料,其并行实现方式主要分为并行k点、并行能带和并行平面波,具有较高的并行效率和大量的软件实现。并行k点方式具有较好的扩展性,但不适合于计算大晶胞体系;并行能带方式对于中小晶胞体系效率较高;并行平面波方式适合于大晶胞体系,但对全局通讯的依赖性较高,并行扩展性较差。充分利用最新的硬件技术,如加速卡、众核技术等,改写或重新设计材料科学计算软件已成为最近的发展趋势。
High performance computing is a powerful tool to understand composition- structure- property relationships in materials. Density functional theory is mainly used to study the materials from atomistic scale to micrometer scale in the computational simulation of materials science,and is parallelized over k-points,bands and plane wave in many computing softwares of materials science with high parallel efficiency. Paralleling over k- points can be scaled well but has poor performance for big unit cell. Paralleling over bands has better efficiency for small or middle size of unit cell. Paralleling over plane wave has better performance but poor scalability for big size of unit cell,and relies on global communication over whole CPU. Rewriting or redesigning computing softwares of materials science to take full advantage of the latest hardware technology such as accelerator or many-core technology has become a recent trend.
High performance computing is a powerful tool to understand composition- structure- property relationships in materials. Density functional theory is mainly used to study the materials from atomistic scale to micrometer scale in the computational simulation of materials science,and is parallelized over k-points,bands and plane wave in many computing softwares of materials science with high parallel efficiency. Paralleling over k- points can be scaled well but has poor performance for big unit cell. Paralleling over bands has better efficiency for small or middle size of unit cell. Paralleling over plane wave has better performance but poor scalability for big size of unit cell,and relies on global communication over whole CPU. Rewriting or redesigning computing softwares of materials science to take full advantage of the latest hardware technology such as accelerator or many-core technology has become a recent trend.
引文
[1]Jensen F.Introduction to computational chemistry[M].Chichester:John Wiley&Sons Ltd,1999.
[2]Dreizler R,Gross E.Density functional theory[M].New York:Plenum Press,1995.
[3]Parr R G,Yang W T.Density-functional theory of atoms and molecules[M].New York:Oxford University Press,1989.
[4]Larsson P,Hess B,Lindahl E.Algorithm improvements for molecular dynamics simulations[J].Wiley Interdisciplinary Reviews:Computational Molecular Science,2011,1(1):93-108.
[5]Friesner1 R A,Guallar V.Ab initio quantum chemical and mixed quantum mechanics/molecular mechanics(QM/MM)methods for studying enzymatic catalysis[J].Annual Review of Physical Chemistry,2005,56:389-427.
[6]Gao J,Truhlar D G.Quantum mechanical methods for enzyme kinetics[J].Annual Review of Physical Chemistry,2002,53:467-505.
[7]van de Walle A.Multicomponent multisublattice alloys,nonconfigurational entropy and other additions to the alloy theoretic automated toolkit[J].Calphad,2009,33(2):266-278.
[8]Kresse G,Furthüller J.Efficiency of ab-initio total energy calculations for metals and semiconductors using a planewave basis set[J].Computational Materials Science,1996,6(1):15-50.
[9]Blaha P,Schwarz K,Sorantin P,et al.Full-potential,linearized augmented plane-wave programs for crystalline systems[J].Computer Physics Communications,1990,59(2):399-415.
[10]Bowler D R,Fattebert J L,Gillan M J,et al.Introductory remarks:linear scaling methods—preface[J].Journal of Physics:Condensed Matter,2008,20(29):290301.
[11]Bowler D R,Miyazaki T.O(N)methods in electronic structure calculations[J].Reports on Progress in Physics,2012,75(3):036503.
[12]Cheng H P.The motion of protons in water-ammonia clusters[J].The Journal of Chemical Physics,1996,105(16):6844-6855.
[13]Mao Keke,Li Lei,Zhang Wenhua,et al.A theoretical study of single-atom catalysis of CO oxidation using Au embedded2D h-BN monolayer:a co-promoted O2activation[J].Scientific Reports,2014,4:5441.
