Eigenvalues Driven Gaussian Selection in continuous speech recognition
分子轨道
普通化学 I 实验
一、实验目的
1. 了解原子轨道线性组合成分子轨道的原理,以及原子轨道之间相位的含义。
2. 掌握电子按照构造原理依次填充分子轨道的过程。
3. 了解分子轨道的能量和分子的键能。
4. 了解分子轨道的节面和对称性符号。
5. 掌握成键轨道和反键轨道的概念和判别方法。
6. 掌握键级的定义和计算方法。
Molecular orbitals
注意两个原子轨道 2 pyA 和 2 pyB 的正负符号与线性组合方程式中的系数符号、以及与图中
原子轨道波函数的相位(红色为正,蓝色为负)是一致的。以此类推,分别画出序号为 3、 5、7 的三个分子轨道是怎样由不同的原子轨道、按照不同的波函数相位组合而成的(组合 系数之间的相对大小可以不必表示出来)。
1 1 H 1S
0.58489 0.96364
2 2 H 1S
0.58489 -0.96364
这一段记录了每个分子轨道的具体信息。第二行横向排列的数字 1 和 2 是分子轨道按能量
5
普通化学 I 实验 由低往高的编号,第三行的对称性符号 SGG、SGU 以及表示占有和空轨道的符号 O、V 与
分子轨道的编号相对应。第四行的 eigenvalues 就是各个分子轨道的能量计算值,单位是
9
普通化学 I 实验 4. 在 O2 的分子轨道中,有几对是能量简并的(能量相差万分之一以内可认为是简并的)? 直观地解释为什么会出现能量简并的分子轨道。 (4)N2 与 O2 的比较 1. 根据分子轨道中电子的排布方式,解释为什么 O2 是顺磁性的,而 N2 是反磁性的。 2. 在 N2 与 O2 中,各有几个电子占据了成键轨道和反键轨道?按照以下定义公式计算 N2 和 O2 的键级:
Mathematica 函数集
最接近的整数 不大于 x 的最大整数 不小于 x 的最小 绝对值 取符号函数 取整数部分 小数 多个数或数组的最大值 最小值
复变量 Re[z] Im[z] Comjugate[z] Abs[z] Arg[z]
z=x+I y 取实部 虚部 共轭 模 幅角
实数或虚数 Exp[z] Log[z] Log[b,z] Sin[z],Cos[z],Tan[z],Cot[z], Csc[z],Sec[z] ArcSin[z],ArcCos[z],Arctan[z],Arccot[z], ArcCsc[z],ArcSec[z] Sinh[z],Cosh[z],Tanh[z],Coth[z], Csch[z],Sech[z] ArcSinh[z],ArcCosh[z],……
Reduce[方程, 变量]:什么情况下方城有解,尽量化简方程并保留方程所有解
Eliminate[方程 s, 变量 s]:消去变量并重组方程组 如:eqns = {x= =1+a/2,y= =1+2 x};
Eliminate[eqns,x]
2.2.4 不等式方程和递归方程
InequalitySolve[ineq,x] InequalitySolve[{ineq1,ineq2},{x,y}
抽象函数的导数表示 f[x_]:=Sin[x^2] 定义函数 f[x] f[x]+f’[x]+f’’[x] 一阶导,二阶导
D[x g[2x],x]
全微分 df
全导数 df dx
多重全导数 全导数,说明 c1,c2, ……为常数
置 dy =0 dx
D[h[x,y],x,x,y]
计算
∂ ∂x2
∂ ∂y
h(3) (x,
臭氧物理计算
输入文件:#T RHF/6-31+G(D) Stable=Opt TestOzone Stability0,1OO,1,1.272O,2,1.272,1,116.8输出文件:#T RHF/6-31+G(D) Stable=Opt Test-----------------------------------------------Ozone Stability---------------Symbolic Z-matrix:Charge = 0 Multiplicity = 1OO 1 1.272O 2 1.272 1 116.8Distance matrix (angstroms):1 2 31 O 0.0000002 O 1.272000 0.0000003 O 2.166793 1.272000 0.000000Framework group C2V[C2(O),SGV(O2)]Deg. of freedom 2Standard orientation:---------------------------------------------------------------------Center Atomic Atomic Coordinates (Angstroms)Number Number Type X Y Z---------------------------------------------------------------------1 8 0 0.000000 1.083397 -0.2221702 8 0 0.000000 0.000000 0.4443403 8 0 0.000000 -1.083397 -0.222170---------------------------------------------------------------------Rotational constants (GHZ): 106.6873911 13.4595422 11.951727857 basis functions, 96 primitive gaussians, 57 cartesian basis functions12 alpha electrons 12 beta electronsnuclear repulsion energy 68.8807036279 Hartrees.NAtoms= 3 NActive= 3 NUniq= 2 SFac= 2.76D+00 NAtFMM= 60 Big=FHarris functional with IExCor= 205 diagonalized for initial guess.ExpMin= 8.45D-02 ExpMax= 5.48D+03 ExpMxC= 8.25D+02 IAcc=2 IRadAn= 4 AccDes= 0.00D+00HarFok: IExCor= 205 AccDes= 0.00D+00 IRadAn= 4 IDoV=1ScaDFX= 1.000000 1.000000 1.000000 1.000000Initial guess orbital symmetries:Occupied (A1) (B2) (A1) (A1) (B2) (A1) (B2) (A1) (B1) (A2)(B2) (A1)Virtual (B1) (A1) (A1) (B2) (B1) (A1) (B2) (B2) (A2) (A1)(A1) (B1) (B2) (A1) (B2) (A1) (A1) (B2) (B1) (B2)(A1) (A2) (B1) (B2) (A1) (A2) (B1) (A1) (B2) (A1)(B2) (A2) (B1) (A1) (B2) (A1) (B2) (B1) (A2) (A1)(B2) (A1) (A1) (B2) (A1)The electronic state of the initial guess is 1-A1.SCF Done: E(RHF) = -224.255923694 A.U. after 12 cyclesConvg = 0.4407D-08 -V/T = 2.0050S**2 = 0.0000**********************************************************************Population analysis using the SCF density.**********************************************************************Orbital symmetries:Occupied (A1) (B2) (A1) (A1) (B2) (A1) (A1) (B2) (B1) (B2)(A1) (A2)Virtual (B1) (A1) (A1) (B2) (B1) (A1) (B2) (A2) (B1) (A1)(B2) (A1) (A1) (B2) (B2) (A1) (B2) (A1) (B1) (A1)(B2) (A2) (B1) (A1) (B2) (A2) (B1) (A1) (A1) (B2)(B2) (A2) (B1) (A1) (B2) (A1) (B1) (B2) (A2) (A1)(B2) (A1) (A1) (B2) (A1)The electronic state is 1-A1.Alpha occ. eigenvalues -- -20.93754 -20.72957 -20.72951 -1.76350 -1.44168Alpha occ. eigenvalues -- -1.09742 -0.83811 -0.80473 -0.78850 -0.56768Alpha occ. eigenvalues -- -0.55671 -0.49227Alpha virt. eigenvalues -- -0.05246 0.16571 0.17766 0.17978 0.21738Alpha virt. eigenvalues -- 0.25108 0.27001 0.28193 0.29916 0.30777Alpha virt. eigenvalues -- 0.34719 0.36552 0.39788 0.43546 0.44115Alpha virt. eigenvalues -- 1.18604 1.25074 1.27328 1.29296 1.32645Alpha virt. eigenvalues -- 1.34353 1.39828 1.40179 1.41297 1.44924Alpha virt. eigenvalues -- 1.62681 1.68627 1.69884 1.76486 1.76964Alpha virt. eigenvalues -- 2.04381 2.04459 2.07563 2.10705 2.35764Alpha virt. eigenvalues -- 2.58498 2.73854 2.77367 2.86928 3.04472Alpha virt. eigenvalues -- 3.28070 3.31532 4.07728 4.38728 4.54391 Condensed to atoms (all electrons):Mulliken atomic charges:11 O -0.1624432 O 0.3248853 O -0.162443Sum of Mulliken charges= 0.00000Atomic charges with hydrogens summed into heavy atoms:11 O -0.1624432 O 0.3248853 O -0.162443Sum of Mulliken charges= 0.00000Electronic spatial extent (au): <R**2>= 111.5045Charge= 0.0000 electronsDipole moment (field-independent basis, Debye):X= 0.0000 Y= 0.0000 Z= 0.8429 Tot= 0.8429 NROrb= 57 NOA= 12 NOB= 12 NV A= 45 NVB= 45**** Warning!!: The largest alpha MO coefficient is 0.24136347D+02Orbital symmetries:Occupied (A1) (B2) (A1) (A1) (B2) (A1) (A1) (B2) (B1) (B2)(A1) (A2)Virtual (B1) (A1) (A1) (B2) (B1) (A1) (B2) (A2) (B1) (A1)(B2) (A1) (A1) (B2) (B2) (A1) (B2) (A1) (B1) (A1)(B2) (A2) (B1) (A1) (B2) (A2) (B1) (A1) (A1) (B2)(B2) (A2) (B1) (A1) (B2) (A1) (B1) (B2) (A2) (A1)(B2) (A1) (A1) (B2) (A1)24 initial guesses have been made.Iteration 1 Dimension 24 NMult 24New state 1 was old state 2Iteration 2 Dimension 48 NMult 48Iteration 3 Dimension 54 NMult 54Cease iterating as an instability has been found.*********************************************************************** Stability analysis using <AA,BB:AA,BB> singles matrix:***********************************************************************Eigenvectors of the stability matrix:Eigenvector 1: Triplet-B2 Eigenvalue=-0.211647112 -> 13 0.6830612 -> 17 0.11302Eigenvector 2: Triplet-B1 Eigenvalue=-0.01388317 -> 13 -0.1185511 -> 13 0.65960Eigenvector 3: Triplet-A2 Eigenvalue= 0.01141148 -> 13 -0.1298810 -> 13 0.6328212 -> 15 -0.1118612 -> 24 0.18654Eigenvector 4: Triplet-A1 Eigenvalue= 0.04021569 -> 13 0.683619 -> 21 -0.10643Eigenvector 5: Singlet-B1 Eigenvalue= 0.079062011 -> 13 0.68240Eigenvector 6: Singlet-A2 Eigenvalue= 0.096341510 -> 13 0.6794512 -> 24 0.11407The wavefunction has an RHF -> UHF instability.Rare condition: small coef for last iteration: 0.000D+00SCF Done: E(UHF) = -224.341434740 A.U. after 17 cyclesConvg = 0.6525D-08 -V/T = 2.0026S**2 = 0.9324Annihilation of the first spin contaminant:S**2 before annihilation 0.9324, after 0.1225QCSCF skips out because SCF is already converged.NROrb= 57 NOA= 12 NOB= 12 NV A= 45 NVB= 45 **** Warning!!: The largest alpha MO coefficient is 0.23411970D+02**** Warning!!: The largest beta MO coefficient is 0.23411970D+02Orbital symmetries:Alpha Orbitals:Occupied (A1) (?A) (?A) (B2) (B2) (B2) (?B) (B2) (B2) (?B)(B2) (B2)Virtual (?B) (B2) (B2) (B2) (?B) (B2) (B2) (?B) (B2) (?B)(B2) (B2) (B2) (B2) (B2) (B2) (B2) (?B) (B2) (B2)(B2) (?B) (B2) (B2) (?B) (?B) (?B) (B2) (B2) (B2)(?B) (B2) (?B) (B2) (B2) (B2) (?B) (B2) (?B) (B2)(B2) (B2) (?C) (?C) (?C)Beta Orbitals:Occupied (A1) (?A) (?A) (B2) (B2) (B2) (?B) (B2) (B2) (?B)(B2) (B2)Virtual (?B) (B2) (B2) (B2) (?B) (B2) (B2) (?B) (B2) (?B)(B2) (B2) (B2) (B2) (B2) (B2) (B2) (?B) (B2) (B2)(B2) (?B) (B2) (B2) (?B) (?B) (?B) (B2) (B2) (B2)(?B) (B2) (?B) (B2) (B2) (B2) (?B) (B2) (?B) (B2)(B2) (B2) (?C) (?C) (?C)12 initial guesses have been made.Iteration 1 Dimension 12 NMult 12Iteration 2 Dimension 24 NMult 24Iteration 3 Dimension 27 NMult 27Iteration 4 Dimension 30 NMult 30Iteration 5 Dimension 33 NMult 33*********************************************************************** Stability analysis using <AA,BB:AA,BB> singles matrix:*********************************************************************** Eigenvectors of the stability matrix:Excited state symmetry could not be determined.Eigenvector 1: ?Spin -?Sym Eigenvalue= 0.03620078A -> 13A -0.1347811A -> 13A 0.2109212A -> 13A -0.5972212A -> 17A 0.1296912A -> 22A -0.167668B -> 13B 0.1347811B -> 13B -0.2109212B -> 13B 0.5972212B -> 17B -0.1296912B -> 22B 0.16766The wavefunction is stable under the perturbations considered.The wavefunction is already stable.The wavefunction is already stable.********************************************************************** Population analysis using the SCF density.**********************************************************************Orbital symmetries:Alpha Orbitals:Occupied (A1) (?A) (?A) (B2) (B2) (B2) (?B) (B2) (B2) (?B)(B2) (B2)Virtual (?B) (B2) (B2) (B2) (?B) (B2) (B2) (?B) (B2) (?B)(B2) (B2) (B2) (B2) (B2) (B2) (B2) (?B) (B2) (B2)(B2) (?B) (B2) (B2) (?B) (?B) (?B) (B2) (B2) (B2)(?B) (B2) (?B) (B2) (B2) (B2) (?B) (B2) (?B) (B2)(B2) (B2) (?C) (?C) (?C)Beta Orbitals:Occupied (A1) (?A) (?A) (B2) (B2) (B2) (?B) (B2) (B2) (?B)(B2) (B2)Virtual (?B) (B2) (B2) (B2) (?B) (B2) (B2) (?B) (B2) (?B)(B2) (B2) (B2) (B2) (B2) (B2) (B2) (?B) (B2) (B2)(B2) (?B) (B2) (B2) (?B) (?B) (?B) (B2) (B2) (B2)(?B) (B2) (?B) (B2) (B2) (B2) (?B) (B2) (?B) (B2)(B2) (B2) (?C) (?C) (?C)Unable to determine electronic state: an orbital has unidentified symmetry.Alpha occ. eigenvalues -- -20.80084 -20.74413 -20.70332 -1.72528 -1.42648 Alpha occ. eigenvalues -- -1.06693 -0.82177 -0.79872 -0.77924 -0.57974 Alpha occ. eigenvalues -- -0.57745 -0.53074Alpha virt. eigenvalues -- 0.06967 0.17140 0.18093 0.18626 0.22382 Alpha virt. eigenvalues -- 0.24714 0.27212 0.28767 0.31520 0.31620 Alpha virt. eigenvalues -- 0.35236 0.37958 0.40840 0.43722 0.47906 Alpha virt. eigenvalues -- 1.20108 1.27392 1.28382 1.28543 1.34302 Alpha virt. eigenvalues -- 1.35570 1.38208 1.42662 1.45313 1.46918 Alpha virt. eigenvalues -- 1.65238 1.71747 1.72365 1.76911 1.79741 Alpha virt. eigenvalues -- 2.02221 2.02761 2.09198 2.12283 2.35839 Alpha virt. eigenvalues -- 2.61521 2.75744 2.80436 2.90174 3.06618 Alpha virt. eigenvalues -- 3.30959 3.34331 4.08920 4.38238 4.59708 Beta occ. eigenvalues -- -20.80084 -20.74413 -20.70332 -1.72528 -1.42648 Beta occ. eigenvalues -- -1.06693 -0.82177 -0.79872 -0.77924 -0.57974 Beta occ. eigenvalues -- -0.57745 -0.53074Beta virt. eigenvalues -- 0.06967 0.17140 0.18093 0.18626 0.22382 Beta virt. eigenvalues -- 0.24714 0.27212 0.28767 0.31520 0.31620 Beta virt. eigenvalues -- 0.35236 0.37958 0.40840 0.43722 0.47906 Beta virt. eigenvalues -- 1.20108 1.27392 1.28382 1.28543 1.34302 Beta virt. eigenvalues -- 1.35570 1.38208 1.42662 1.45313 1.46918 Beta virt. eigenvalues -- 1.65238 1.71747 1.72365 1.76911 1.79741 Beta virt. eigenvalues -- 2.02221 2.02761 2.09198 2.12283 2.35839 Beta virt. eigenvalues -- 2.61521 2.75744 2.80436 2.90174 3.06618 Beta virt. eigenvalues -- 3.30959 3.34331 4.08920 4.38238 4.59708 Condensed to atoms (all electrons):Mulliken atomic charges:11 O -0.0212062 O 0.0424123 O -0.021206Sum of Mulliken charges= 0.00000Atomic charges with hydrogens summed into heavy atoms:11 O -0.0212062 O 0.0424123 O -0.021206Sum of Mulliken charges= 0.00000Atomic-Atomic Spin Densities.1 2 31 O 1.042685 -0.125884 0.0000002 O -0.125884 0.000000 0.1258843 O 0.000000 0.125884 -1.042685Mulliken atomic spin densities:11 O 0.9168022 O 0.0000003 O -0.916802Sum of Mulliken spin densities= 0.00000Electronic spatial extent (au): <R**2>= 110.5628Charge= 0.0000 electronsDipole moment (field-independent basis, Debye):X= 0.0000 Y= 0.0000 Z= 0.0591 Tot= 0.0591Test job not archived.1|1|UNPC-UNK|Stability|UHF|6-31+G(d)|O3|PCUSER|20-Nov-2014|0||#T RHF/6-31+G(D) STABLE=OPT TEST||Ozone Stability||0,1|O|O,1,1.272|O,2,1.272,1,116.8||Version=x86-Win32-G03RevB.05|State=1-A1|HF=-224.3414347|S2=0.93245|S2-1=0.|S2A=0.122545|RMSD=6.525e-009|Dipole=-0.0197955,0.,0.0121783|PG=C02V [C2(O1),SGV(O2)]||@We find comfort among those who agree with us -- growth among those who don't.-- Frank A. ClarkJob cpu time: 0 days 0 hours 0 minutes 6.0 seconds.File lengths (MBytes): RWF= 16 Int= 0 D2E= 0 Chk= 7 Scr= 1Normal termination of Gaussian 03 at Thu Nov 20 16:21:43 2014.。
高斯常见错误
高斯常见错误第一篇:高斯常见错误近来一直在学习高斯,因为不精通常遇到各种错误。
结合自学的东西和查阅的资料总结出来一些错误,希望对和我一样的高斯初学者有所帮助。
1、Q:Error termination in NtrErr: ntran open failure returned to fopen.Segmentation fault E:Can't open a file.2、Q:Internal consistency error detected in FileIO for unit 1 I= 4 J=0 I Fail= 1.E:Gaussian is limited to 16 GB of scratch space on the 32-bit nodes.3、Q:Out-of-memory error in routine UFChkP(IEnd= 12292175MxCore= 6291456)Use %Mem=12MW to provide the minimum amount of memory required to complete this step.Error termination via Lnk1e at Thu Feb 2 13:05:32 2006.Eefault memory(6 MW, set in $GAUSS_MEMDEF)is too small for unfchk.4、Q:galloc: could not allocate memory.: Resource temporarily unavailable orOut-of-memory error in routine...orEnd of file in GetChg.Error termination via Lnk1e...E:Not enough memory.5、Q:IMax=3 JMax=2 DiffMx= 0.00D+00Unable to allocate space to process matrices in G2DrvN:NAtomX= 58 NBasis= 762 NBas6D= 762 MDV1= 6291106 MinMem= 105955841.E:Gaussian has 6 MW free memory(MDV1)but requires at least 106 MW(MinMem).6、Q;Estimate disk for full transformation-677255533 words.Semi-Direct transformation.Bad length for file.E:MaxDisk has been set too low.7、Q:Error termination in NtrErr:NtrErr Called from FileIO.E:The calculation has exceeded the maximum limit of maxcyc.8、Q:Erroneous read.Read 0instead of 6258688.fd = 4g_readE:Disk quota or disk size exceeded.Could also be disk failure or NFS timeout.9、Q:Erroneous write.Write 8192 instead of 12288.fd = 4E:Disk quota or disk size exceeded.Could also be disk failure or NFS10、Q:orig len = 12288 left = 12288 g_writeE:timeout11、另有link错误:如:Error termination request processed by link 9999对于优化不收敛,即L9999错误,实际上是在规定的步数内没有完成优化,即还没有找到极小值点。
