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SIESTA程序简介
Siesta (Spanish Initiative for Electronic Simulations
with Thousands of Atoms)。适用于分子和固体的电子
结构和分子动力学计算。
主要特点:
•DFT+LDA/LSD/GGA；
•模守恒赝势，非局域可分离（Kleinman-Bylander）；
•数值原子轨道基底，准激发态轨道；
•允许valence-bond/Wannier-like functions的线性组合；
•Fortran 90，内存动态分配技术；
•可并行计算。
•量子输运的计算（TranSiesta）
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研发人员及单位
•Emilio Artacho, University of Cambridge
•Julian D. Gale, Curtin University of Technology, Perth
•Alberto Garcia, Universidad del Pais Vasco, Bilbao
•Javier Junquera, Universidad de Cantabria, Santander
•Richard M. Martin, U. of Illinois at Urbana-Champaign
•Pablo Ordejon, Institut de Ciencia de Materials, CSIC,
Barcelona
•Daniel Sanchez-Portal, Unidad de Fisica de Materiales,
Centro Mixto CSIC-UPV/EHU, San Sebastian
•Jose M. Soler, Universidad Autonoma de Madrid
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计算能力:尤其是O(N)算法
• Total and partial energies.
• Atomic forces， Stress tensor.
• Electric dipole moment.
• Atomic, orbital and bond populations (Mulliken).
• Electron density.
• Geometry relaxation, fixed or variable cell.
• Constant-temperature molecular.
• Variable cell dynamics (Parrinello-Rahman).
• Spin polarized calculations (collinear or not).
• k-sampling of the Brillouin zone.
• Local and orbital-projected density of states.
• Band structure.
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The documentation
•赝势的使用文档及例子
•V3.0 的使用所明书，82页
•部分算例和安装测试程序
Opium赝势程序也可生成siesta
格式的赝势.
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related papers worth reading
• P. Ordejón, D. A. Drabold, M. P. Grumbach and R. M.
Martin, Phys. Rev. B 48, 14646 (1993); Phys. Rev. B 51
1456 (1995),
• P. Ordejón, E. Artacho and J. M. Soler, Phys. Rev. B 53,
10441, (1996)
• Sánchez-Portal, P. Ordejón, E. Artacho and J. M. Soler,
Int. J. Quantum Chem., 65, 453 (1997).
• E. Artacho, D. Sánchez-Portal, P. Ordejón, A. García and
J. M. Soler, Phys. Stat. Sol. (b) 215, 809 (1999)
• J. Junquera, O. Paz, D. Sánchez-Portal, and E. Artacho,
Phys. Rev. B 64, 235111, (2001).
• D. Sánchez-Portal, P. Ordejón, and E. Canadell, Structure
and Bonding 113, 103-170 (2004).
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下载地址
• 下载地址：
http://www.uam.es/siesta
• 当前版本：Siesta v3.2
2013-7
• 不需要注册，是免费的软件
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编译程序
• 解压缩：
gunzip siesta3.2.tar.gz,
tar –xvf siesta3.2.tar
• 系统检测：到 Src 目录,
./configure
• 编译：make
• 测试：到 tests 目录,
make
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生成赝势：
(You must realize that this is a tricky
business that you must master before
using Siesta responsibly. Every
pseudopotential must be thoroughly
checked before use.)
$ cd ∼/siesta/Pseudo/atom
$ make
$ cd Tutorial/O
$ sh ../pg.sh O.tm2.inp
$ cp O.tm2.psf ∼/whateveryourworkingdir/h2o/O.psf
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赝势输入文件例
pg Oxygen
tm2 2.0
n=O c=ca
0.0 0.0 0.0 0.0 0.0 0.0
1 4
2 0 2.00 0.00
2 1 4.00 0.00
3 2 0.00 0.00
4 3 0.00 0.00
1.15 1.15 1.15 1.15
由 Jose Luis Martins提供的许多原子赝势的输入文件在:
~/siesta-2.0/Pseudo/atom/Contrib/atom_table.txt
(但需要略做修改, 增加一些空轨道)
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运行主程序
Go to your favorite working directory and:
$ mkdir h2o
$ cd h2o
$ cp ∼/siesta/Examples/H20/h2o.fdf .
$ siesta < h2o.fdf | tee h2o.out
注意：out.fdf 输出文件包含了所有的程序输
入参数也包括省却参数。
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输入文件格式
The Flexible Data Format (FDF)
• FDF 由字符串标记及其值构成,没有说明的取
省缺值
• FDF字符串标记与大小写无关,“_”,“-”被忽略
• # 打头的行为说明
• 逻辑变量为 T, true, .true., yes, F, false, .false.