[14]Car R,Parrinello M.Unified approach for molecular dynamics and density-functional theory[J].Physical Review Letters,1985,55(22):2471-2474.
[15]Kühne T,Krack M,Mohamed F,et al.Efficient and accurate Car-Parrinello-like approach to Born-Oppenheimer molecular dynamics[J].Physical Review Letters,2007,98(6):066401.
[16]Ceperley D M,Alder B J.Ground-state of the electron gas by a stochastic method[J].Physical Review Letters,1980,45(7):566-569.
[17]Perdew J P,Zunger A.Self-interaction correction to densityfunctional approximations for many-electron systems[J].Physical Review B,1981,23(10):5048-5079.
[18]Perdew J P,Chevary J A,Vosko S H,et al.Atoms,molecules,solids,and surfaces-applications of the generalized gradient approximation for exchange and correlation[J].Physical Review B,1992,46(11):6671-6687.
[19]Perdew J P,Burke K,Ernzerhof M.Generalized gradient approximation made simple[J].Physical Review Letters,1996,77(18):3865-3868.
[20]Gorling A,Levy M.Exact Kohn-Sham scheme based on perturbation theory[J].Physical Review A,1994,50(1):196-204.
[21]Austin B J,Sham L J,Heine V.General theory of pseudopotentials[J].Physical Review,1962,127(1):276-276.
[22]Yin M T,Cohen M L.Theory of ab initio pseudopotential calculations[J].Physical Review B,1982,25(12):7403-7412.
[23]Bachelet G B,Hamann D R,Schluter M.Pseudopotentials that work:from H to Pu[J].Physical Review B,1982,26(8):4199-4228.
[24]Hamann D R.Generalized norm-conserving pseudopotentials[J].Physical Review B,1989,40(5):2980-2987.
[25]Bl?chl P E.Projector augmented-wave method[J].Physical Review B,1994,50(24):17953-17979.
[26]Bylaska E J,Valiev M,Kawai R,et al.Parallel implementation of the projector augmented plane wave method for charged systems[J].Computer Physics Communications,2002,143(1):11-28.
[27]Clarke L J,Stich I,Payne M C.Large-scale ab initio total energy calculations on parallel computers[J].Computer Physics Communications,1992,72(1):14-28.
[28]Nelson J S,Plimpton S J,Sears M P.Plane-wave electronicstructure calculations on a parallel supercomputer[J].Physical Review B,1993,47(4):1765-1774.
[29]Wiggs J,Jonsson H.A parallel implementation of the CarParrinello method by orbital decomposition[J].Computer Physics Communications,1994,81(1/2):1-18.
[30]Ashcroft N W,Mermin N D.Solid state physics[M].Philadelphia:Holt Saunders,1976.
[31]Bush I J,Tomi?S,Searle B G,et al.Parallel implementation of the ab initio CRYSTAL program:electronic structure calculations for periodic systems[J].Proceedings of the Royal Society A,2011,467(2131):2112-2126.
[32]Hamilton T P,Pulay P.Direct inversion in the iterative subspace(DIIS)optimization of open-shell,excited-state,and small multiconfiguration SCF wave functions[J].The Journal of Chemical Physics,1986,84(10):5728-5734.
[33]Gygi F.Architecture of Qbox:a scalable first-principles molecular dynamics code[J].IBM Journal of Research and Development,2008,52(1/2):137-144.
[34]Canning A,Raczkowski D.Scaling first-principles planewave codes to thousands of processors[J].Computer Physics Communications,2005,169(1/3):449-453.
[35]Delley B.From molecules to solids with the DMol3approach[J].The Journal of Chemical Physics,2000,113(18):7756-7764.
[36]Clark S J,Segall M D,Pickard C J,et al.First principles methods using CASTEP[J].Zeitschrift für KristallographieCrystalline Materials,2005,220(5/6):567-570.
[37]Artacho E,Anglada E,Diéguez O,et al.The SIESTA method:developments and applicability[J].Journal of Physics:Condensed Matter,2008,20(6):064208.