线性代数-常用单词词组-中英对照
Dual problem对偶问题442,446EEconomics 经济学435,439Eigencourse 457,458Eigenvalue 特征值283,287,374,499 Eigenvalue changes 特征值变换439284,294,300 Eigenvalues of 的特征值297Eigenvalues of 的特征值362Eigenvalues of 的特征值Eigenvector basis 基底的特征向量399Eigenvectors 特征向量283,287,374Eigshow 290,368Elimination 消元法45-66,83,86,135Ellipse 椭圆290,346,366,382Energy 能量343,409Engineering 工程409,419Error 误差211,218,219,225,481,483 Error equation 误差方程477Euler angles 欧拉角474Euler’s formula 欧拉公式311,426,430,497Even 偶数113,246,258,452 Exponential 指数的314,319,327FFactorization 因式分解95,110,235,348,370,374 False proof 假证明305,338Fast Fourier Transform 快速傅立叶变换393,493,511,565Feasible set 可行集440,441FFT(see Fast见快速傅里叶变换509-514Fourier Transform)Fibonacci 菲波那契75,266,268,301,302,306,308 Finite difference 有限差分315-317,417Finite elements 有限元412,419First-order system 一阶方程组315,326Fixed-free 固定-自由410,414,417,419Force balance 平衡力412FORTRAN 16,38Forward difference 前向差分30Four Fundamental Subspaces 四个基本子空间184-199,368,424,507 Fourier series 傅立叶序列233,448,450,452Fourier Transform 傅立叶变换393,509-514Fredholm Alternative 弗雷德霍姆择一203Free 自由133,135,137,144,146,155 Full column rank 列满秩157,170,405Full row rank 行满秩159,405Function space 函数空间121,448,449 Fundamental Theorem of Linear线性代数基本定理188,198,368Algebra(see Four Fundamental Subspaces)GGaussian elimination 高斯消元法45,49,135Gaussian probability distribution 高斯概率分布455Gauss-Jordan 高斯-约当83,84,91,469Gauss-Seidel 高斯-塞德尔481,484,485,489Gene expression data 基因表达数据457Geometric series 等比数列436Gershgorin circles 格尔什戈林圆491Gibbs phenomenon 吉布斯效应451Givens rotation 吉文斯旋转471Google 谷歌368,369,434Gram-Schmidt 格拉姆-施密特223,234,236,241,370,469 Graph 图表74,143,307,311,420,422,423 Group 群119,354HHalf-plane 半平面7Heat equation 热方程式322,323Heisenberg 海森堡305,310Hilbert space 希尔伯特空间447,449Hook e’s Law 虎克定律410,412Householder reflections 镜像变换237,469,472Hyperplane 超平面30,42IIll-conditioned matrix 病态矩阵371,473,474Imaginary 虚数289Independent 独立的26,27,134,168,200,300 Initial value 初值313Inner product 内积11,56,108,448,502,506 Input and output basis 基底输入输出399Integral 积分24,385,386Interior point method 内点法445Intersection of spaces 交空间129,183Inverse matrix 逆矩阵24,81,27082Inverse of的逆Invertible 可逆的86,173,200,248Iteration 迭代481,482,484,489,492JJacobi 雅可比481,483,485,489Jordan form 约当型356,357,358,361,482 JPEG 364,373KKalman filter 卡尔曼滤波器93,214Kernel 核377,380Kirchhoff’s Laws 基尔霍夫定律143,189,420,424-427 Krylov 克雷洛夫491,492L225,480norm 和范数Lagrange multiplier 拉格朗日乘子445Lanczos method 兰索斯方法490,492LAPACK 线性代数软件包98,237,486Leapfrog method 跳步法317,329Least squares 最小平方218,219,236,405,408,453184,186,192,425Left nullspace左零空间Left-inverse 左逆的81,86,154,405Length 长度12,232,447,448,501Line 线34,40,221,474Line of springs 线弹簧411Linear combination 线性组合1,3Linear equation 线性方程23Linear programming 线性规划440Linear transformation 线性变换44,375-398Linearity 线性关系44,245,246Linearly independent 线性独立26,134,168,169,200 LINPACK 线性系统软件包465Loop 环路307,425,426Lower triangular 下三角9598,100,474Lucas numbers 卢卡斯数306MMaple 38,100Mathematica 38,100MATLAB 17,37,237,243,290,337,513 Matrix(see full page 570) 矩阵22,384,387Matrix exponential 矩阵指数314,319,327Matrix multiplication 矩阵乘法58,59,67,389----。
车辆控制系统说明书
IndexAactuation layer, 132average brightness,102-103adaptive control, 43Badaptive cruise control, 129backpropagation algorithm, 159adaptive FLC, 43backward driving mode,163,166,168-169adaptive neural networks,237adaptive predictive model, 283Baddeley-Molchanov average, 124aerial vehicles, 240 Baddeley-Molchanov fuzzy set average, 120-121, 123aerodynamic forces,209aerodynamics analysis, 208, 220Baddeley-Molchanov mean,118,119-121alternating filter, 117altitude control, 240balance position, 98amplitude distribution, 177bang-bang controller,198analytical control surface, 179, 185BCFPI, 61-63angular velocity, 92,208bell-shaped waveform,25ARMAX model, 283beta distributions,122artificial neural networks,115Bezier curve, 56, 59, 63-64association, 251Bezier Curve Fuzzy PI controller,61attitude angle,208, 217Bezier function, 54aumann mean,118-120bilinear interpolation, 90, 300,302automated manual transmission,145,157binary classifier,253Bo105 helicopter, 208automatic formation flight control,240body frame,238boiler following mode,280,283automatic thresholding,117border pixels, 101automatic transmissions,145boundary layer, 192-193,195-198autonomous robots,130boundary of a fuzzy set,26autonomous underwater vehicle, 191braking resistance, 265AUTOPIA, 130bumpy control surface, 55autopilot signal, 228Index 326CCAE package software, 315, 318 calibration accuracy, 83, 299-300, 309, 310, 312CARIMA models, 290case-based reasoning, 253center of gravity method, 29-30, 32-33centroid defuzzification, 7 centroid defuzzification, 56 centroid Method, 106 characteristic polygon, 57 characterization, 43, 251, 293 chattering, 6, 84, 191-192, 195, 196, 198chromosomes, 59circuit breaker, 270classical control, 1classical set, 19-23, 25-26, 36, 254 classification, 106, 108, 111, 179, 185, 251-253classification model, 253close formation flight, 237close path tracking, 223-224 clustering, 104, 106, 108, 251-253, 255, 289clustering algorithm, 252 clustering function, 104clutch stroke, 147coarse fuzzy logic controller, 94 collective pitch angle, 209 collision avoidance, 166, 168 collision avoidance system, 160, 167, 169-170, 172collision avoidance system, 168 complement, 20, 23, 45 compressor contamination, 289 conditional independence graph, 259 confidence thresholds, 251 confidence-rated rules, 251coning angle, 210constant gain, 207constant pressure mode, 280 contrast intensification, 104 contrast intensificator operator, 104 control derivatives, 211control gain, 35, 72, 93, 96, 244 control gain factor, 93control gains, 53, 226control rules, 18, 27, 28, 35, 53, 64, 65, 90-91, 93, 207, 228, 230, 262, 302, 304-305, 315, 317control surfaces, 53-55, 64, 69, 73, 77, 193controller actuator faulty, 289 control-weighting matrix, 207 convex sets, 119-120Coordinate Measurement Machine, 301coordinate measuring machine, 96 core of a fuzzy set, 26corner cube retroreflector, 85 correlation-minimum, 243-244cost function, 74-75, 213, 282-283, 287coverage function, 118crisp input, 18, 51, 182crisp output, 7, 34, 41-42, 51, 184, 300, 305-306crisp sets, 19, 21, 23crisp variable, 18-19, 29critical clearing time, 270 crossover, 59crossover probability, 59-60cruise control, 129-130,132-135, 137-139cubic cell, 299, 301-302, 309cubic spline, 48cubic spline interpolation, 300 current time gap, 136custom membership function, 294 customer behav or, 249iDdamping factor, 211data cleaning, 250data integration, 250data mining, 249, 250, 251-255, 259-260data selection, 250data transformation, 250d-dimensional Euclidean space, 117, 124decision logic, 321 decomposition, 173, 259Index327defuzzification function, 102, 105, 107-108, 111 defuzzifications, 17-18, 29, 34 defuzzifier, 181, 242density function, 122 dependency analysis, 258 dependency structure, 259 dependent loop level, 279depth control, 202-203depth controller, 202detection point, 169deviation, 79, 85, 185-188, 224, 251, 253, 262, 265, 268, 276, 288 dilation, 117discriminated rules, 251 discrimination, 251, 252distance function, 119-121 distance sensor, 167, 171 distribution function, 259domain knowledge, 254-255 domain-specific attributes, 251 Doppler frequency shift, 87 downhill simplex algorithm, 77, 79 downwash, 209drag reduction, 244driver’s intention estimator, 148 dutch roll, 212dynamic braking, 261-262 dynamic fuzzy system, 286, 304 dynamic tracking trajectory, 98Eedge composition, 108edge detection, 108 eigenvalues, 6-7, 212electrical coupling effect, 85, 88 electrical coupling effects, 87 equilibrium point, 207, 216 equivalent control, 194erosion, 117error rates, 96estimation, 34, 53, 119, 251, 283, 295, 302Euler angles, 208evaluation function, 258 evolution, 45, 133, 208, 251 execution layer, 262-266, 277 expert knowledge, 160, 191, 262 expert segmentation, 121-122 extended sup-star composition, 182 Ffault accommodation, 284fault clearing states, 271, 274fault detection, 288-289, 295fault diagnosis, 284fault durations, 271, 274fault isolation, 284, 288fault point, 270-271, 273-274fault tolerant control, 288fault trajectories, 271feature extraction, 256fiber glass hull, 193fin forces, 210final segmentation, 117final threshold, 116fine fuzzy controller, 90finer lookup table, 34finite element method, 318finite impulse responses, 288firing weights, 229fitness function, 59-60, 257flap angles, 209flight aerodynamic model, 247 flight envelope, 207, 214, 217flight path angle, 210flight trajectory, 208, 223footprint of uncertainty, 176, 179 formation geometry, 238, 247 formation trajectory, 246forward driving mode, 163, 167, 169 forward flight control, 217 forward flight speed, 217forward neural network, 288 forward velocity, 208, 214, 217, 219-220forward velocity tracking, 208 fossil power plants, 284-285, 296 four-dimensional synoptic data, 191 four-generator test system, 269 Fourier filter, 133four-quadrant detector, 79, 87, 92, 96foveal avascular zone, 123fundus images, 115, 121, 124 fuselage, 208-210Index 328fuselage axes, 208-209fuselage incidence, 210fuzz-C, 45fuzzifications, 18, 25fuzzifier, 181-182fuzzy ACC controller, 138fuzzy aggregation operator, 293 fuzzy ASICs, 37-38, 50fuzzy binarization algorithm, 110 fuzzy CC controller, 138fuzzy clustering algorithm, 106, 108 fuzzy constraints, 286, 291-292 fuzzy control surface, 54fuzzy damage-mitigating control, 284fuzzy decomposition, 108fuzzy domain, 102, 106fuzzy edge detection, 111fuzzy error interpolation, 300, 302, 305-306, 309, 313fuzzy filter, 104fuzzy gain scheduler, 217-218 fuzzy gain-scheduler, 207-208, 220 fuzzy geometry, 110-111fuzzy I controller, 76fuzzy image processing, 102, 106, 111, 124fuzzy implication rules, 27-28 fuzzy inference system, 17, 25, 27, 35-36, 207-208, 302, 304-306 fuzzy interpolation, 300, 302, 305- 307, 309, 313fuzzy interpolation method, 309 fuzzy interpolation technique, 300, 309, 313fuzzy interval control, 177fuzzy mapping rules, 27fuzzy model following control system, 84fuzzy modeling methods, 255 fuzzy navigation algorithm, 244 fuzzy operators, 104-105, 111 fuzzy P controller, 71, 73fuzzy PD controller, 69fuzzy perimeter, 110-111fuzzy PI controllers, 61fuzzy PID controllers, 53, 64-65, 80 fuzzy production rules, 315fuzzy reference governor, 285 Fuzzy Robust Controller, 7fuzzy set averages, 116, 124-125 fuzzy sets, 7, 19, 22, 24, 27, 36, 45, 115, 120-121, 124-125, 151, 176-182, 184-188, 192, 228, 262, 265-266fuzzy sliding mode controller, 192, 196-197fuzzy sliding surface, 192fuzzy subsets, 152, 200fuzzy variable boundary layer, 192 fuzzyTECH, 45Ggain margins, 207gain scheduling, 193, 207, 208, 211, 217, 220gas turbines, 279Gaussian membership function, 7 Gaussian waveform, 25 Gaussian-Bell waveforms, 304 gear position decision, 145, 147 gear-operating lever, 147general window function, 105 general-purpose microprocessors, 37-38, 44genetic algorithm, 54, 59, 192, 208, 257-258genetic operators, 59-60genetic-inclined search, 257 geometric modeling, 56gimbal motor, 90, 96global gain-scheduling, 220global linear ARX model, 284 global navigation satellite systems, 141global position system, 224goal seeking behaviour, 186-187 governor valves80, 2HHamiltonian function, 261, 277 hard constraints, 283, 293 heading angle, 226, 228, 230, 239, 240-244, 246heading angle control, 240Index329heading controller, 194, 201-202 heading error rate, 194, 201 heading speed, 226heading velocity control, 240 heat recovery steam generator, 279 hedges, 103-104height method, 29helicopter, 207-212, 214, 217, 220 helicopter control matrix, 211 helicopter flight control, 207 Heneghan method, 116-117, 121-124heuristic search, 258 hierarchical approaches, 261 hierarchical architecture, 185 hierarchical fuzzy processors, 261 high dimensional systems, 191 high stepping rates, 84hit-miss topology, 119home position, 96horizontal tail plane, 209 horizontal tracker, 90hostile, 223human domain experts, 255 human visual system, 101hybrid system framework, 295 hyperbolic tangent function, 195 hyperplane, 192-193, 196 hysteresis thres olding, 116-117hIIF-THEN rule, 27-28image binarization, 106image complexity, 104image fuzzification function, 111 image segmentation, 124image-expert, 122-123indicator function, 121inert, 223inertia frame, 238inference decision methods, 317 inferential conclusion, 317 inferential decision, 317 injection molding process, 315 inner loop controller, 87integral time absolute error, 54 inter-class similarity, 252 internal dependencies, 169 interpolation property, 203 interpolative nature, 262 intersection, 20, 23-24, 31, 180 interval sets, 178interval type-2 FLC, 181interval type-2 fuzzy sets, 177, 180-181, 184inter-vehicle gap, 135intra-class