• 数值要有单位
• 复杂数据结构用blocks括起来:
%block label <index>
%endblock label
• 还有高级用法: 可读入数据等
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SystemName Water molecule
SystemLabel h2o
输 NumberOfAtoms
NumberOfSpecies 2
3
入
MeshCutoff 50 Ry
%block ChemicalSpeciesLabel
1 8 O # Species index, atomic number, species label
文 2 1 H
%endblock ChemicalSpeciesLabel
件 AtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies
例 0.000 0.000 0.000 1
0.757 0.586 0.000 2
-0.757 0.586 0.000 2
%endblock AtomicCoordinatesAndAtomicSpecies
save-rho T
save-delta-rho T
save-total-potential T
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输入信息种类
• General system descriptors (一般描述)
• Basis definition(基底定义)
• Lattice, coordinates, k-sampling(几何相关)
• DFT, Grid, SCF
• Eigenvalue problem: order-N or diagonalization
• Molecular dynamics and relaxations
• Output options
• Efficiency options
• Options for saving/reading information
• Parallel options
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水分子的计算所有输入参数
• #FDF: Opened INPUT_TMP.0 for input. Unit: 12
• fdf-debug 0 # Default value
• SystemName Water molecule
• SystemLabel h2o
• WriteXML T # Default value
• alloc_report_level 0 # Default value
• xc.functional LDA # Default value
• xc.authors PZ # Default value
• user-basis F # Default value
• user-basis-netcdf F # Default value
• PAO.BasisSize standard # Default value
• PAO.BasisType split # Default value
• Number_of_species 2
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•%block ChemicalSpeciesLabel
• 1 8 O # Species index, atomic number, species label
•2 1 H
•%endblock ChemicalSpeciesLabel
•PAO.EnergyShift 0.2000000000E-01 Ry # Default value
•PAO.SplitNorm 0.1500000000 # Default value
•PAO.SplitNorm 0.1500000000 # Default value
•PAO.EnergyShift 0.2000000000E-01 Ry # Default value
•PAO.SplitNorm 0.1500000000 # Default value
•PAO.SplitNorm 0.1500000000 # Default value
•PAO.BasisType split # Default value
•Atom-Setup-Only F # Default value
•MD.UseStructFile F # Default value
•LatticeConstant 0.000000000 Bohr # Default value
•AtomicCoordinatesFormat Ang
•NumberOfAtoms 3
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•ZM.UnitsLength Bohr # Default value
•ZM.UnitsAngle rad # Default value
•ZM.ForceTolLength 0.1555740000E-02 Ry/Bohr # Default value
•ZM.ForceTolAngle 0.3565490000E-02 Ry/rad # Default value
•ZM.MaxDisplLength 0.2000000000 Bohr # Default value
•ZM.MaxDisplAngle 0.3000000000E-02 rad # Default value
•ZM.CalcAllForces F # Default value
•%block AtomicCoordinatesAndAtomicSpecies
• 0.000 0.000 0.000 1
• 0.757 0.586 0.000 2
•-0.757 0.586 0.000 2
•%endblock AtomicCoordinatesAndAtomicSpecies
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•SpinPolarized F # Default value
•NonCollinearSpin F # Default value
•SystemName Water molecule
•LongOutput F # Default value
•NumberOfSpecies 2
•WriteDenchar F # Default value
•WriteMullikenPop 0 # Default value
•MeshCutoff 50.00000000 Ry
•# Above item originally: MeshCutoff 50.00000000 Ry
•NetCharge 0.000000000 # Default value
•MaxSCFIterations 50 # Default value
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•DM.NumberPulay 0 # Default value
•DM.NumberBroyden 0 # Default value
•DM.MixSCF1 F # Default value
•DM.PulayOnFile F # Default value
•DM.MixingWeight 0.2500000000 # Default value
•DM.OccupancyTolerance 0.1000000000E-11 # Default value
•DM.NumberKick 0 # Default value
•DM.KickMixingWeight 0.5000000000 # Default value
•DM.Tolerance 0.1000000000E-03 # Default value
•DM.RequireEnergyConvergence F # Default value
•DM.EnergyTolerance 0.7349806700E-05 Ry # Default value
•UseSaveData F # Default value
•DM.UseSaveDM F # Default value
•NeglNonOverlapInt F # Default value
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•SolutionMethod diagon # Default value
•Diag.DivideAndConquer T # Default value
•Diag.Memory 1.000000000 # Default value
•ElectronicTemperature 0.1900000000E-02 Ry # Default value
•FixSpin F # Default value
•ON.MaxNumIter 1000 # Default value
•ON.etol 0.1000000000E-07 # Default value
•ON.eta 0.000000000 Ry # Default value