[38]Giannozzi P,Baroni S,Bonini N,et al.QUANTUM ESPRESSO:a modular and open-source software project for quantum simulations of materials[J].Journal of Physics:Condensed Matter,2009,21(39):395502.
[39]Gonze X,Amadon B,Anglade P-M,et al.ABINIT:firstprinciples approach to material and nanosystem properties[J].Computer Physics Communications,2009,180(12):2582-2615.
[40]Andreoni W,Curioni A.New advances in chemistry and materials science with CPMD and parallel computing[J].Parallel Computing,2000,26(7/8):819-842.
[41]Hutter J,Iannuzzi M,Schiffmann F,et al.CP2K:atomistic simulations of condensed matter systems[J].Wiley Interdisciplinary Reviews:Computational Molecular Science,2014,4(1):15-25.
[42]Plimpton S.Fast parallel algorithms for short-range molecular dynamics[J].Journal of Computational Physics,1995,117(1):1-19.
[43]Metz S,K?estner J,Sokol A A,et al.Chem Shell—a modular software package for QM/MM simulations[J].Wiley Interdisciplinary Reviews:Computational Molecular Science,2014,4(2):101-110.
[44]Barbatti M,Ruckenbauer M,Plasser F,et al.Newton-X:a surface-hopping program for nonadiabatic molecular dynamics[J].Wiley Interdisciplinary Reviews:Computational Molecular Science,2014,4(1):26-33.
[45]Geudtner G,Calaminici P,Carmona-Espíndola J,et al.deMon2k[J].Wiley Interdisciplinary Reviews:Computational Molecular Science,2012,2(4):548-555.
[46]Bochevarov A D,Harder E,Hughes T F,et al.Jaguar:a high-performance quantum chemistry software program with strengths in life and materials sciences[J].International Journal of Quantum Chemistry,2013,113(18):2110-2142.
[47]ApràE,Bylaska E J,Dean D J,et al.NWChem for materials science[J].Computational Materials Science,2003,28(2):209-221.
[48]Skylaris C K,Haynes P D,Mostofi M C,et al.Introducing ONETEP:linear-scaling density functional simulations on parallel computers[J].The Journal of Chemical Physics,2005,122(8):084119.
[49]Vande Vondele J,Krack M,Mohamed F,et al.Quickstep:fast and accurate density functional calculations using a mixed Gaussian and plane waves approach[J].Computer Physics Communications,2005,167(2):103-128.
[50]Brown P,Woods C,Mc Intosh-Smith S,et al.Massively multicore parallelization of Kohn-Sham theory[J].Journal of Chemical Theory and Computation,2008,4(10):1620-1626.
[51]Brown P,Woods C J,Mc Intosh-Smith S,et al.A massively multicore parallelization of the Kohn-Sham energy gradients[J].Journal of Computational Chemistry,2010,31(10):2008-2013.
[52]Yasuda K.Two-electron integral evaluation on the graphics processor unit[J].Journal of Computational Chemistry,2008,29(3):334-342.
[53]Yasuda K.Accelerating density functional calculations with graphics processing unit[J].Journal of Chemical Theory and Computation,2008,4(8):1230-1236.
[54]Vogt L,Olivares-Amaya R,Kermes S,et al.Accelerating resolution-of-the-identity second-order Moller-Plesset quantum chemistry calculations with graphical processing units[J].The Journal of Physical Chemistry A,2008,112(10):2049-2057.
[55]Ufimtsev I S,Martinez T J.Graphical processing units for quantum chemistry[J].Computing in Science and Engineering,2008,10(6):26-34.
[56]Ufimtsev I S,Martinez T J.Quantum chemistry on graphical processing units 1.Strategies for two-electron integral evaluation[J].Journal of Chemical Theory and Computation,2008,4(2):222-231.
[57]Ufimtsev I S,Martinez T J.Quantum chemistry on graphical processing units 2.Direct self-consistent field implementation[J].Journal of Chemical Theory and Computation,2009,5(4):1004-1015.