similarity, 252inverse dynamics control, 228, 230 inverse dynamics method, 227 inverse kinema c, 299tiJ - Kjoin, 180Kalman gain, 213kinematic model, 299kinematic modeling, 299-300 knowledge based gear position decision, 148, 153knowledge reasoning layer, 132 knowledge representation, 250 knowledge-bas d GPD model, 146eLlabyrinths, 169laser interferometer transducer, 83 laser tracker, 301laser tracking system, 53, 63, 65, 75, 78-79, 83-85, 87, 98, 301lateral control, 131, 138lateral cyclic pitch angle, 209 lateral flapping angle, 210 leader, 238-239linear control surface, 55linear fuzzy PI, 61linear hover model, 213linear interpolation, 300-301, 306-307, 309, 313linear interpolation method, 309 linear optimal controller, 207, 217 linear P controller, 73linear state feedback controller, 7 linear structures, 117linear switching line, 198linear time-series models, 283 linguistic variables, 18, 25, 27, 90, 102, 175, 208, 258Index 330load shedding, 261load-following capabilities, 288, 297 loading dock, 159-161, 170, 172 longitudinal control, 130-132 longitudinal cyclic pitch angle, 209 longitudinal flapping angle, 210 lookup table, 18, 31-35, 40, 44, 46, 47-48, 51, 65, 70, 74, 93, 300, 302, 304-305lower membership functions, 179-180LQ feedback gains, 208LQ linear controller, 208LQ optimal controller, 208LQ regulator, 208L-R fuzzy numbers, 121 Luenburger observer, 6Lyapunov func on, 5, 192, 284tiMMamdani model, 40, 46 Mamdani’s method, 242 Mamdani-type controller, 208 maneuverability, 164, 207, 209, 288 manual transmissions, 145 mapping function, 102, 104 marginal distribution functions, 259 market-basket analysis, 251-252 massive databases, 249matched filtering, 115 mathematical morphology, 117, 127 mating pool, 59-60max member principle, 106max-dot method, 40-41, 46mean distance function, 119mean max membership, 106mean of maximum method, 29 mean set, 118-121measuring beam, 86mechanical coupling effects, 87 mechanical layer, 132median filter, 105meet, 7, 50, 139, 180, 183, 302 membership degree, 39, 257 membership functions, 18, 25, 81 membership mapping processes, 56 miniature acrobatic helicopter, 208 minor steady state errors, 217 mixed-fuzzy controller, 92mobile robot control, 130, 175, 181 mobile robots, 171, 175-176, 183, 187-189model predictive control, 280, 287 model-based control, 224 modeless compensation, 300 modeless robot calibration, 299-301, 312-313modern combined-cycle power plant, 279modular structure, 172mold-design optimization, 323 mold-design process, 323molded part, 318-321, 323 morphological methods, 115motor angular acceleration, 3 motor plant, 3motor speed control, 2moving average filter, 105 multilayer fuzzy logic control, 276 multimachine power system, 262 multivariable control, 280 multivariable fuzzy PID control, 285 multivariable self-tuning controller, 283, 295mutation, 59mutation probability, 59-60mutual interference, 88Nnavigation control, 160neural fuzzy control, 19, 36neural networks, 173, 237, 255, 280, 284, 323neuro-fuzzy control, 237nominal plant, 2-4nonlinear adaptive control, 237non-linear control, 2, 159 nonlinear mapping, 55nonlinear switching curve, 198-199 nonlinear switching function, 200 nonvolatile memory, 44 normalized universe, 266Oobjective function, 59, 74-75, 77, 107, 281-282, 284, 287, 289-291,Index331295obstacle avoidance, 166, 169, 187-188, 223-225, 227, 231 obstacle avoidance behaviour, 187-188obstacle sensor, 224, 228off-line defuzzification, 34off-line fuzzy inference system, 302, 304off-line fuzzy technology, 300off-line lookup tables, 302 offsprings, 59-60on-line dynamic fuzzy inference system, 302online tuning, 203open water trial, 202operating point, 210optical platform, 92optimal control table, 300optimal feedback gain, 208, 215-216 optimal gains, 207original domain, 102outer loop controller, 85, 87outlier analysis, 251, 253output control gains, 92 overshoot, 3-4, 6-7, 60-61, 75-76, 94, 96, 193, 229, 266Ppath tracking, 223, 232-234 pattern evaluation, 250pattern vector, 150-151PD controller, 4, 54-55, 68-69, 71, 74, 76-77, 79, 134, 163, 165, 202 perception domain, 102 performance index, 60, 207 perturbed plants, 3, 7phase margins, 207phase-plan mapping fuzzy control, 19photovoltaic power systems, 261 phugoid mode, 212PID, 1-4, 8, 13, 19, 53, 61, 64-65, 74, 80, 84-85, 87-90, 92-98, 192 PID-fuzzy control, 19piecewise nonlinear surface, 193 pitch angle, 202, 209, 217pitch controller, 193, 201-202 pitch error, 193, 201pitch error rate, 193, 201pitch subsidence, 212planetary gearbox, 145point-in-time transaction, 252 polarizing beam-splitter, 86 poles, 4, 94, 96position sensor detectors, 84 positive definite matrix, 213post fault, 268, 270post-fault trajectory, 273pre-defined membership functions, 302prediction, 251, 258, 281-283, 287, 290predictive control, 280, 282-287, 290-291, 293-297predictive supervisory controller, 284preview distance control, 129 principal regulation level, 279 probabilistic reasoning approach, 259probability space, 118Problem understanding phases, 254 production rules, 316pursuer car, 136, 138-140 pursuer vehicle, 136, 138, 140Qquadrant detector, 79, 92 quadrant photo detector, 85 quadratic optimal technology, 208 quadrilateral ob tacle, 231sRradial basis function, 284 random closed set, 118random compact set, 118-120 rapid environment assessment, 191 reference beam, 86relative frame, 240relay control, 195release distance, 169residual forces, 217retinal vessel detection, 115, 117 RGB band, 115Riccati equation, 207, 213-214Index 332rise time, 3, 54, 60-61, 75-76road-environment estimator, 148 robot kinematics, 299robot workspace, 299-302, 309 robust control, 2, 84, 280robust controller, 2, 8, 90robust fuzzy controller, 2, 7 robustness property, 5, 203roll subsidence, 212rotor blade flap angle, 209rotor blades, 210rudder, 193, 201rule base size, 191, 199-200rule output function, 191, 193, 198-199, 203Runge-Kutta m thod, 61eSsampling period, 96saturation function, 195, 199 saturation functions, 162scaling factor, 54, 72-73scaling gains, 67, 69S-curve waveform, 25secondary membership function, 178 secondary memberships, 179, 181 selection, 59self-learning neural network, 159 self-organizing fuzzy control, 261 self-tuning adaptive control, 280 self-tuning control, 191semi-positive definite matrix, 213 sensitivity indices, 177sequence-based analysis, 251-252 sequential quadratic programming, 283, 292sets type-reduction, 184setting time, 54, 60-61settling time, 75-76, 94, 96SGA, 59shift points, 152shift schedule algorithms, 148shift schedules, 152, 156shifting control, 145, 147shifting schedules, 146, 152shift-schedule tables, 152sideslip angle, 210sigmoidal waveform, 25 sign function, 195, 199simplex optimal algorithm, 80 single gimbal system, 96single point mass obstacle, 223 singleton fuzzification, 181-182 sinusoidal waveform, 94, 300, 309 sliding function, 192sliding mode control, 1-2, 4, 8, 191, 193, 195-196, 203sliding mode fuzzy controller, 193, 198-200sliding mode fuzzy heading controller, 201sliding pressure control, 280 sliding region, 192, 201sliding surface, 5-6, 192-193, 195-198, 200sliding-mode fuzzy control, 19 soft constraints, 281, 287space-gap, 135special-purpose processors, 48 spectral mapping theorem, 216 speed adaptation, 138speed control, 2, 84, 130-131, 133, 160spiral subsidence, 212sporadic alternations, 257state feedback controller, 213 state transition, 167-169state transition matrix, 216state-weighting matrix, 207static fuzzy logic controller, 43 static MIMO system, 243steady state error, 4, 54, 79, 90, 94, 96, 98, 192steam turbine, 279steam valving, 261step response, 4, 7, 53, 76, 91, 193, 219stern plane, 193, 201sup operation, 183supervisory control, 191, 280, 289 supervisory layer, 262-264, 277 support function, 118support of a fuzzy set, 26sup-star composition, 182-183 surviving solutions, 257Index333swing curves, 271, 274-275 switching band, 198switching curve, 198, 200 switching function, 191, 194, 196-198, 200switching variable, 228system trajector192, 195y,Ttail plane, 210tail rotor, 209-210tail rotor derivation, 210Takagi-Sugeno fuzzy methodology, 287target displacement, 87target time gap, 136t-conorm maximum, 132 thermocouple sensor fault, 289 thickness variable, 319-320three-beam laser tracker, 85three-gimbal system, 96throttle pressure, 134throttle-opening degree, 149 thyristor control, 261time delay, 63, 75, 91, 93-94, 281 time optimal robust control, 203 time-gap, 135-137, 139-140time-gap derivative, 136time-gap error, 136time-invariant fuzzy system, 215t-norm minimum, 132torque converter, 145tracking error, 79, 84-85, 92, 244 tracking gimbals, 87tracking mirror, 85, 87tracking performance, 84-85, 88, 90, 192tracking speed, 75, 79, 83-84, 88, 90, 92, 97, 287trajectory mapping unit, 161, 172 transfer function, 2-5, 61-63 transient response, 92, 193 transient stability, 261, 268, 270, 275-276transient stability control, 268 trapezoidal waveform, 25 triangular fuzzy set, 319triangular waveform, 25 trim, 208, 210-211, 213, 217, 220, 237trimmed points, 210TS fuzzy gain scheduler, 217TS fuzzy model, 207, 290TS fuzzy system, 208, 215, 217, 220 TS gain scheduler, 217TS model, 207, 287TSK model, 40-41, 46TS-type controller, 208tuning function, 70, 72turbine following mode, 280, 283 turn rate, 210turning rate regulation, 208, 214, 217two-DOF mirror gimbals, 87two-layered FLC, 231two-level hierarchy controllers, 275-276two-module fuzzy logic control, 238 type-0 systems, 192type-1 FLC, 176-177, 181-182, 185- 188type-1 fuzzy sets, 177-179, 181, 185, 187type-1 membership functions, 176, 179, 183type-2 FLC, 176-177, 180-183, 185-189type-2 fuzzy set, 176-180type-2 interval consequent sets, 184 type-2 membership function, 176-178type-reduced set, 181, 183-185type-reduction,83-1841UUH-1H helicopter, 208uncertain poles, 94, 96uncertain system, 93-94, 96 uncertain zeros, 94, 96underlying domain, 259union, 20, 23-24, 30, 177, 180unit control level, 279universe of discourse, 19-24, 42, 57, 151, 153, 305unmanned aerial vehicles, 223 unmanned helicopter, 208Index 334unstructured dynamic environments, 177unstructured environments, 175-177, 179, 185, 187, 189upper membership function, 179Vvalve outlet pressure, 280vapor pressure, 280variable structure controller, 194, 204velocity feedback, 87vertical fin, 209vertical tracker, 90vertical tracking gimbal, 91vessel detection, 115, 121-122, 124-125vessel networks, 117vessel segmentation, 115, 120 vessel tracking algorithms, 115 vision-driven robotics, 87Vorob’ev fuzzy set average, 121-123 Vorob'ev mean, 118-120vortex, 237 WWang and Mendel’s algorithm, 257 WARP, 49weak link, 270, 273weighing factor, 305weighting coefficients, 75 weighting function, 213weld line, 315, 318-323western states coordinating council, 269Westinghouse turbine-generator, 283 wind–diesel power systems, 261 Wingman, 237-240, 246wingman aircraft, 238-239 wingman veloc y, 239itY-ZYager operator, 292Zana-Klein membership function, 124Zana-Klein method, 116-117, 121, 123-124zeros, 94, 96µ-law function, 54µ-law tuning method, 54。
机器学习经典书目汇总
机器学习经典书目汇总本文总结了机器学习的经典书籍,包括数学基础和算法理论的书籍。
入门书单《数学之美》作者吴军大家都很熟悉。
以极为通俗的语言讲述了数学在机器学习和自然语言处理等领域的应用。
《Programming Collective Intelligence》(《集体智慧编程》)作者Toby Segaran也是《BeautifulData : The Stories Behind Elegant Data Solutions》(《数据之美:解密优雅数据解决方案背后的故事》)的作者。
这本书最大的优势就是里面没有理论推导和复杂的数学公式,是很不错的入门书。
目前中文版已经脱销,对于有志于这个领域的人来说,英文的pdf是个不错的选择,因为后面有很多经典书的翻译都较差,只能看英文版,不如从这个入手。
还有,这本书适合于快速看完,因为据评论,看完一些经典的带有数学推导的书后会发现这本书什么都没讲,只是举了很多例子而已。
《Algorithms of the Intelligent Web》(《智能web算法》)作者Haralambos Marmanis、Dmitry Babenko。
这本书中的公式比《集体智慧编程》要略多一点,里面的例子多是互联网上的应用,看名字就知道。
不足的地方在于里面的配套代码是BeanShell而不是python或其他。
总起来说,这本书还是适合初学者,与上一本一样需要快速读完,如果读完上一本的话,这一本可以不必细看代码,了解算法主要思想就行了。
《统计学习方法》作者李航,是国内机器学习领域的几个大家之一,曾在MSRA 任高级研究员,现在华为诺亚方舟实验室。
书中写了十个算法,每个算法的介绍都很干脆,直接上公式,是彻头彻尾的“干货书”。
每章末尾的参考文献也方便了想深入理解算法的童鞋直接查到经典论文;本书可以与上面两本书互为辅助阅读。
《Machine Learning》(《机器学习》)作者Tom Mitchell是CMU的大师,有机器学习和半监督学习的网络课程视频。
热力学性质计算-Gaussian
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Alpha virt. eigenvalues -- 2.90063 2.90063 3.18837 4.19106 4.19106
Alpha virt. eigenvalues -- 4.19106 25.15683
布居数分析缺省是用SCF密度,如果想用当前方法(此例为MP2方法),Pop (density=Current)
• 自洽场:
SCF Done: E(RHF) = -40.2089173552 A.U. after 1 cycles 自洽场收敛
Convg = 0.3754D-11 -V/T = 2.0014 自洽场收敛判据值和维里系数
S**2 = 0.0000
自旋平方
维里系数应该为2(一般计算的值都会接近这个数)
Alpha virt. eigenvalues -- 0.16167 0.23702 0.23702 0.23702 0.42707 的本征值 Alpha virt. eigenvalues -- 0.42707 0.42707 0.75271 0.81186 0.81186 (能量)
计算化学-7
另一种等价表示方法是: %mem=32mb %chk=H2O #P B3LYP/6-311G OPT=z-matrix POP=FULL The geometry optimization of water 0,1 O H,1,r H,1,r,2,a Variables a=105.4 Constants r=1.0
最大值
均方值
各原子受力情况
(Enter d:\G09W\l103.exe) GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad Berny optimization. Internal Forces: Max 0.021560519 RMS 0.017964017 Search for a local minimum. Step number 1 out of a maximum of 20 …… Second derivative matrix not updated -- first step. The second derivative matrix: R1 R2 A1 R1 0.47688 R2 0.00000 0.47688 A1 0.00000 0.00000 0.16000 Eigenvalues --- 0.16000 0.47688 0.47688 RFO step: Lambda=-2.17751054D-03 EMin= 1.60000000D-01 Linear search not attempted -- first point. Iteration 1 RMS(Cart)= 0.02871456 RMS(Int)= 0.00060649 Iteration 2 RMS(Cart)= 0.00068611 RMS(Int)= 0.00000019 Iteration 3 RMS(Cart)= 0.00000012 RMS(Int)= 0.00000000 ClnCor: largest displacement from symmetrization is 3.60D-15 for atom 3. Variable Old X -DE/DX Delta X Delta X Delta X New X (Linear) (Quad) (Total) R1 1.88973 -0.02156 0.00000 -0.04501 -0.04501 1.84472 R2 1.88973 -0.02156 0.00000 -0.04501 -0.04501 1.84472 A1 1.83958 0.00620 0.00000 0.03821 0.03821 1.87779 Item Value Threshold Converged? Maximum Force 0.021561 0.000450 NO RMS Force 0.017964 0.000300 NO Maximum Displacement 0.029439 0.001800 NO RMS Displacement 0.028794 0.001200 NO Predicted change in Energy=-1.094755D-03 GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