•ON.eta_alpha 0.000000000 Ry # Default value
•ON.eta_beta 0.000000000 Ry # Default value
•On.RcLWF 9.500000000 Bohr # Default value
•ON.UseSaveLWF F # Default value
•ON.functional kim # Default value
•ON.ChemicalPotentialUse F # Default value
•ON.ChemicalPotential F # Default value
•ON.ChemicalPotentialRc 9.500000000 Bohr # Default value
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•ON.ChemicalPotentialTemperature 0.5000000000E-01 Ry # default
•ON.ChemicalPotentialOrder 100 # Default value
•MD.VariableCell F # Default value
•MD.TypeOfRun verlet # Default value
•MD.NumCGsteps 0 # Default value
•MD.MaxCGDispl 0.2000000000 Bohr # Default value
•MD.MaxForceTol 0.1555740000E-02 Ry/Bohr # Default
•MD.MaxStressTol 0.6797730000E-04 Ry/Bohr**3 # Default
•MD.InitialTimeStep 1 # Default value
•MD.FinalTimeStep 1 # Default value
•MD.LengthTimeStep 1.000000000 fs # Default value
•MD.Quench F # Default value
•MD.InitialTemperature 0.000000000 K # Default value
•MD.TargetTemperature 0.000000000 K # Default value
•MD.TargetPressure 0.000000000 Ry/Bohr**3 # Default
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•MD.NoseMass 100.0000000 Ry*fs**2 # Default value
•MD.ParrinelloRahmanMass 100.0000000 Ry*fs**2 # Default
•MD.AnnealOption TemperatureAndPressure # Default value
•MD.TauRelax 100.0000000 fs # Default value
•MD.BulkModulus 0.6797730000E-02 Ry/Bohr**3 # Default
•MD.FCDispl 0.4000000000E-01 Bohr # Default value
•MD.FCfirst 1 # Default value
•MD.FClast 3 # Default value
•Harris_functional F # Default value
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•WriteKpoints F # Default value
•WriteForces F # Default value
•WriteDM T # Default value
•WriteBands F # Default value
•WriteKbands F # Default value
•WriteEigenvalues F # Default value
•WriteCoorStep F # Default value
•WriteCoorInitial T # Default value
•WriteMDhistory F # Default value
•WriteMDXmol T # Default value
•UseSaveData F # Default value
•MD.UseSaveXV F # Default value
•MD.UseSaveZM F # Default value
•SaveHS F # Default value
•FixAuxillaryCell F # Default value
•ReInitialiseDM F # Default value
•MullikenInSCF F # Default value
•WarningMinimumAtomicDistance 1.000000000 Bohr # Default value
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•BornCharge F # Default value
•Diag.ParallelOverK F # Default value
•Output-Structure-Only F # Default value
•RcSpatial 0.000000000 Bohr # Default value
•ProcessorGridX 1 # Default value
•ProcessorGridY 1 # Default value
•ProcessorGridZ 1 # Default value
•NumberOfEigenStates 23 # Default value
•kgrid_cutoff 0.000000000 Bohr # Default value
•LongOutput F # Default value
•WriteWaveFunctions F # Default value
•AtomicCoordinatesFormat Ang
•AtomCoorFormatOut Ang # Default value
•LatticeConstant 0.000000000 Bohr # Default value
•Harris_functional F # Default value
•MeshSubDivisions 2 # Default value
•LatticeConstant 0.000000000 Bohr # Default value
•DirectPhi F # Default value
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•LatticeConstant 0.000000000 Bohr # Default value
•Diag.AllInOne F # Default value
•Diag.DivideAndConquer T # Default value
•Diag.NoExpert F # Default value
•Diag.PreRotate F # Default value
•Diag.Use2D T # Default value
•SingleExcitation F # Default value
•OccupationFunction FD # Default value
•OccupationFunction FD # Default value
•DM.FormattedFiles F # Default value
•DM.FormattedInput F # Default value
•DM.FormattedOutput F # Default value
•WriteCoorXmol F # Default value
•WriteCoorCerius F # Default value
•OpticalCalculation F # Default value
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• SaveRho T
• SaveDeltaRho T
• SaveElectrostaticPotential F # Default value
• SaveTotalPotential T
• SaveIonicCharge F # Default value
• SaveTotalCharge F # Default value
众多的参数说明其功能强大！
量子输运的计算和运行需
要其它理论才能理解。
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How to run Siesta?
•How to run Siesta?
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自学软件使用的建议：活学活用
按步学习siesta中的文档
算一个你感兴趣的体系
研究并修改原代码
随时补充和
更新知识
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• end