[58]Ufimtsev I S,Martinez T J.Quantum chemistry on graphical processing units 3.Analytical energy gradients and first principles molecular dynamics[J].Journal of Chemical Theory and Computation,2009,5(10):2619-2628.
[59]Hacene M,Anciaux-Sedrakian A,Rozanska X,et al.Accelerating VASP electronic structure calculations using graphic processing units[J].Journal of Computational Chemistry,2012,33(32):2581-2589.
[60]Woods C J,Brown P S,Manby F R.Multicore parallelization of Kohn-Sham theory[J].Journal of Chemical Theory and Computation,2009,5(7):1776-1784.
[61]Leang S S,Rendell A P,Gordon M S.Quantum chemical calculations using accelerators:migrating matrix operations to the NVIDIA Kepler GPU and the Intel Xeon Phi[J].Journal of Chemical Theory and Computation,2014,10(3):908-912.
[2]Dreizler R,Gross E.Density functional theory[M].New York:Plenum Press,1995.
[3]Parr R G,Yang W T.Density-functional theory of atoms and molecules[M].New York:Oxford University Press,1989.
[4]Larsson P,Hess B,Lindahl E.Algorithm improvements for molecular dynamics simulations[J].Wiley Interdisciplinary Reviews:Computational Molecular Science,2011,1(1):93-108.
[5]Friesner1 R A,Guallar V.Ab initio quantum chemical and mixed quantum mechanics/molecular mechanics(QM/MM)methods for studying enzymatic catalysis[J].Annual Review of Physical Chemistry,2005,56:389-427.
[6]Gao J,Truhlar D G.Quantum mechanical methods for enzyme kinetics[J].Annual Review of Physical Chemistry,2002,53:467-505.
[7]van de Walle A.Multicomponent multisublattice alloys,nonconfigurational entropy and other additions to the alloy theoretic automated toolkit[J].Calphad,2009,33(2):266-278.
[8]Kresse G,Furthüller J.Efficiency of ab-initio total energy calculations for metals and semiconductors using a planewave basis set[J].Computational Materials Science,1996,6(1):15-50.
[9]Blaha P,Schwarz K,Sorantin P,et al.Full-potential,linearized augmented plane-wave programs for crystalline systems[J].Computer Physics Communications,1990,59(2):399-415.
[10]Bowler D R,Fattebert J L,Gillan M J,et al.Introductory remarks:linear scaling methods—preface[J].Journal of Physics:Condensed Matter,2008,20(29):290301.
[11]Bowler D R,Miyazaki T.O(N)methods in electronic structure calculations[J].Reports on Progress in Physics,2012,75(3):036503.
[12]Cheng H P.The motion of protons in water-ammonia clusters[J].The Journal of Chemical Physics,1996,105(16):6844-6855.
[13]Mao Keke,Li Lei,Zhang Wenhua,et al.A theoretical study of single-atom catalysis of CO oxidation using Au embedded2D h-BN monolayer:a co-promoted O2activation[J].Scientific Reports,2014,4:5441.
[14]Car R,Parrinello M.Unified approach for molecular dynamics and density-functional theory[J].Physical Review Letters,1985,55(22):2471-2474.
[15]Kühne T,Krack M,Mohamed F,et al.Efficient and accurate Car-Parrinello-like approach to Born-Oppenheimer molecular dynamics[J].Physical Review Letters,2007,98(6):066401.
[16]Ceperley D M,Alder B J.Ground-state of the electron gas by a stochastic method[J].Physical Review Letters,1980,45(7):566-569.
[17]Perdew J P,Zunger A.Self-interaction correction to densityfunctional approximations for many-electron systems[J].Physical Review B,1981,23(10):5048-5079.
[18]Perdew J P,Chevary J A,Vosko S H,et al.Atoms,molecules,solids,and surfaces-applications of the generalized gradient approximation for exchange and correlation[J].Physical Review B,1992,46(11):6671-6687.