Gaussian中IOP关键词使用详解
Technical Support InformationLast update: 16 April 2003Overlay 15 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 88 89 90 91 92 94 95 96 97 98 101 102 103 104 105 106 107 108 109 110 111 112 113 114Overlay 29 10 11 12 13 14 15 16 17 18 19 20 29 30 40 41Overlay 35 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 67 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106Overlay 45 6 7 8 9 10 11 13 14 15 16 17 18 19 20 21 22 23 24 25 26 28 29 31 33 34 35 36 37 38 43 44 45 46 47 48 60 61 62 63 64 65 66 67 68 69 71 72 80 81 82 110Overlay 55 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102Overlay 615 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 70 71 72 73 74 75 76 77 78 79 80 81 82 83Overlay 76 7 8 9 10 11 12 13 14 15 16 18 25 29 30 31 32 40 41 42 43 44 45 52 53 64 65 70 71 72 74 75 76 77 87Overlay 85 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 27 28 29 30 31 32 35 36 38 39 40 41 42 43 44 45 46 47Overlay 95 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 25 26 27 28 30 31 36 37 38 40 41 42 43 44 45 46 47 48 49 60 61 62 70 71 72 73 74 75 81 82 83 84 85 86Overlay 105 6 7 8 9 10 11 13 14 15 16 17 18 19 20 21 22 28 29 30 31 32 45 46 47 48 60 61 62 63 72 72 74 75 76 77 78 79Overlay 115 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 26 27 28 29 30 31 32 33 39 40 41 42 43 45 46 53 60 61 62 63 70 71 75Overlay 99995 6 7 8 9 10 11 12 13 14 15 16 17 18 33Technical Support InformationLast update: 22 March 2003Overlay 15 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 88 89 90 91 92 94 95 96 97 98 101 102 103 104 105 106 107 108 109 110 111 112 113 114IOp(1/5)L103 MODE OF OPTIMIZATION 0 FIND LOCAL MINIMUM 1 FIND A SADDLE POINT N FIND A STATIONARY POINT ON THE ENERGY SURFACE WITH N NEGATIVE EIGENVALUES OF THE 2ND DERIVATIVE MATRIX L107: MODE OF SEARCH 0 LOCATE THE MAXIMUM IN THE LST PATH. 1 SCAN THE LST PATH.IOp(1/6)L102, L103, L105, L107, L109, L112, L113, L114: MAXIMUM NUMBER OF STEPS (OR NUMBER OF STEPS FOR AN LST SCAN). 0 NSTEP = Max(20,NVAR+10) (L103, L112) = Min(20,NVAR+10) (L102, L105, L109) = Min(40,NVar+20) (L113, L114) N NSTEP = NIOp(1/7)L103, L105, L109, L112, L113, L114: CONVERGENCE ON THE FIRST DERIVATIVE AND ESTIMATED DISPLACEMENT FOR THE OPTIMIZATION RMS FIRST DERIVATIVE .LT. CONFV, RMS EST. DISPLACEMENT .LT. CONVX=4*CONVF -1 ConvF = 1/600 HARTREE/BOHR OR RADIAN 0 CONVF = 0.0003 HARTREE/BOHR OR RADIAN N CONVF = N*10**-6 L116, L117: Convergence on electric field/charges -1 Default value for optimizations: 10**-7. 0 Default value for single-points: 10**-5 in L116, 10**-7 in L117. N 10**-N.IOp(1/8)L103, L109, L112: MAXIMUM STEP SIZE ALLOWED DURING OPT. 0 DXMAXT = 0.1 BOHR OR RADIAN (L103, Estm or UnitFC). = 0.3 Bohr or Radian (L103, Read or CalcFC). = 0.2 Bohr or Radian (L105). = 0.3 Bohr or Radian (L113, L114). DXMAXT = 0.01 * NNL117: General control. 0 Which type of basin to use to partition the density isosurface. Default is 4 1 GradVne 2 GradRho 3 Don't Use Basins, Use only the Center of NuclearCharge 4 Use Interlocking Spheres N0 Order of Adam's-Bashforth-Moulton (ABM) predictorcorrector method to use in solving diff. eqns. for the grad RHO or Vne trajectories. Default is 4, max is 9. N00 Number of small steps per ABM step to be used in starting ABM and when "slow down" is needed in ABM. Default is 5. N000 Which approximation to make. Default is III for Tomasi (interlocking spheres) and IV for general surface. 1000 Apprx. I - Don't Do Self-Polarization or "Compensation" 2000 Apprx. II - Do-Self Polarization, But No Compensation. 3000 Apprx. III - Do Self-Polarization and Compensation. 4000 Apprx. IV - Do III and Allow Surface To "Relax" in Solution if no spheres N0000 Whether to evaluate densities using orbitals or density matrix. Default is to use density. 10000 Use MOs. 20000 Use density. L121: Time step, N*0.0001 fs, default 0.1IOp(1/9)L103: Use of Trust radius. 0 Whether to update trust radius (DXMaxT, default Yes). Default is Yes for minima, no for TS. 1 2 No. Yes.00 Whether to scale or search the sphere when reducing the step size to the trust radius (Default search for minima, scale for transition states.). 10 20 Scale. Search.L107: WHETHER TO MAINTAIN SYMMETRY ALONG THE SEARCH PATH. 0 1 YES. NO.L117: Whether to delete points which are too close together: 0 1 No Yes, using a default criteria (0.05 Angstroms)-N Yes, using a (10**-N Angstroms) criteria. How close to get to the isosurface in search. 0 N Approx 1.0D-6 (N=20) 2.0**-NL121: Whether to read in initial velocities: 0 1 2 3 Default (same as 1) Generate random initial velocity Read in initial cartesian velocity (Bohr/sec) Read in initial MW cartesian velocity (sqrt(amu)*Bohr/sec)IOp(1/10)L103, L105, L109, L112, L113, L114: Input of initial Hessian: All values must be in atomic units (Hartree, Bohr, and radians). 0 1 2 3 Use defaults (not valid for L109). Read ((FC(I,J),J=1,I),I=1,NVAR) (8F10.6) (L103 only). Read I,J,FC(I,J), (5I3,F20.0) (L103 only). End with a blank card. Read from checkpoint file in internal coordinates.4 Second derivative matrix calculated analytically. (not valid for L109). 5 Read cartesian forces and force constants from the checkpoint file are convert to internal coordinates. 6 Read cartesian forces followed by cartesian force constants (both in format 6F12.8) from input stream. followed by a blank line. 7 8 9 10 Use semiempirical force constants. Use unit matrix (default for L105; only recognized by 103). Estimate force constants using valence force field. Use unit matrix throughout.IOp(1/11)L103: TEST OF CURVATURE. BOMB THE JOB IF THE SECOND SECOND DERIVATIVE MATRIX HAS THE WRONG NUMBER OF NEGATIVE EIGENVALUES. 0 DEFAULT (TEST for z-matrix or cartesian TS but not for LST/QST or for minimum). 1 2 DON'T TEST. TEST.L117: Scaling Factor for Determining Overlaps of VDW atoms -1 0 N Turn off scaling Default is 1.010 1.000 + N*(0.001)Step size for ABM method in Trudge for isodensity method. 0 N 0.05 (N=2) 0.1/NIOp(1/12)L103: OPTIMIZATION CONTROL PARAMETERS 0 USE DEFAULT VALUES1 READ IN NEW VALUES FOR ALL PARAMETERS (SEE INITBS)IOp(1/13)L103,L113,L114,L115: Type of Hessian Update: 0 Default (9 for L103 minimization, 7 for L103 TS, D2Corr and L115, Powell for L113 and L114). 1 2 3 4 5 6 7 8 9 Powell (not in L103). BFGS (not in L103) BFGS, safeguarding positive definateness (not inL103 or L115) D2Corr (New, only in L103 and L115). D2Corr (Old, only in L103 and L115). D2Corr (BFGS) D2Corr (Bofill Powell+MS for transition states). D2Corr (No update, use initial Hessian). D2Corr (New if energy rises, otherwise BFGS).L121: Multi-time step parameter (NDtrC,NDtrP) 0 NN No multi-time stepping Iterate density constraints NN times per stepMM00 Do gradient once every MM stepsIOp(1/14)L103: Max. number of bad steps to allow before attempting a linear minimization (i.e., no quadratic step). 0 N Default (0 for TS, 1 for minima). Allow N -- linear only starts with the N+1st.IOp(1/15)L103,L109: ABORT IF DERIVATIVES TOO LARGE -1 or 0 N No force test at all. FMAXT = 0.1 * NIOp(1/16)L103,L113,L114: MAXIMUM ALLOWABLE MAGNITUDE OF THE EIGENVALUESOF THE SECOND DERIVATIVE MATRIX. IF THE LIMIT IS EXCEEDED, THE SIZE OF THE EIGENVALUE IS REDUCED TO THE MAXIMUM, AND PROCESSING CONTINUES. 0 N EIGMAX = 25.0 HARTREE / BOHR**2 OR RADIAN**2 EIGMAX = 0.1 * NIOp(1/17)L103,L113,L114: MINIMUM ALLOWABLE MAGNITUDE OF THE EIGENVALUES OF THE SECOND DERIVATIVE MATRIX. SIMMILAR TO IOp(16) 0 N EIGMIN = 0.0001 EIGMIN = 1. / NIOp(1/18)L103: Coordinate system. 0 Proceed normally1 Second derivatives will be computed as directed on the variable definition cards. No optimization will occur. 10 20 30 40 Do optimization in cartesian coordinates. Do full optimization in redundant internal coord. Do full optimization in pruned distance matrix coords. Do optimization in Z-matrix coordinates.50 Do full optimization in redundant internal coords with large molecular tools. 100 1000 2000 3000 Read the AddRedundant input section for each structure. Do not define H-bonds Define H-bonds with no related coordinates (default) Define H-bonds and related coordinates10000 Reduce the number of redundant internals 20000 Define all redundant internals 100000 0000000 Old definition of redundant internals. Default (2000000).1000000 Skip MM atoms in internal coordinate definitions and do microiterations the old way, in L103. 2000000 Include MM atoms in internal coordinate definitions (no microiterations). 3000000 Skip MM atoms in internal coordinate definitions and do microiterations the new way, in L120. 4000000 Microiterations for pure MM, done in L402.IOp(1/19)L103: SEARCH SELECTION 0 2 Default (same as 6). LINEAR AND STEEPEST DESCENT.3 STEEPEST DESCENT AND LINEAR ONLY WHEN ESSENTIAL. 4 5 6 7 8 9 10 11 13 Quadratic if curvature is correct; RFO if not. Linear as usual. Quadratic if curvature is correct; RFO if not. No linear search. RFO and linear. RFO without linear. Newton-Raphson and linear. Newton-Raphson only. GDIIS and linear GDIIS only. First-order simultaneous optimization.L113,L114: Search Selection: 0 P-RFO OR RFO STEP ONLY (DEFAULT)1 P-RFO OR RFO STEP FOR "WRONG" HESSIAN OTHERWISE NEWTON-RAPHSONIOp(1/20)L101, L106, L108, L109, L110: INPUT UNITS 0 1 2 3 ANGSTROMS DEGREES BOHRS DEGREESANGSTROMS RADIANS BOHRS RADIANSIOp(1/21)L103,L113,L114: EXPERT SWITCH. 0 NORMAL MODE.1 EXPERT MODE: CERTAIN CUTOFFS USED TO CONTROL THE OPTIMIZATION WILL BE RELAXED. THESE INCLUDE FMAXT, DXMAXT, EIGMAX AND EIGMIN.IOp(1/22)L107: Whether to reorder coordinates for maximum coincidence. 0 1 2 Yes. Assume reactant order equals product order. Read in a re-ordering vector from the input.L115: KIND OF SEARCH: 0 1 2 3 4 5 6 7 BOTH DIRECTIONS AND GENERATE SEARCH VECTOR FORWARD DIRECTION AND GENERATE S. VECTOR BACKWARD DIRECTION AND GENERATE S. VECTOR BOTH DIRECTIONS AND GENERATE S. VECTOR FORWARD DIRECTION AND READ S. VECTOR 8F10.6 FORWARD DIRECTION AND READ S. VECTOR 8F10.6 BACKWARD DIRECTION AND READ S. VECTOR 8F10.6 BOTH DIRECTIONS AND READ S. VECTOR 8F10.6IOp(1/23)L112: Derivative availability. 0 1 2 Energy only. Energy + Forces. Energy + Forces + Force constantsIOp(1/24)Whether to round tetrahedral angles. 0 1 2 Default (Yes). Yes, round angles within 0.001 degree. No.IOp(1/25)Wether SCRF is used with numerical polarizability: 0 1 No. Yes, the field in /Gen/ must be cleared each time.IOp(1/26)Accuracy of function being optimized: -NNMM Energy 10**-(NN), Gradient 10**-(MM). -1 0 1 2 3 Read in values Default (same as 1). Normal accuracy for HF (energy and gradient both 1.d-7). Standard grid accuracy for DFT (Energy 1.d-5, gradient 1.d-4) Fine grid accuracy for DFT (Energy 1.d-7, gradient 1.d-6)IOp(1/27)= IJKL (i.e. 1000*I+100*J+10*K+L) Transition state searching using QST and redundant internal coordinates L= 0,1 Input one structure, either initial guess of the minimizing structure or transition structure without QST. L= 2 Input 2 structures, the first one is the reactant, the second one is the product. The union of the two redundant coordinates are taken as the redundant coords for the TS. The values of the TS coord are estimated by interpolating the sturcture of R and P. R and P are used to guide the QST optimization of the TS. L= 3 Input 3 structures. The first one is reactant the second one is the product. The third one is the initial guess of the transition structure. R and P are used to guide the QST optimization of the TS. K = 1-9 Interpolation of initial guess of TS between R and P (TS=0.1*J*R + 0.1*(10-J)*P, default J=5) J=1 J=2 J=3 J=4 LST constraint in internals QST constraint in internals LST constraint in distance matrix space QST constraint in distance matrix spaceI = 0-9 Control parameters for climbing phase of QST (e.g. QSTRad = 0.01*I, default QSTrad = 0.05)IOp(1/28)L103: Number of translations and rotations to remove during redundant coordinate transformations: -2 -1 0 N 0. Normal (6 or 5 for linear molecules). Default, same as -1. N.IOp(1/29)L101: SPECIFICATION OF NUCLEAR CENTERS 0 BY Z-MATRIX1 BY DIRECT COORDINATE INPUT (must set IOp(29) in L202). 2 GET Z-MATRIX AND VARIABLES FROM THE CHECKPOINT FILE. 3 GET CARTESIAN COORDINATES ONLY FROM THE CHECKPOINT FILE. 4 5 By model builder, model A. By model builder, model B.6 Get Z-matrix from the checkpoint file, but read new values for some variables from the input stream. 7 Get all input (title, charge and multiplicity, structure) from the checkpoint file. 10 000 Print details of the model building process. Default (same as 100).100 Do not abort job if model builder generates a z-matrix with too many variables. 200 Abort job if model builder generates a z-matrix with too many variables. 1000 2000 3000 4000 5000 00000 Read optimization flags in format 50L1 after the z-matrix. Set all optimization flags to optimize. Purge flags except the frozen variables. Rebuild the coordinate system. (2+3) Purge all flags but keep the coordinate definition. Default, same as 10000.10000 Mark Z-matrix constants as frozen variables rather than wired-in constants. 20000 Do not retain symbolic constants.100000 Generate a symbolic z-matrix using all Cartesians if none is present on the checkpoint file (a hack to make IRCs work with Cartesian input). 200000 Same as one, but retain the redudant internal coordinate definitions.IOp(1/30)L103: ARE THE READ-WRITE FILES TO BE UPDATED? THIS OPTION IS SET FOR THE LAST CALL TO 103 IN FREQUENCY CALCULATIONS IN ORDER TO PRESERVE THE VALUES OF THE VARIABLES FOR ARCHIVING. It also suppresses error termination on large gradients. 0 1 YES NOIOp(1/32)TITLE CARD PUNCH CONTROL. 0 1 DON'T PUNCH. PUNCH.IOp(1/33)L101: L102 L103 L106 L109 L110 L113 L114 0 1 OFF ON DEBUG PRINTIOp(1/34)L101 L102 L103: DEBUG + DUMP PRINT 0 1 OFF ONIOp(1/35)RESTART (L102-L112). 0 NORMAL OPTIMIZATION.1 FIRST POINT OF A RESTART. GET GEOMETRY, WAVEFUNCTION, ET. FROM THE CHECKPOINT FILE.IOp(1/36)CHECKPOINT. 0 1 NORMAL CHECKPOINT OF OPTIMIZATION. SUPPRESS CHECKPOINTING.IOp(1/37)D2E CLEANUP (obsolete) 0 NO CLEANUP.1 THIS IS THE LAST POINT AT WHICH ANALYTIC SECOND DERIVATIVES WILL BE DONE. DELETE THE D2E FILE AND THE BUCKETS AND TRUNCATE THE READ/WRITE FILES.IOp(1/38)Entry control option (currently only by L106, L107, L108, L109, L110, L111, and L112 but not L102, L103, and L105). 0 1 N>1 . Continuation of run. Initial entry. In L103: Initial entry of guided optimization using N levels.N0 In L106: differentiate Nth derivatives once. In L110 and L111: differentiate energy N times. 000 100 200 In L106: differentiate wrt nuclear coordinates. In L106: differentiate wrt electric field. In L106: differentiate wrt field and nuclear.IOp(1/39)Step size control for numerical differentiation. (L106, L109, L110, L111). Path step size in L115. 0 Use internal default (0.001 Angstroms in L106, 0.005 A in L109, 0.01 Angstrom in L110, 0.001 au in L111). N Use step-size of 0.0001*N (angstroms in L106, L109, L110, electric field au in L111). -1 Read stepsize (up to 2 for L106, 1 for others), free-format.-N>1 Use step-size of 0.0001*N atomic units everywhere.IOp(1/40)L113, L114: Hessian recalculation. -1 0 N Pick up analytic second derivatives every time. Just update. The default, execpt for CalcAll. Recalculation the Hessian every N steps.L116: Whether to read initial E-field: 0 1 2 Start with 0.0. Read from checkpoint file. Read from input stream.IOp(1/41)Step number of optimization from which to take geometry. -1 for the initial geometryIOp(1/42)L103, L115: Number of points along the reaction path in each direction. Default is 6. L117: Cutoff to be used in evaluating densities. 0 N 1.0D-10 1.0D-NIOp(1/43)L116: Extent of Reaction Field. 0 1 2 3 Dipole Quadrupole Octapole HexadecapoleL117: How to define Radii 0 1 2 10 20 30 Default is 11 Use internally stored Radii, centers will be on atoms Read-in centers and radii on cards Force Merz-Kollman radii (Default) Force CHELP (Francl) recommended radii. Force CHELPG (Breneman) recommended radii.100 Read in replacement radii for selected atom types as pairs (IAn,Rad) or (Symbol,Rad), terminated by a blank line. 200 Read in replacment radii for selected atoms as pairs (I,Rad), terminated by a blank line. Initial radius of spheres to be placed around attractors to "capture" the gradient trajectories. The final radius is then automatically optimized separately for each atom. 0 NM 0.1 N.M = NM/10IOp(1/44)IRC Type 0 1 2 3 Default (same as 3). Cartesian. Internal. Mass-weighted.L117: Maximum distance between a nucleus and its portion of the isosurface - used in Trudge only to eliminate, from the outset, points which clearly lie in another basin. This parameter should be chosen with the parameter Cont in mind 0 NM 10.0 au N.M au = NM/10L121: Seed for random number generator (ISeed) -1 Use system time initialize iseed (Note each run will give different results) 0 N Use default seed value (ISeed = 398465) Set random number seed to NIOp(1/45)Read isotopes in L115. 0 1 Do not read isotopes. Read Isotopes.IOp(1/46)Order of multipoles in numerical SCRF: 0 1 2 3 Dipole Quadrupole Octapole Hexadecapole.IOp(1/47)Number of redundant internal coordinates to allow for. 0 N Default: 50000 N.IOp(1/48)IRCMax control. 1 20 Do IRCMax Include zero-point energy.CIOp(1/49)Options to IRC path relaxation (IJKL) L 2/1 dont/do optimize reactant structure. Default: 1K2/1 dont/do optimize product structure. Default: 1J 3/2/1 dont/QST3/QST2 optimize TS structure (for QST input). Default: 1 I 2/1 unimolecular/bimolecular reaction. Default: unimolecularIOp(1/52)L101 and L120: Type of ONIOM calculation: 0/1 2 3 00 10 20 100 One layer, normal calculation Two layers Three layers Default (20) Include electrostatics in model systems using MM charges. No electrostatics included in the model systems Do full square for testing.N000 Use atomic charge type N-1 during microiterations. The default is MK charges.IOp(1/53)L120: Action of each invocation of L120: 0 1 Do nothing Set up point MM on rwf from initial data2 Set up point MM on rwf from initial data and restore point MM on chk file if ONIOM data is present there. 3 4 5 6 Restore point M from data on the rwf. Integrate energy Integrate energy and gradient Integrate energy, gradient, and hessian7 Restore point MM from RWF but do not create a new model system. NN0 Save necessary information (some rwf's, energy, gradients, hessian) of point NN of the ONIOM grid. NN = MaxLev**2 + 1 (currently 17) to restore real system. MM000 Calc Level High ||| Mid ||| Low SML 1--3--6 system size 2--5--8 4--7--9* Next point to do is MM.IOp(1/54)Whether to recover initial energy during IRCMax from chk file: 0 1 No. Yes.IOp(1/55)L103: Options for GDIIS: ICos*1000+IChkC*100+IMix*10+Method form. L115: IRC optimization. 0 1 Default, use gradients to find the next geometry. Use displacements to find the next geometry.IOp(1/56)Set of atom type names to parse: 0 1 2 Accept any. Dreiding/UFF. Amber.3 Amber allowing any symbol, for use with parameters in input stream.IOp(1/57)Whether to produce connectivity: 0 Default (4 if reading geom from chk file and connectivity is there, otherwise 3). 1 2 3 4 5 10 No. Yes, read from input stream Yes, generate connectivity. Yes, read from checkpoint file. Yes, read from rwf file. Read modifications.100 Connectivity input is in terms of z-matrix entries, including dummy atoms.IOp(1/58)IRCMax control in L115.IOp(1/59)Update of coordinates in L103 0 1 2 Default (1 for large opt, 2 for regular) New versions. Old version.IOp(1/60)Interpret extra integer and fp values in z-matrix as scan information. 0 1 2 Default (No). Yes. No.IOp(1/61)How ONIOM should leave the rwf at the end of each geomtry: 0 Default (1).1 Normal: leave the rwf set up for the low-level calculation on the real system. 2 MOMM: leave the rwf set up for the real system, but with NBasis and NBsUse for the high-level calc on the model system. Useful for treating the full system as having electrons only on the QM atoms.IOp(1/62)Counterpoise control. NN NN fragments, NN < 50.IOp(1/63)Step in counterpoise calculation: MNN NN = 0 1-NFrag M = order of derivatives (1=Energy, 2=Gradient, Supermolecule Fragments with ghost atomsNFrag+1 - 2*NFrag -- lone fragmentsIOp(1/64)Molecular mechanics force field selection: 0 1 2 3 4 5 6 7 000 100 200 300 None. Dreiding. UFF. AMBER. MM2 (NYI). MM3 (NYI). MMFF (NYI). Quartic fitting field (NYI). Use only hard-wired. Use soft and hard-wired, hard-wired has priority. Use soft and hard-wired, soft has priority. Use only soft. Lowest 2 digits then have no meaning.0000 Do not read modifications to parameter set. 1000 Read modifications to parameter set. 00000 With soft parameters, abort when different parameters match to the same degree. 10000 Use the first when there are equivalent matches. 20000 Use the last when there are equivalent matches. If IOp(67)=3, then the default is to apply soft parameters with higher priority.IOp(1/65)Control of which terms are included in MM, corresponding to the 'classes' in FncInf. 0 1 10 100 1000 10000 Do all (default) Non-bonded Stretching Bending Torsion Out-of-planeIOp(1/66)Whether to generate QEQ charges, over-written the values in AtChMM, or to use the values already there. 0 1 2 00 10 20 000 100 200 Default (2, 1==> 221) Do QEq. Don't do QEq. Default (10) Do for atoms which were not explicitly typed. Do for all atoms regardless of typing. Default (100) Do for atoms which have charge specified or defaulted to 0. Do for all atoms regardless of initial charge.IOp(1/67)Source of MM parameters. 0 1 2 3 Default: 2 if reading geom from chk file, else 1. Generate here, reading from input if requested by IOp(64). Copy from chk file. Pick up non-standard parameters from chk file.IOp(1/70)L118 Type of sampling (Nact) 0 1 2 3 4 Defalt (same as 3) Orthant sampling Microcanonical normal mode sampling Fixed normal mode energy Local mode sampling ( now only Nact = 0 or 3 OK )IOp(1/71)Whether to print out input files for each structure along an IRC: 0 1 No. Yes.IOp(1/72)L103: Algorithm choice for microiterations. L121: Lagrangian constrain method for ADMP (ICType) Half*Gamma*Tr[(P*P-P)**2] + Lambda*[Tr(P)-Ne] + Eta*Tr(P*P-P) 0 Default Same as 7 if no Mass-Weighting (IOp(76) < 0) Same as 10 if Mass-Weighting (IOp(76) > 0) 1 2 Use Lambda and Eta only. (Gamma=0) Use Lambda, Eta, Gamma. Gamma = .23 Use Lambda, Eta, Gamma. Gamma = 1. Constraints for scalar Mass case: 4 Use exact constraint Sum(ij)[Vij*(P**2-P)ij]5-7 Iterative Scheme same as 4. Different initial guesses. 7 is default for scalar mass case. Constraints for tensorial Mass: 8-11 Mass-weighting constraints. Documentation maybe found in DVelV1. 10 is default.IOp(1/73)L103: NInit for microiterations. L121: Initial Kinetic energy of the Nuclei (EStrtC) 0 Default (.1 Hartree)N>0 N*micro-Hartree N<0 0.0 HartreeIOp(1/74)Charge scaling for charge embedding in ONIOM. IJKLMN 6th through 1st nearest neighbors of current layer scaled by I*0.2, J*0.2, etc. 0 ==> 5 (no scaling); all layers are scaled by at least as much as ones farther out. The default is 500. M L0 Factor for charges one bond away from link atom Factor for charges two bonds away from link atomK00 Factor for charges three bonds away from link atom IJ etc. The actual factors used are: 0: 1.0 1: 0.0 2: 0.2 3: 0.4 4: 0.6 5: 0.8 6-9: 1.0IOp(1/75)ADMP control flag (ICntrl) 0 1 2 3 00 10 20 Standard ADMP Read converged density at every step Fix the nuclear coordinates Test time reversability (MaxStp must be even) Default (20). Read stopping parameters from input. Do not read stopping parameters.IOp(1/76)+/- XXXXZYYYY = Ficticous electron mass (EMass) YYYY Default (1000) IOp(76)>0 YYYY*.0001 AMU MW core functions more than valence functions. IOp(76)<0 YYYY*.0001 AMU. Use uniform scaling for all basis functions (Note YYYY > 9999 makes no sense) Z Mass-weighting option. If IOp(76)<0, Z is meaningless.XXXX If PBC: Mass of Box Coordinates (BoxMas) = XXXX*.0001 AMU BoxMas=0 Box coordinates not propagated (default).IOp(1/77)Initial Kinetic energy of the density matrix (EStrtP) (For UHF, Alpha and Beta each get half this energy) and Option Number to compute initial kinetic energy. Format of Input: XXYYYY (six digits) IWType = XX N = YYYY (For UHF, Alpha and Beta each get half this energy) 0 Default (0.0 Hartree)N>0 N*micro-Hartree IWType is used to figure out how the initial velocity is is computed (in gnvelp). If XXYYYY < 0 : Initial velocity = 0.0 Hartee (i.e., currently same as N=0 above)IOp(1/78)Sparse in L121 -N 0 1 Sparse here with cutoff 10**(-N), full elsewhere Use full matrices or spase based on standard settings. Use sparse fixed formIOp(1/79)IRCMax convergence in L115 Stopping criteria in L118 and L121.IOp(1/80)L106: 0/1/2 Cartesian/Normal mode/Internal coordinate differentiation. 2 is NYI. L118: .eq.1 to surpress the 5th order correction after surface hop has been made in Trajectory Surface Hopping calculations. Needs also IOp(10/80=1) Nuclear Kinetic Energy Thermostat Option. (Currently only Velocity scaling is implemented) 0 No Thermostat.11XXXXX Velocity scaling, but only for the first XXXXX simulation steps. (This options is useful, if thermostating in only required during equilibration. 1000000 Velocity scaling, all the way through the simulation.IOp(1/81)Nuclear KE thermostat in ADMP -- temperate is checked and scaled every IOp(81) steps.IOp(1/82)Temperature for nuclear KE thermostat in L121.IOp(1/83)Whether to read in frequencies for electric and magnetic perturbations. 0 1 2 Default (No). Yes. No.IOp(1/84)Differentiation of frequency-dependent properties. 0 N No. Mask for which properties on file 721 will be differentiated.IOp(1/85)Band gap calculation in PBC ADMP: 0 1 2 Default (No). Diagonalizae Fock matrix to get band gap, evolution, etc. No.IOp(1/86)Printing for NMR for ONIOM. 0 1 2 Default (1). Print tensors and eigenvalues. Print eigenvectors as well.IOp(1/87)ONIOM integration of density. 