[19]Perdew J P,Burke K,Ernzerhof M.Generalized gradient approximation made simple[J].Physical Review Letters,1996,77(18):3865-3868.
[20]Gorling A,Levy M.Exact Kohn-Sham scheme based on perturbation theory[J].Physical Review A,1994,50(1):196-204.
[21]Austin B J,Sham L J,Heine V.General theory of pseudopotentials[J].Physical Review,1962,127(1):276-276.
[22]Yin M T,Cohen M L.Theory of ab initio pseudopotential calculations[J].Physical Review B,1982,25(12):7403-7412.
[23]Bachelet G B,Hamann D R,Schluter M.Pseudopotentials that work:from H to Pu[J].Physical Review B,1982,26(8):4199-4228.
[24]Hamann D R.Generalized norm-conserving pseudopotentials[J].Physical Review B,1989,40(5):2980-2987.
[25]Bl?chl P E.Projector augmented-wave method[J].Physical Review B,1994,50(24):17953-17979.
[26]Bylaska E J,Valiev M,Kawai R,et al.Parallel implementation of the projector augmented plane wave method for charged systems[J].Computer Physics Communications,2002,143(1):11-28.
[27]Clarke L J,Stich I,Payne M C.Large-scale ab initio total energy calculations on parallel computers[J].Computer Physics Communications,1992,72(1):14-28.
[28]Nelson J S,Plimpton S J,Sears M P.Plane-wave electronicstructure calculations on a parallel supercomputer[J].Physical Review B,1993,47(4):1765-1774.
[29]Wiggs J,Jonsson H.A parallel implementation of the CarParrinello method by orbital decomposition[J].Computer Physics Communications,1994,81(1/2):1-18.
[30]Ashcroft N W,Mermin N D.Solid state physics[M].Philadelphia:Holt Saunders,1976.
[31]Bush I J,Tomi?S,Searle B G,et al.Parallel implementation of the ab initio CRYSTAL program:electronic structure calculations for periodic systems[J].Proceedings of the Royal Society A,2011,467(2131):2112-2126.
[32]Hamilton T P,Pulay P.Direct inversion in the iterative subspace(DIIS)optimization of open-shell,excited-state,and small multiconfiguration SCF wave functions[J].The Journal of Chemical Physics,1986,84(10):5728-5734.
[33]Gygi F.Architecture of Qbox:a scalable first-principles molecular dynamics code[J].IBM Journal of Research and Development,2008,52(1/2):137-144.
[34]Canning A,Raczkowski D.Scaling first-principles planewave codes to thousands of processors[J].Computer Physics Communications,2005,169(1/3):449-453.
[35]Delley B.From molecules to solids with the DMol3approach[J].The Journal of Chemical Physics,2000,113(18):7756-7764.
[36]Clark S J,Segall M D,Pickard C J,et al.First principles methods using CASTEP[J].Zeitschrift für KristallographieCrystalline Materials,2005,220(5/6):567-570.
[37]Artacho E,Anglada E,Diéguez O,et al.The SIESTA method:developments and applicability[J].Journal of Physics:Condensed Matter,2008,20(6):064208.
[38]Giannozzi P,Baroni S,Bonini N,et al.QUANTUM ESPRESSO:a modular and open-source software project for quantum simulations of materials[J].Journal of Physics:Condensed Matter,2009,21(39):395502.
[39]Gonze X,Amadon B,Anglade P-M,et al.ABINIT:firstprinciples approach to material and nanosystem properties[J].Computer Physics Communications,2009,180(12):2582-2615.
[40]Andreoni W,Curioni A.New advances in chemistry and materials science with CPMD and parallel computing[J].Parallel Computing,2000,26(7/8):819-842.
[41]Hutter J,Iannuzzi M,Schiffmann F,et al.CP2K:atomistic simulations of condensed matter systems[J].Wiley Interdisciplinary Reviews:Computational Molecular Science,2014,4(1):15-25.
[42]Plimpton S.Fast parallel algorithms for short-range molecular dynamics[J].Journal of Computational Physics,1995,117(1):1-19.