0 1 2 K0 L00 Do not integrate. Integrate current densities. Integrate densities specified by following digits: Density to use from gridpoint 1 Density to use from gridpoint 2M000 etc. K,L,M,etc: 0: SCF 1: MP first order 2: MP2 3: MP3 4: MP4 5: CI one-particle 6: CI 7: QCI/CC 8: Correct to second orderIOp(1/88)Whether to read in atomic masses (isotopes): 0 Default (1 if geometry read from input, 4 if geometry read from chk) 1 Use most abundant isotopes.2 Read isotopes from input. The temperature and pressure are read first, for backwards compatibility. 3 4 Read isotopes from rwf. Read isotopes from chk.IOp(1/89)Maximum allowed deviation from average nuclear KE during ADMP, in Kelvin.IOp(1/90)To read in the velocity in cartesian coordinates Nuclear Kinetic Energy Thermostat Option. Average energy (in microhartree) to be maintained during Simulation, as required by IOp(80).IOp(1/91)Thermostat Option.IOp(1/92)Maximum allowed deviation from average nuclear KE specified in IOp(81). Also in microhartree. IOp(1/94, 95, 96, 97, 98) IOp(94): Davidson control for quadratic micro-iterations (see MMOpt2) IOp(95): RFO/Davidson control for quadratic microiterations (see MMOpt2) IOp(96): Davidson control for coupled QM/MM macro step (see MMOpt2)IOp(97):RFO/Davidson control for coupled QM/MM macro step (see MMOpt2)IOp(98):Control of quadratic micro-iterations and coupled QM/MM quadratic macro step. <0 0 1 2 3 4 5 10 20 30 40 50 Do not use dynamic convergence criteria for the micro-iterations. Default(15). Regular non-coupled macro step. Coupled macro step, full diagonalization. Coupled macro step, direct /w full Hessian incore. Coupled macro step, direct /w MM Hessian incore. Coupled macro step, fully direct. Regular micro-iterations. Quadratic micro-iterations, full diagonalization. Quadratic micro-iterations, direct /w prepared Hessian incore. Quadratic micro-iterations, direct /w raw MM Hessian incore. Quadratic micro-iterations, fully direct.IOp(1/101, 102, 103, 104)Phase control in L115 and L118: N1, N2, N3, N4IOp(1/105)Reaction direction 00 10 Default (Same as 10) Forward direction20 Reverse direction Damped-Velocity Verlet (DVV) options for Dynamic Reaction Path Following 0 1 2 00 10 20 000 100 200 step 300 0000 1000 2000 Default (Same as 2) Use DVV Do not use DVV Default (Same as 10) Follow the rxn path in the forward direction Follow the rxn path in the reverse direction Default (Same as 200) Time step correction not used Time step correction used but not to recalculate current DVVTime step correction used and current DVV step recalculated Default (Same as 1000) Use DVV stopping criteria Do NOT use DVV stopping criteriaIOp(1/106)Damping constant for DVV Dynamic Rxn Path following (v0) 0 N Default v0=0.04 (N=400) v0 is set to N*0.0001IOp(1/107)Error tolerance for DVV time step correction (Error) 0 N Default Error=0.003 (N=30) Error=N*0.0001IOp(1/108)Gradient magnitude for DVV stopping criteria (Crit1) 0 N Default (N=15) N*0.0001IOp(1/109)Force-Velocity angle for DVV stopping criteria (Crit2) 0 N Default (90 Degrees) Use N DegreesIOp(1/110)Scaling of rigid fragment steps during microiterations. 0 1 2 -n Do not scale Scale with 1/NRA (NRA = number of atoms in fragment)Scale with 1/Sqrt(NRA) Scale with 1/nIOp(1/111)Step-size to use with steepest descent when L103 is having trouble: -N -1 0 N Scale up to RMS step of N/1000 if DXRMS is less. Effectively disables the scaling Default (50) Scale up or down to maximum change in a variable of N/1000IOp(1/112)Temperature for thermochemistry. 0 N Default (standard temperature, unless read in). N/1000 degrees.IOp(1/113)Pressure for thermochemistry. 0 N Default (1 atomosphere, unless read in). N/1000 atmospheres.IOp(1/114)Scale factor for harmonic frequencies for use in thermochemistry and harmonic vibration-rotation analysis. 0 N Default (1 unless specified by IOp in overlay 7 or read in). N/1000000.。
衡量芳香性的方法以及在Multiwfn中的计算
衡量芳香性的方法以及在Multiwfn中的计算补充:在此文撰文之后Multiwfn又支持了ICSS方法图形化分析芳香性,见此贴《通过Multiwfn绘制等化学屏蔽表面研究芳香性》(/sobereva/item/9e672259b67d4d9408be1768)衡量芳香性的方法以及在Multiwfn中的计算文/SoberevaFirst release: 2013-Jan-23 Last update: 2014-Nov-20图文摘要本文首先先介绍芳香性的基本概念,然后对比较重要、目前比较流行的和近年来新提出的衡量芳香性的方法依次进行介绍,并谈谈笔者的看法。
其中可以在Multiwfn程序中实现的方法会介绍操作过程。
最后对实际应用中芳香性指标的选择进行讨论。
1 什么是芳香性芳香性是一个十分古老,重要,又含糊的化学概念。
苯是最具典型的芳香性分子,也是芳香性的原型分子。
与芳香性有关的文章近十几年来增速十分迅猛,如今可以说已经过热、被过分炒作。
新的衡量芳香性的指标也不断被提出,同样在近年来增速迅猛,目前总计已有数十种。
这些指标体现了芳香性的不同侧面,其中绝大部分依赖于量子化学计算。
芳香性难以给出一个确切、唯一的定义,实际上芳香性这个词包含的内容被不断地广义化,以至于越来越不可能给出一个既简单、精确又能被所有研究者接受的定义。
芳香性分子在能量、结构、反应性、磁性质、电子结构等方面都展现出独特的特征。
对于大量芳香性体系,利用统计分析,可以发现它们总是同时具有很多特征,如:键长均衡化、电子呈高度整体离域性、外磁场下能形成整体诱导环电流、有较大离域化能、结构稳定等等,因此这样来看只要考察某分子的某个方面特征就能衡量其芳香性高低。
但是对于不少分子,它们具有的各种特征之间的相关性并不满足上述大规律,这被称为芳香性的多维性,因此为了合理地描述芳香性就不得不同时考虑数种基于分子不同性质的芳香性指标。
下面的表格列举了芳香性、非芳香性和反芳香性体系一部分常见特征,有的内容并不很准确,仅供参考,取自Chem.Rev.,105,3716(2005)。
合同标准型 线性代数
合同标准型线性代数Linear algebra is an important branch of mathematics that deals with the study of vectors, vector spaces, linear transformations, and systems of linear equations. 线性代数是数学的一个重要分支,它研究向量、向量空间、线性变换和线性方程组。
It is a fundamental subject that has applications in various fields such as physics, engineering, computer science, and economics. 这是一个基本学科,在物理学、工程学、计算机科学和经济学等各个领域都具有应用。
Understanding the concepts and principles of linear algebra is crucial for students and professionals in these fields. 理解线性代数的概念和原理对于这些领域的学生和专业人士至关重要。
One of the key topics in linear algebra is the concept of a vector space. 在线性代数中一个关键的主题是向量空间的概念。
A vector spaceis a set of vectors that satisfy certain properties such as closure under addition and scalar multiplication. 向量空间是一组满足一定性质的向量,例如在加法和数量乘法下封闭。
The properties of vector spaces provide a framework for understanding and working with vectors ina systematic manner. 向量空间的性质为系统地理解和处理向量提供了一个框架。
高斯使用中的问题汇总
⾼斯使⽤中的问题汇总如何从下⾯的Gaussian输出⽂件中找出轨道系数及轨道能!!(新⼿多谢),请帮忙标出来求助]如何从下⾯的Gaussian输出⽂件中找出轨道系数及轨道能!!(新⼿多谢),请帮忙标出来The electronic state is 1-A1.Alpha occ. eigenvalues -- -20.58265 -11.33946 -1.39265 -0.87259 -0.69715 Alpha occ. eigenvalues -- -0.63950 -0.52294 -0.44073Alpha virt. eigenvalues -- 0.13573 0.24842 0.33338 0.37329 0.73660 Alpha virt. eigenvalues -- 0.80783 0.84685 0.94689 1.10445 1.10700 Alpha virt. eigenvalues -- 1.13937 1.27145 1.33529 1.62050 1.78192 Alpha virt. eigenvalues -- 1.79416 1.99239 2.18347 2.23684 2.45514 Alpha virt. eigenvalues -- 2.64513 2.87165 2.97616 3.27576 4.09792 Alpha virt. eigenvalues -- 4.47637Molecular Orbital Coefficients1 2 3 4 5(A1)--O (A1)--O (A1)--O (A1)--O (B2)--O EIGENVALUES -- -20.58265 -11.33946 -1.39265 -0.87259 -0.697151 1 C 1S 0.00000 0.99566 -0.11060 -0.16262 0.000002 2S 0.00047 0.02675 0.20981 0.33995 0.000003 2PX 0.00000 0.00000 0.00000 0.00000 0.000004 2PY 0.00000 0.00000 0.00000 0.00000 0.420175 2PZ -0.00007 0.00066 0.17259 -0.18451 0.000006 3S -0.00024 -0.00743 0.08051 0.31309 0.000007 3PX 0.00000 0.00000 0.00000 0.00000 0.000008 3PY 0.00000 0.00000 0.00000 0.00000 0.157609 3PZ -0.00048 0.00135 -0.01160 -0.07970 0.0000010 4XX -0.00002 -0.00272 -0.01628 -0.01333 0.0000011 4YY -0.00006 -0.00202 -0.01365 0.03019 0.0000012 4ZZ -0.00074 -0.00123 0.03302 -0.00166 0.0000013 4XY 0.00000 0.00000 0.00000 0.00000 0.0000014 4XZ 0.00000 0.00000 0.00000 0.00000 0.0000015 4YZ 0.00000 0.00000 0.00000 0.00000 -0.0139416 2 O 1S 0.99472 -0.00038 -0.19672 0.08889 0.0000017 2S 0.02094 0.00025 0.44184 -0.20351 0.0000018 2PX 0.00000 0.00000 0.00000 0.00000 0.0000019 2PY 0.00000 0.00000 0.00000 0.00000 0.3212220 2PZ -0.00153 -0.00029 -0.13537 -0.14216 0.0000021 3S 0.00436 -0.00058 0.37895 -0.27048 0.0000022 3PX 0.00000 0.00000 0.00000 0.00000 0.0000023 3PY 0.00000 0.00000 0.00000 0.00000 0.1797624 3PZ 0.00006 0.00108 -0.04718 -0.06799 0.0000025 4XX -0.00418 0.00015 -0.00022 -0.00041 0.0000026 4YY -0.00383 -0.00011 -0.00073 -0.00413 0.0000027 4ZZ -0.00356 -0.00019 0.01969 0.00906 0.0000028 4XY 0.00000 0.00000 0.00000 0.00000 0.0000029 4XZ 0.00000 0.00000 0.00000 0.00000 0.0000030 4YZ 0.00000 0.00000 0.00000 0.00000 -0.0233931 3 H 1S -0.00002 -0.00020 0.03017 0.17902 0.1908232 2S -0.00013 0.00210 -0.00537 0.06479 0.1202633 4 H 1S -0.00002 -0.00020 0.03017 0.17902 -0.1908234 2S -0.00013 0.00210 -0.00537 0.06479 -0.120266 7 8 9 10(A1)--O (B1)--O (B2)--O (B1)--V (A1)--V EIGENVALUES -- -0.63950 -0.52294 -0.44073 0.13573 0.248421 1 C 1S 0.01942 0.00000 0.00000 0.00000 -0.122122 2S -0.06075 0.00000 0.00000 0.00000 0.148963 2PX 0.00000 0.32517 0.00000 0.40259 0.000004 2PY 0.00000 0.00000 -0.19811 0.00000 0.000005 2PZ -0.37597 0.00000 0.00000 0.00000 -0.210866 3S 0.03971 0.00000 0.00000 0.00000 1.980967 3PX 0.00000 0.21231 0.00000 0.71124 0.000008 3PY 0.00000 0.00000 -0.04477 0.00000 0.000009 3PZ -0.08856 0.00000 0.00000 0.00000 -0.7497710 4XX 0.00549 0.00000 0.00000 0.00000 -0.0027311 4YY 0.02734 0.00000 0.00000 0.00000 -0.0126512 4ZZ -0.01933 0.00000 0.00000 0.00000 -0.0045913 4XY 0.00000 0.00000 0.00000 0.00000 0.0000014 4XZ 0.00000 0.03558 0.00000 -0.03288 0.0000015 4YZ 0.00000 0.00000 0.06035 0.00000 0.00000Sample Text相关回复:作者: lixiaona158 发布⽇期: 2008-04-03EIGENVALUES 后⾯的数字就是这个轨道对应的能量,但是它的单位是HF,⼀般使的时候需要换成电⼦福特,⽤这个系数乘27.2116就可以了。
找过渡态的基本经验
[交流]找过渡态的一些经验已有10人参与★ ★ ★ ★ ★gmy1990(金币+5): 谢谢分享! 2011-06-06 22:14:36zhou2009:编辑内容 2011-06-22 09:54zhou2009:标题高亮 2011-06-22 10:43小红豆:提升帖子 2011-07-14 18:44小红豆:提升帖子 2011-07-20 19:24小红豆:提升帖子 2011-07-22 19:33最近经常见虫友问关于过渡态怎么找的问题,正好我最近比较郁闷就给大家写个简单的教程,仅限新手入门。
过渡态简单点说就是化学反应中瞬间形成的高自由能的不稳定复合物,形象点说就是就是反应势能面上的一个鞍点,所谓的找过渡态也就是要找到这个反应势能面上的这个鞍点,这里以DA反应作为例子简单说下我用gaussian找过渡态的经验。
Gaussian里面找过渡态主要有3种方法:TS、QST2以及QST3。
这里套用gaussian手册里的说明。
TS是进行过渡态而不是局部最小值的优化计算。
QST2是使用STQN 方法寻找过渡态结构。
这个选项需要输入反应物和产物分子结构,先后通过两组连续的标题和分子说明部分定义。
注意在这两个结构中的原子顺序必需一致。
TS 不能和QST2 合用。
QST3是使用STQN 方法寻找过渡态结构。
这个选项需要输入反应物,产物和最初的过渡态结构,先后由三组连续的标题和分子说明部分定义。
注意在这三个结构中的原子顺序必需一致。
TS 不能和QST3 合用。
接下来贴出几个例子来说明下TS、QST2和QST3的输入文件该怎么写%chk=c2h4_c4h6_ts%nproc=1%mem=200mb# opt=(ts,calcfc) freq=noraman b3lyp/6-31g*Title Card Required0 1C -0.37960200 1.41026100 0.50972400H -0.06409400 1.04025400 1.48028400H -0.26589500 2.48067200 0.40089100C -1.26020300 0.70558300 -0.28508700H -1.84635800 1.22289600 -1.04415700C -1.26023800 -0.70552500 -0.28508700H -1.84641800 -1.22280900 -1.04415900C -0.37967300 -1.41024700 0.50972300H -0.06414500 -1.04025600 1.48028200H -0.26601500 -2.48066300 0.40088700C 1.45648200 0.69084700 -0.25401700H 1.98402400 1.24692000 0.51079100H 1.29283800 1.24312300 -1.17152100C 1.45645300 -0.69091000 -0.25401800H 1.29278400 -1.24317800 -1.17152200H 1.98396500 -1.24700700 0.51079200qst2%chk=c2h4_c4h6_qst2%nproc=1%mem=200mb# opt=(calcfc,qst2) freq=noraman b3lyp/6-31g*Title Card Required0 1C -3.17791906 1.13289796 -1.01187682H -2.64475531 0.20519304 -1.01187682H -4.24791906 1.13289796 -1.01187682 C -2.50264475 2.30787525 -1.01187682 H -3.03580850 3.23558018 -1.01187682 C -0.96264475 2.30787525 -1.01187682 H -0.42948100 3.23558018 -1.01187682 C -0.28040135 1.13693077 -1.01187682 H -0.80804382 0.20607449 -1.01187682 H 0.78957977 1.14328807 -1.01187682 C -2.59776413 0.98894279 1.10133233 H -3.14031063 0.06692559 1.12200992 H -3.12699887 1.91846375 1.07302387 C -1.24260873 0.98347968 1.11087410 H -0.70006223 1.90549689 1.09019651 H -0.71337398 0.05395873 1.13918256Title Card Required0 1C 1.41432400 0.09460100 0.31826800 H 1.42370000 0.10775400 1.42899000 H 2.47445600 0.12780100 0.00402400 C 0.66866000 1.30146700 -0.16992700 H 1.26438900 2.14276400 -0.50621500 C -0.66890700 1.30134300 -0.16992700 H -1.26479300 2.14252900 -0.50621700 C -1.41434600 0.09433800 0.31826600 H -1.42372700 0.10749400 1.42898900 H -2.47448400 0.12734000 0.00402000 C 0.77040400 -1.21422100 -0.17552700 H 1.14229400 -2.05288100 0.44176200 H 1.12544800 -1.41421500 -1.20543600 C -0.77017000 -1.21437000 -0.17552800 H -1.12517200 -1.41443600 -1.20543700 H -1.14189800 -2.05310200 0.44176200qst3%chk=c2h4_c4h6_qst3%nproc=1%mem=200mb# opt=(calcall,qst3,noeigentest) freq=noraman b3lyp/6-31g*Title Card Required0 1C -3.17791906 1.13289796 -1.01187682 H -2.64475531 0.20519304 -1.01187682 H -4.24791906 1.13289796 -1.01187682 C -2.50264475 2.30787525 -1.01187682 H -3.03580850 3.23558018 -1.01187682 C -0.96264475 2.30787525 -1.01187682 H -0.42948100 3.23558018 -1.01187682 C -0.28040135 1.13693077 -1.01187682 H -0.80804382 0.20607449 -1.01187682 H 0.78957977 1.14328807 -1.01187682 C -2.59776413 0.98894279 1.10133233 H -3.14031063 0.06692559 1.12200992 H -3.12699887 1.91846375 1.07302387 C -1.24260873 0.98347968 1.11087410 H -0.70006223 1.90549689 1.09019651 H -0.71337398 0.05395873 1.13918256Title Card Required0 1C 1.41432400 0.09460100 0.31826800 H 1.42370000 0.10775400 1.42899000 H 2.47445600 0.12780100 0.00402400 C 0.66866000 1.30146700 -0.16992700 H 1.26438900 2.14276400 -0.50621500 C -0.66890700 1.30134300 -0.16992700 H -1.26479300 2.14252900 -0.50621700 C -1.41434600 0.09433800 0.31826600 H -1.42372700 0.10749400 1.42898900 H -2.47448400 0.12734000 0.00402000 C 0.77040400 -1.21422100 -0.17552700 H 1.14229400 -2.05288100 0.44176200 H 1.12544800 -1.41421500 -1.20543600 C -0.77017000 -1.21437000 -0.17552800 H -1.12517200 -1.41443600 -1.20543700 H -1.14189800 -2.05310200 0.44176200Title Card Required0 1C 0.39335100 -1.40752200 0.50945100 H 0.07415700 -1.04074500 1.48001500 H 0.28923500 -2.47884000 0.39989000C 1.26702700 -0.69422900 -0.28512700H 1.85846600 -1.20567200 -1.04409200C 1.25346800 0.71680900 -0.28478600H 1.83499300 1.23987800 -1.04346600C 0.36574900 1.41309100 0.50971100H 0.05414500 1.04053600 1.48056200H 0.24248700 2.48246500 0.40066900C -1.45041500 -0.70335800 -0.25427100H -1.97290400 -1.26432600 0.51044000H -1.28115600 -1.25385900 -1.17177300C -1.46240700 0.67835900 -0.25370700H -1.30467900 1.23254800 -1.17112400H -1.99537500 1.22910700 0.51125200这里需要注意下反应物的构型以及产物的构型都必须是优化过的。
线性代数_常用单词词组_中英对照
有限差分
315-317,417
Finite elements
有限元
412,419
First-order system
一阶方程组
315,326
Fixed-free
固定-自由
410,414,417,419
Force balance
平衡力
412
FORTRAN
16,38
Forward difference
Index
A
Addition of vectors
向量的加法
2,3,33,121
All combinations
所有组合
5,122,123
Angle between vectors
向量间的夹角
14,15
Anti-symmetric
(see Skew-symmetric)
反对称
109
Area
面积
272,273,280
Gauss-Seidel
高斯-塞德尔
481,484,485,489
Gene expression data
基因表达数据
457
Geometric series
等比数列
436
Gershgorin circles
格尔什戈林圆
491
Gibbs phenomenon
吉布斯效应
451
Givens rotation
Dependent
相关的
26,27,169,170
Derivative
导数
24,109,229,384,395
Determinant
行列式
matlab工具箱遗传算法使用方法
简单的遗传算法可以使用Matlab自带的遗传算法工具箱,但是要从Matlab2010版本之后才会自带这个工具箱,且调用命令也有变化,分别是gatool和optimtool。
GUI界面如下图所示:1、problem setup and results设置与结果(1)Solver:求解程序,选择要用的求解程序(遗传算法,遗传算法多目标等)(2)problem:1)fitness function适应度函数,求最小,这里的使用度函数要自己编写,书写格式是“@函数名”。
2)number of variable变量数,必须是整数,即,使用这个GUI界面的适应度函数的变量必须是[1*n]的向量,而不能是[m*n]的矩阵。
3)constraints约束4)linear inequalities线性不等式,A*x〈=b形式,其中A是矩阵,b是向量5)linear equalities线性等式,A*x=b形式,其中A是矩阵,b是向量6)bounds定义域,lower下限,upper上限,列向量形式,每一个位置对应一个变量7)nonlinear constraint function非线性约束,用户定义,非线性等式必须写成c=0形式,不等式必须写成c<=0形式8)integer variable indices整型变量标记约束,使用该项时Aeq和beq必须为空,所有非线性约束函数必须返回一个空值,种群类型必须是实数编码举例,若是想让第一个、第三个、第五个变量保持是整数的话,则直接在此处填写[1 3 5]9)run solver and view results求解use random states from previous run使用前次的状态运行,完全重复前次运行的过程和结果2、population(1)population type编码类型1)double vector实数编码,采用双精度。
整数规划的种群类型必须是实数编码。
第三章Gaussian软件使用new
例6: 乙炔分子 直线形分子
第三章Gaussian软件使用new
练习
• 写出分子 H2C=C=O分子输入坐标 • 其中C=C: 1.35 C=O: 1.20 C-H: 1.09 • 写出苯分子内坐标 • C=C: 1.30 C-H: 1.09
第三章Gaussian软件使用new
Gaussian的文件
• Gjf 计算任务文件 • Chk 临时文件 • Rwf 读写文件 • Out 输出文件
第三章Gaussian软件使用new
Gaussian程序界面和输入文件的构造
第三章Gaussian软件使用new
Gaussian作业的格式
%chk=water.chk %rwf=water.rwf #p hf/6-31g scfcyc=250 scfcon=8
变量部分
a1=105.0
d1=120.0
d1=120.0
r2=1.4
常量部分
通过对两个键长和键角使用同
一变量定义可以控制分子的对
通过设定常量,可以使程序
称性
-转动耦合 • 电子亲和能和电离势 • 极化和超极化率(静态的
和含频的) • 静电势和电子密度 • NMR 屏蔽和磁化系数 • 自旋-自旋耦合常数
第三章Gaussian软件使用new
几何构型的构建
GaussianView
第三章Gaussian软件使用new
例1:使用HF方法,优化 H2O2分子
第三章Gaussian软件使用new
相互作用 CI CI
超超HFHF
微扰处理 微扰处理 多组态 自多洽组场态 自洽场
基组的选择
第三章Gaussian软件使用new
➢ Route Section采用自由格式,大小写不敏感
Gaussian软件应用激发态计算
Gaussian软件应用——激发态计算第九章激发态计算本章探讨激发态的计算.激发态是指分子体系的稳定的,高能级的电子结构状态. 比如在高能紫外可见光谱中的激发态的分子.激发态在化学的很多领域都有用, 包括光化学,电子光谱.对于激发态分子的模拟是困难的,因为很难避免体系向基态变化.模拟激发态的理论很少,在Gaussian中,提供的是结构相关方法(Configuration Interaction approach),采用Hartree-Fock单置换,所以也被称为CI-Singles.这一方法被认为是很多分子激发态的零级处理的有效方法.在定性上有比较好的结果,但在定量方面,并不总是好的.和Hartree-Fock方法一样,CI-Singles方法也不昂贵.9.1 运行激发态计算下面是激发态计算的关键词CIS 进行CI-Silgles激发态计算,这是方法关键词,在其前面可以加上R和U作为闭壳层分子和开壳层分子的标识.CIS=(Root=n) 确定研究哪一个激发态,默认为1CIS=(NStates=n) 确定研究的激发态的数量.默认为3CIS=50-50 同时计算单重态和三重态.Triplets选项为计算单重态,默认为单重态.当选择Triplets时,一定要设置NStates数量.CIS=Read 从临时文件中读入初始猜测.用于利用前一个工作中的结果进行计算,与Guess=Read和Geom=Check一起使用.Density=Current 要求计算激发态的布局分析Pop=Reg 要求较详细的布局分析结果,包括分子轨道系数例9.1 文件e9_01 乙烯的激发态本例计算乙烯的最低的四个激发态.乙烯的激发态已经有了很好的研究,最低的四个如下多重度Modern标记Mulliken标记跃迁1 3 B1u T pi --> pi*2 3 B3u TR pi --> 3s3 1 B3u R pi --> 3s4 1 B1u V pi --> pi*计算设置如下# RCIS=(NStates=2, 50-50)/6-31+G(d) Test由于即需要单重态,也需要三重态,所以设置50-50,每个状态计算两个.注意这里使用了弥散基组,弥散基组在计算过渡态方面有好的结果.输出文件中有Excited State 1: Triplet-B1U 3.7768eV 328.27 nm f=0.000多重度对称性激发能振荡强度8 --> 11 0.52952跃迁轨道数激发态波函数系数8 --> 17 -0.45942This State for optimization and/or second-order correction:Total Energy, E(Cis) = -77.8969983928激发态能量Copying the Cisingles density for this state as the1-particle RhoCI density.计算结果是1 2 3 4对称性3B1u 3B3u 1B3u 1B1u能量3.78 7.43 7.83 7.98实验值4.36 7.66 6.98 7.15总的说计算的结果与实验值符合的不错,更加精确的结果就需要大的基组计算了.9.2 激发态优化和频率分析在Gaussian中可以进行激发态的优化和频率分析.步骤是,首先进行能量计算得到激发态,然后在此结构基础上进行结构优化和频率分析例9.2 文件e9_02 甲醛的激发态优化下面是输入文件%Chk=es_form#T RCIS/6-31+G(d) Testformaldehyde Excited States0 1Ground sate molecule specification--Link1--%Chk=se_form%NoSave#T RCIS(Root=1,Read)/6-31+G(d) Opt Freq Geom=Check Guess=Read Test第一个步骤计算最低的三个激发态,第二步骤是利用其结果进行结构优化和频率分析在本例的计算中,得到的激发态出现了虚频,其结构显示碳原子要离开原子平面. 由于原来的分子结构中,所有原子都在同一平面上,所以,也得到一个共平面的激发态结构.这样,就要设法产生一个正确的几个结构.(激发态的结构优化目前没有包含内坐标冗余,所以在初始结构中定义一个平面结构,得到的激发态结构就也是共平面的).我们将在练习9.2中继续讨论.练习练习9.1 文件9_01 亚甲基环丙烯的激发态亚甲基环丙烯在二十世纪八十年代中期发现的,其紫外光谱有三个峰,位置(nm) 对称性能量(ev) 相对面积309 1B2 4.01 0.2242 1B1 5.12 0.01206 1A1 6.02 1.5该分析结构如下H H\ /C1||C2/ \C3==C4/ \H H半经验方法的计算结果显示在1A1下面另一个1B1的激发态,最初的解释为其可能被206峰掩盖了.在MP2/6-31G(d)水平进行结构优化,然后进行激发态计算# RCIS(NStates=5)/6-31+G(d) Density=All Test得到了五个激发态,如下状态对称性能量(eV) 强度1 1B2 5.48 4.01 0.052 1B1 5.91 5.12 0.023 1A2 6.30 0.04 1B1 6.38 0.035 1A1 6.41 6.02 0.37得到的一,二,五三个激发态都与实验符合.对于第三个和第四个,第三个激发态的强度为零,自然观测不到,第四个激发态的强度很弱,而且与第五个激发态位置相近,也被其掩盖了.下面得到的是偶极矩和原子电荷方法偶极矩C1 C2 C3 C4SCF -2.39z -0.5 -0.2 -0.1 -0.1CI 1-Particle 4.75z -0.004 -0.06 -0.4 -0.4CI 2.56z -0.2 -0.2 -0.3 -0.3两个激发态偶极矩计算的结果都表明偶极矩的符号变化,其中CI 1-particle方法夸大了这一变化,这表明了在激发态电子密度的迁移.这一计算偶极矩的方法仍然利用了传统的方法,由于其根据波函数的平方来进行计算,就倾向于产生这样的趋势.据此,我们强烈推荐采用波函数的解析导数来进行偶极矩计算.设置为Density=CI或在CI-Silgles中的Density=Current练习9.2 文件9_02 甲醛的激发态优化确定甲醛第一激发态的结构,比较红外光谱.下面是分子的Z-矩阵CO 1 RCOX 1 1.0 2 ACOH 1 RCH 3 ACH 2 90.H 1 RCH 3 ACH 2 -90.RCO=1.25RCH=1.08ACO=145.0ACH=60.这里使用了虚原子,使得对于分子的描述更加简单,这个分子也不再是共平面的结构.计算采用校正因子0.8929,结果如下计算值校正值实验值平面外弯曲495 442 683CH2摇摆978 873 898CH2剪式1426 1273 1290CO伸缩1647 1471 1173对称CH伸缩3200 2857 2847反对称CH伸缩3295 2942 2968基本与实验值相符练习9.3 文件9_03 丙烯醛的激发态优化丙烯醛的激发态结构仍然是平面结构练习9.4 文件9_04a~b 苯的激发态优化在CI-Singlets方法的研究过程中,有这样的文字,进一步,我们可以得出结论,CI-Singlets方法的成功很大程度上依赖所选用的基组,弥撒的激发态往往需要在分裂的价键轨道基组上增加弥散函数.苯是这一结论的好的例子.苯的激发态研究也显示了如下两点* 理论预测必须与高精度的实验比较.允许跃迁可以与普通的单光子光谱结果比较,但禁阻跃迁要有多光子实验证明.* 当需要确定预测的和观测的状态时,必须应用激发态的对称性.一般的,Gaussian提供激发态的对称性,但当不能提供时,需要检验跃迁的波函数.本例中,没有使用弥散基组得到的激发态与实验结果相差较大,缺少了三个低能量的激发态,而使用弥散基组的计算结果与实验吻合较好.练习9.5 文件9_05a~b 使用CASSCF方法研究激发态练习使用CASSCF(Conplete Active Space Multiconfiguration SCF)方法.研究体系为练习9.3研究的丙烯醛.这练习9.3中,第一激发态的能量相差较大,本练习试图寻找减小误差的办法.CASSCF计算在SCF计算基础上增加了完全电子相关计算.由于SCF计算有倾向基态的趋势,CASSCF是其的改进.关键词就是CASSCF,需要两个参数,活性空间的(Active Space)电子数量和轨道数量.活性空间指CI计算中的轨道.活性空间的电子从HOMO轨道中取得,轨道由活性空间电子的HOMO轨道和一些LUMO轨道组成.例如一个单重态体系的CASSCF(4,6),表示活性空间由两个HOMO轨道(4个电子), 和4个LUMO轨道组成.Guess=Alter用于指定组成活性空间的轨道.一个快速的Guess=Only和/或Pop=Full计算用于生成具体的轨道信息,来确定参与活性空间的轨道.采用CASSCF方法确定丙烯醛的第一激发态能量,需要如下步骤,* 运行UHF/STO-3G Pop=NaturalOrbitals计算三重态丙烯醛的初始轨道和对称性,选择将要组成活性空间的轨道.由于第一激发态电子由氧原子的孤对电子跃迁到CO键的pi轨道,所需要的组成活性空间的轨道就要包括氧的孤对电子以及羰基的pi轨道.* 在6-31G(d)基组确定基态和激发态的能量.由于CASSCF波函数很难收敛,我们需要做如下工作* 运行CASSCF(6,5,UNO)/STO-3G Guess=(Read, Alter)计算三重态丙烯醛,改进临时文件中的轨道.之所以采用三重态,是因为它比较容易收敛.* 从STO-3G的波函数,6-31G(d)基组进行第二个计算.* 采用6-31G(d)基组计算能量,然后,在前一个计算得到的波函数基础上,设置多重度为1,Geom=Check,进行计算,这里需要给出NRoot=2来确定激发态.* 运行另一个CASSCF(6,5)/6-31G(d)计算得到基态能量,方法与得到激发态结果的方法相同.CASSCF方法不再是个黑箱子,它需要使用者的参与,而且必须很小心,很有耐心.注意从默认的猜测进行的CASSCF计算几乎肯定是要失败的.选择合适的活性空间轨道需要对所研究的体系有深刻的认识.下面是计算的具体方法首先是第一组计算,检验轨道,确定活性空间组成.%Chk=acro_cas#T UHF/STO-3G Test Pop=NaturalOrbotalsUHF on triplet acrolein at CAS(6,5) 6-31G(d) geometry0 3molecule specification--Link1--%Chk=acro_cas%Chk=acro_cas#T CAS(6,5,UNO) Guess=(Read,Only) Test Geom=Check...下面是从第二次得到的收敛的波函数的对称性.Orbital Symmetries:Occupied (A') (A') (A') (A') (A') (A") (A') (A') (A')(A') (A') (A') (A") (A') (A")Virtual (A") (A') (A') (A') (A') (A') (A') (A')活性空间将要由4个最高占据轨道和一个最低空轨道组成.我们需要四个A"和一个A'轨道,这样,我们就必须讲第6号轨道与13或15号轨道置换.这样,我们就必须检验这些轨道究竟代表什么,在分子的什么地方.这里,15号轨道在氧原子的2px,2py轨道上有很大的系数,而其他几乎为零,所以需要保留这条轨道.这样,就要置换6和13号轨道,输入文件如下%Chk=acro_cas#T CAS(6,5,UNO)/STO-3G Test Geom=Check Guess=(Read,Alter)CAS 6,5 Using triplet UNO orbitals0 3! Bring A" into the active space6 13这个计算的输出文件就是新的三重态的CASSCF表述.我们要用这个结果进行进一步的计算,首先是更大基组的CASSCF计算,然后是单重态的CASSCF计算. --Link1--%Chk=acro_cas%Chk=acro_cas#T CAS(6,5)/6-31G(d) Test Geom=Check Guess=ReadCAS 6,5 in extended basis set0 3--Link1--%Chk=acro_cas#T CAS(6,5,NRoot=2)/6-31G(d) Test Geom=Check Guess=Read)Singlet n-pi state (should have similar orbitals)0 1最后是基态的能量计算--Link1--%Chk=acro_cas%NoSave#T CAS(6,5)/6-31G(d) Test Geom=Check Guess=ReadGround state starting from excited state orbitals0 1最终得到的能量差是4.035eV,与实验值3.71eV比较,已经很接近了.练习9.6 文件9_06a~d CASSCF方法研究丁二烯光化学当光照射丁二烯分子时,分子由基态升至激发态,然后激发态又要通过一个非辐射(不发射光子)衰减回到基态势能面.这个非辐射衰减有两个方法解释.传统观点认为分子从激发态的势能面通过其和基态势能面的最接近的点转到基态的势能面,这一点上,激发态的势能面仅比基态势能面高一点.另外的观点认为,存在一个区域,两个势能面相交,跃迁在相交的区域完成.具体描述可以是,丁二烯(包括顺式和反式,我们这里讨论的是顺式)首先受激跃迁至第一激发态,这一激发态是单重态的1Bu状态,表示的是pi体系的HOMO到LUMO的跃迁.第二激发态是1Ag状态,表示的是HOMO到LUMO的双重跃迁,这两个激发态的顺序并不清楚,但是1Bu在飞秒的时间内很快转换到1Ag.然后反应从1Ag状态的势能面变化到接近,穿过基态的势能面,在接近或穿过基态势能面的时候,分子降到基态.本练习只研究这个体系的一小部分,在基态结构下研究三个状态的相对能量,并确定两个势能面相交的点.对于基态,完成如下步骤,* 在RHF/3-21G水平检验轨道,来确定活性空间.这里将采用4电子空间,6条活性轨道.轨道要包括pi轨道,并且具有A2,B1对称性(对应两个激发态的对称性)* 使用选区的活性空间,在基态进行一系列态平均(State Average)4,4 CAS计算,一般的,CAS计算优化轨道和所研究状态的波函数,而态平均计算提供符合所需要的群的所有轨道的最佳描述.在这个计算中,需要定义NRoot选项,在其所指定的状态和基态之间的所有状态都将要被平均化.同时,各个状态的权重也需要提供.这里我们关心最低的三个状态,所以,NRoot=3,设权重=0.333333.我们将在3-21G, 4-31G, 6-31G(d),6-31+G(d)四个基组水平上运行平均化.在最后一个计算的设置行设定#P选项来输出各个状态的表述.表述如下VERTOR EIGENvalueS CORRESPONDING EIGENVECTOR1 -154.87477374 0.95038483 -0.32993992E-01 .....状态序号能量各个电子结构的系数下面是4,4 CAS计算中的前两个激发态结构PRIMARY BASIS FUNCTION=1 2 1 22 SYMMETRY TYPE=0结构序号1 21 3活性空间中的电子位置3 SYMMETRY TYPE=01 31 3结构2是单重激发态,一个电子从活性空间的第二条轨道跃迁到第三条轨道,结构3是双重激发态,活性空间第二轨道中的两个电子都跃迁到第三轨道* 计算完成后,表征两个激发态,比较能量* 可以进行第二系列的4,6CAS计算,考察结果的变化研究相交点,步骤如下* 以已经得到的结构为起点,设置UHF/STO-3G Guess=Mix Pop=NaturalOrbitals NoSymm计算,检验轨道* 建立好的CAS体系,运行两次4,4CAS态平均计算,在第一次运算中采用STO-3G 基组,设置UNO, NoFullDiog和CASSCF关键词;第二个计算中采用4-31G基组.两个计算都有NoSymm关键词* 运行CAS Opt=Conical, Nosymm, iop(1/8=5)确定相交点* 在优化的相交点的结构上运行态平均计算,采用4-31G基组,部分结果如下方法激发态1 激发态2 能量差CAS(4,4)/6-31+G(d,p) 2 1Ag 1 1Bu 0.03702CAS(4,6)/6-31+G(d,p) 2 1Ag 1 1Bu 0.00540两个结果中,1Ag的能量都比1Bu低,随着方法的改善,能差减小.增加MP2计算可以进一步缩小这个差距.这个寻找相交点的计算还是成功的,这一结构上得到的基态和激发态的差距仅有0.00014Hartree.。
用Gaussian研究化学问题
用Gaussian研究化学问题用Gaussian研究化学问题一:单点能的计算单点能计算是指对给定几何构性的分子的能量以及性质进行计算,由于分子的几何构型是固定不变的,只是\一个点\,所以叫单点能计算。
单点能计算可以用于: ", 计算分子的基本信息", 可以作为分子构型优化前对分子的检查", 在由较低等级计算得到的优化结果上进行高精度的计算 ", 在计算条件下,体系只能进行单点计算", 单点能的计算可以在不同理论等级,采用不同基组进行。
例:甲醛单点能The electronic state of the initial guess is 1-A1. Warning! Cutoffs forsingle-point calculations used.Requested convergence on RMS density matrix=1.00D-04 within 128 cycles. Requested convergence on MAX density matrix=1.00D-02. Requested convergenceon energy=5.00D-05. No special actions if energy rises.Keep R1 integrals in memory in canonical form, NReq= 649414. SCFDone: E(RHF) = -113.863702135 A.U. after 6 cycles Convg= 0.4799D-04 -V/T = 2.0031 S**2 = 0.0000********************************************************************* Population analysis using the SCF density.*********************************************************************二:几何优化收敛标准当一阶导数为零的时候优化结束,但实际计算上,当变化很小,小于某个量的时候,就可以认为得到优化结构。
独立代理变量分析(ISVA)包的说明说明书
Package‘isva’October13,2022Type PackageTitle Independent Surrogate Variable AnalysisVersion1.9Date2017-1-14Author Andrew E TeschendorffMaintainer Andrew Teschendorff<*********************.uk>Depends qvalue,fastICA,JADEDescription Independent Surrogate Variable Analysis is an algorithmfor feature selection in the presence of potential confoundingfactors(see Teschendorff AE et al2011,<doi:10.1093/bioinformatics/btr171>).License GPL-2LazyLoad yesRepository CRANNeedsCompilation noDate/Publication2017-01-1401:35:23R topics documented:DoISV A (2)EstDimRMT (4)isva (5)isvaFn (6)simdataISV A (7)Index81DoISVA Feature selection using independent surrogate variablesDescriptionGiven a data matrix and a phenotype of interest,this function performs feature selection to identify features associated with the phenotype of interest in the presence of potential confounding factors.The algorithmfirstfinds the variation in the data matrix not associated with the phenotype of interest (using a linear model),and subsequently performs Independent Component Analysis(ICA)on this residual variation matrix.The number of independent components to be inferred can be prespeci-fied or estimated using Random Matrix Theory(RMT).Independent Surrogate Variables(ISVs)are constructed from the independent components and provide estimates of the effect of confounders on the data.If potential confounders are unknown(default NULL option)there will be as many ISVs as there are independent components in the residual variation space.If potential confounders are known(either exactly or subject to error/uncertainty)the algorithm will select only those indepen-dent components that correlate with the confounders.If potential confounders are specified it can happen that ISV A will not select any ISVs because none of the independent components correlates with the confounders.In this scenario ISV A should be rerun with the default(NULL)option.The constructed ISVs arefinally included as covariates in a multivariate regression model to identify features that correlate with the phenotype of interest independently of the potential confounders.There are two implementations of ICA offered:JADE and fastICA.We note that the former will result in the same solution(therefore deterministic),whereas fastICA may result in convergence to different local minima for different runs.In the latter case,a consensus solution is advised if results vary between runs.UsageDoISVA(data.m,pheno.v,cf.m=NULL,factor.log,pvthCF=0.01,th=0.05,ncomp=NULL,icamethod=c("JADE","fastICA"))Argumentsdata.m Data matrix:rows label features,columns label samples.It is assumed that number of features is much larger