[43]Metz S,K?estner J,Sokol A A,et al.Chem Shell—a modular software package for QM/MM simulations[J].Wiley Interdisciplinary Reviews:Computational Molecular Science,2014,4(2):101-110.
[44]Barbatti M,Ruckenbauer M,Plasser F,et al.Newton-X:a surface-hopping program for nonadiabatic molecular dynamics[J].Wiley Interdisciplinary Reviews:Computational Molecular Science,2014,4(1):26-33.
[45]Geudtner G,Calaminici P,Carmona-Espíndola J,et al.deMon2k[J].Wiley Interdisciplinary Reviews:Computational Molecular Science,2012,2(4):548-555.
[46]Bochevarov A D,Harder E,Hughes T F,et al.Jaguar:a high-performance quantum chemistry software program with strengths in life and materials sciences[J].International Journal of Quantum Chemistry,2013,113(18):2110-2142.
[47]ApràE,Bylaska E J,Dean D J,et al.NWChem for materials science[J].Computational Materials Science,2003,28(2):209-221.
[48]Skylaris C K,Haynes P D,Mostofi M C,et al.Introducing ONETEP:linear-scaling density functional simulations on parallel computers[J].The Journal of Chemical Physics,2005,122(8):084119.
[49]Vande Vondele J,Krack M,Mohamed F,et al.Quickstep:fast and accurate density functional calculations using a mixed Gaussian and plane waves approach[J].Computer Physics Communications,2005,167(2):103-128.
[50]Brown P,Woods C,Mc Intosh-Smith S,et al.Massively multicore parallelization of Kohn-Sham theory[J].Journal of Chemical Theory and Computation,2008,4(10):1620-1626.
[51]Brown P,Woods C J,Mc Intosh-Smith S,et al.A massively multicore parallelization of the Kohn-Sham energy gradients[J].Journal of Computational Chemistry,2010,31(10):2008-2013.
[52]Yasuda K.Two-electron integral evaluation on the graphics processor unit[J].Journal of Computational Chemistry,2008,29(3):334-342.
[53]Yasuda K.Accelerating density functional calculations with graphics processing unit[J].Journal of Chemical Theory and Computation,2008,4(8):1230-1236.
[54]Vogt L,Olivares-Amaya R,Kermes S,et al.Accelerating resolution-of-the-identity second-order Moller-Plesset quantum chemistry calculations with graphical processing units[J].The Journal of Physical Chemistry A,2008,112(10):2049-2057.
[55]Ufimtsev I S,Martinez T J.Graphical processing units for quantum chemistry[J].Computing in Science and Engineering,2008,10(6):26-34.
[56]Ufimtsev I S,Martinez T J.Quantum chemistry on graphical processing units 1.Strategies for two-electron integral evaluation[J].Journal of Chemical Theory and Computation,2008,4(2):222-231.
[57]Ufimtsev I S,Martinez T J.Quantum chemistry on graphical processing units 2.Direct self-consistent field implementation[J].Journal of Chemical Theory and Computation,2009,5(4):1004-1015.
[58]Ufimtsev I S,Martinez T J.Quantum chemistry on graphical processing units 3.Analytical energy gradients and first principles molecular dynamics[J].Journal of Chemical Theory and Computation,2009,5(10):2619-2628.
[59]Hacene M,Anciaux-Sedrakian A,Rozanska X,et al.Accelerating VASP electronic structure calculations using graphic processing units[J].Journal of Computational Chemistry,2012,33(32):2581-2589.
[60]Woods C J,Brown P S,Manby F R.Multicore parallelization of Kohn-Sham theory[J].Journal of Chemical Theory and Computation,2009,5(7):1776-1784.
[61]Leang S S,Rendell A P,Gordon M S.Quantum chemical calculations using accelerators:migrating matrix operations to the NVIDIA Kepler GPU and the Intel Xeon Phi[J].Journal of Chemical Theory and Computation,2014,10(3):908-912.