than number of samples.pheno.v Numeric vector of length equal to number of columns of data matrix.At present only numeric(ordinal)phenotypes are supported,so categorical phenotypes areexcluded.cf.m Matrix of potential confounding factors.Rows label samples,Columns label confounding factors,which may be numeric or categorical.The default option(NULL)is for the case where potential confounding factors are not known orirrelevant.factor.log A logical vector of same length as columns of cf.m.FALSE indicates factor is to be treated as a numeric,TRUE as categorical.pvthCF P-value threshold to call a significant association between an independent sur-rogate variable and a confounding factor.By default this is0.01.th False discovery rate threshold for feature selection.By default this is0.05.ncomp Number of independent surrogate variables to look for.By default this is NULL, and estimation is performed using Random MatrixTheory.icamethod Method implementing ICA to be used.Must be either JADE or fastICA.ValueA list with following entries:spv Sorted P-values.rk Ranked index of features.qv Estimated sorted q-values(False Discovery Rate).ndeg Number of differentially altered features.deg Indices of differentially altered features.lm Matrix of significant feature regression statistics and P-values.isv Matrix of selected independent surrogate variables(ISVs).nsv Number of selected ISVs.pvCF P-value matrix of associations between factors(phenotype of interest plus con-founding factors)and inferred ISVs.Note that this may be a larger set than theselected ISVs.selisv Column indices of selected ISVs.Author(s)Andrew E TeschendorffReferencesIndependent Surrogate Variable Analysis to deconvolve confounding factors in large-scale microar-ray profiling studies.Teschendorff AE,Zhuang JJ,Widschwendter M.Bioinformatics.2011Jun 1;27(11):1496-505.Examples###Example###load in simulated datadata(simdataISVA);data.m<-simdataISVA$data;pheno.v<-simdataISVA$pheno;##factors matrix(two potential confounding factors,e.g chip and cohort)factors.m<-cbind(simdataISVA$factors[[1]],simdataISVA$factors[[2]]);colnames(factors.m)<-c("CF1","CF2");###Estimate number of significant components of variation4EstDimRMT rmt.o<-EstDimRMT(data.m);print(paste("Number of significant components=",rmt.o$dim,sep=""));###this makes sense since1component is associated with the###the phenotype of interest,while the other two are associated###with the confoundersncp<-rmt.o$dim-1;###Do ISVA###run with the confounders as givenisva.o<-DoISVA(data.m,pheno.v,factors.m,factor.log=rep(FALSE,2),pvthCF=0.01,th=0.05,ncomp=ncp,icamethod="fastICA");###Evaluation(ISVs should correlate with confounders)###modeling of CFsprint(cor(isva.o$isv,factors.m));###this shows that CFs are reconstructed fairly well###sensitivity(fraction of detected true positives)print(length(intersect(isva.o$deg,simdataISVA$deg))/length(simdataISVA$deg));###PPV(1-false discovery rate)print(length(intersect(isva.o$deg,simdataISVA$deg))/length(isva.o$deg));###run not knowing what confounders there are and with ncp=3say.isva2.o<-DoISVA(data.m,pheno.v,cf.m=NULL,factor.log=rep(FALSE,2),pvthCF=0.01,th=0.05,ncomp=3,icamethod="fastICA");###sensitivity(fraction of detected true positives)print(length(intersect(isva2.o$deg,simdataISVA$deg))/length(simdataISVA$deg));###PPV(1-false discovery rate)print(length(intersect(isva2.o$deg,simdataISVA$deg))/length(isva2.o$deg));EstDimRMT Estimates dimensionality of a data set using Random Matrix TheoryDescriptionGiven the data matrix,it estimates the number of significant components of variation by comparing the observed distribution of spectral eigenvalues to the theoretical one under a Gaussian Orthogonal Ensemble(GOE).Specifically,a spectral decomposition of the data covariance matrix is performed and the number of eigenvalues larger than the theoretical maximum predicted by the GOE is taken as an estimate of the number of significant components.UsageEstDimRMT(data.m,plot=TRUE)isva5Argumentsdata.m Data matrix.Rows label features,Columns samples.plot Logical.Plots Eigenvalue densities if true.ValueA list with following objectscor Data covariance matrix.dim Estimated intrinsic dimensionality of data.estdens Empirical density of eigenvalues.thdens Theoretical density of eigenvalues.Author(s)Andrew E TeschendorffReferencesRandom matrix approach to cross correlations infinancial data.Plerou et al.Physical Review E (2002),V ol.65.Examples##see example for DoISVAisva Independent Surrogate Variable AnalysisDescriptionIndependent Surrogate Variable Analysis is an algorithm for feature selection in the presence of potential confounding factors,specially designed for the analysis of large-scale high-dimensional quantitative genomic data(e.g microarrays).It uses Independent Component Analysis(ICA)to model the confounding factors as independent surrogate variables(ISVs).These ISVs are included as covariates in a multivariate regression model to subsequently identify features that correlate witha phenotype of interest independently of these confounders.Two ICA implementations are offered:JADE from the JADE R-package and fastICA from the fastICA R-package.DetailsPackage:isvaType:PackageVersion: 1.9Date:2017-01-13License:GPL-2LazyLoad:yes6isvaFn There are two internal functions.One function(EstDimRMT)performs the dimensionality esti-mation using a Random Matrix Theory approximation.The other function(isvaFn)is the main engine function and performs the modelling of confounding factors using Independent Component Analysis(ICA).Briefly,ICA is applied on the residual variation orthogonal to that of the phenotype of interest.DoISV A is the main user function,performing feature selection using the constructed independent surrogate variables as covariates.Author(s)Andrew E Teschendorff Maintainer:<*********************.uk>ReferencesIndependent Surrogate Variable Analysis to deconvolve confounding factors in large-scale microar-ray profiling studies.Teschendorff AE,Zhuang JJ,Widschwendter M.Bioinformatics.2011Jun 1;27(11):1496-505.isvaFn Main engine function for inference of independent surrogate variables(ISVs)DescriptionThis is the main engine function which infers the statistically independent surrogate variables(ISVs) by performing Independent Component Analysis(ICA)on the residual variation matrix.It uses either the ICA implementation of JADE or the one from the fastICA R-package.The residual variation matrix reflects the variation orthogonal to that of a phenotype of interest and is inferred using a linear model.UsageisvaFn(data.m,pheno.v,ncomp=NULL,icamethod)Argumentsdata.m Data matrix.Rows label features.Columns label samples.pheno.v Numeric vector encoding phenotype of interest.ncomp Optionally specify number of ISVs to look for.By default will use Approximate Random Matrix Theory to infer this number.icamethod The ICA method to be used.Input value is taken from DoISV A.ValueA list with following entries:n.isv Number of inferred ISVs.isv Matrix of inferred ISVs.simdataISV A7Author(s)Andrew E TeschendorffReferencesIndependent Surrogate Variable Analysis to deconvolve confounding factors in large-scale microar-ray profiling studies.Teschendorff AE,Zhuang JJ,Widschwendter M.Bioinformatics.2011Jun 1;27(11):1496-505.Examples##see example for DoISVAsimdataISVA Simulated data for ISVADescriptionA synthetic data set of750features and50samples with a binary phenotype and two confoundingfactors.Relative effect size of confounding factors(CFs)to that of phenotype of interest is2.For further details please see reference.UsagesimdataISVAFormatThis synthetic data set is a list object containing the following elements:(i)data is the data matrix (750features,50samples),(ii)pheno is a binary phenotype vector,(iii)factors is a list of length two containing the two binary confounding factors,(iv)deg is the index vector of those truly dif-ferentially"expressed"features,(v)degL is a list of index vectors for features truly differentially altered(first element,degL[[1]]=deg)and those features affected by CFs(2nd and3rd elements). ReferencesIndependent Surrogate Variable Analysis to deconvolve confounding factors in large-scale microar-ray profiling studies.Teschendorff AE,Zhuang JJ,Widschwendter M.Bioinformatics.2011Jun 1;27(11):1496-505.Index∗datasetssimdataISVA,7∗multivariateDoISVA,2EstDimRMT,4isva,5isvaFn,6DoISVA,2EstDimRMT,4isva,5isvaFn,6simdataISVA,78。
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Published online: 3 December 2008 © Springer Science+Business Media, LLC 2008
Abstract In this paper a novel algorithm for Gaussian Selection (GS) of mixtures used in a continuous speech recognition system is presented. The system is based on hidden Markov models (HMM), using Gaussian mixtures with full covariance matrices as output distributions. The purpose of Gaussian selection is to increase the speed of a speech recognition system, without degrading the recognition accuracy. The basic idea is to form hyper-mixtures by clustering close mixtures into a single group by means of Vector Quantization (VQ) and assigning it unique Gaussian parameters for estimation. In the decoding process only those hyper-mixtures which are above a designated threshold are selected, and only mixtures belonging to them are evaluated, improving computational efficiency. There is no problem with the clustering and evaluation if overlaps between the mixtures are small, and their variances are of the same range. However, in real case, there are numerous models which do not fit this profile. A Gaussian selection scheme proposed in this paper addresses this problem. For that purpose, beside the clustering algorithm, it also incorporates an algorithm for mixture grouping. The particular mixture is assigned to a group from the predefined set of groups, based
1 Introduction Hidden Markov model-based (HMM-based) continuous speech recognition (CSR) systems tend to operate several times slower than real-time, which is not practical for most applications. Techniques are therefore required that would reduce the decoding time to at least real-time, while retaining or staying close to the same level of accuracy. To obtain a high level of accuracy, HMM-based CSR systems typically use continuous densities. In such systems, calculation of state likelihoods makes up a significant proportion (between 30–70%) of the computational load [8]. This is a result of the need to use multiple mixture Gaussian output distributions in a state, and each Gaussian component must be separately evaluated in order to determine the overall likelihood. A wide variety of techniques may be used to reduce the amount of computation required. Some of them involve alteration of acoustic feature vector from the full system (Linear Discriminant Analysis) [7, 16], and others involve “tying” of acoustical states (semi-continuous HMM systems) [6]. An alternative approach is to use Gaussian Selection (GS) methods [3, 10] that reduce likelihood computation time by only computing the likelihood of a selected subset of mixtures used for a particular input vector.
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Most of the GS methods in CSR and Speaker Verification tasks were designed for selection of diagonal covariance matrices [1, 3, 10, 13–15, 21]. Nevertheless, the generalization to the full covariance case is straightforward. Bocchieri in [3] firstly introduced Vector Quantized Gaussian Selection. The idea was to generate a set of codewords (clusters). Each codeword is then assigned a shortlist of Gaussians. For clustering of Gaussians, weighted Euclidean distance was used. Knill and Gales in [10] modified the proposed algorithm in order for the distance to take into account the variance of a particular mixture to be clustered. In [15] Watanabe and Shinoda proposed the use of a tree structured probability density function in modeling of the acoustical space applied on Gaussian mixtures. In [14] Simonin and Delphin did something similar. The Gaussian tree was built from successive Gaussian mixture merging. Each node of the tree was associated with a Gaussian hypermixture, and the actual HMM densities are associated to the leaves. In general, they proposed building of a tree structure for partitioning of the acoustical space, but the algorithms were applied to the diagonal Gaussian mixtures. In application to the tied state full covariances in the system used in this work, only one level of hierarchy was acceptable from the aspect of recognition accuracy. In the one level case, it amounts to a VQ technique, i.e. generalization of a method proposed by Bocchieri. That scheme is referred to as Vector Quantization Gaussian Selection (VQGS) and it is used as a baseline approach. The basic idea is to form hyper-mixtures by putting close mixtures into a single cluster and assigning unique Gaussian parameters to it. In the decoding process, after the evaluation of all hyper-mixtures for a particular input acoustic vector, only the hyper-mixtures which are above a predefined threshold are selected. The mixtures belonging to them are evaluated and the rest of the mixtures are approximated with some sufficiently general value. A problem emerges if there are significant overlaps between the mixtures to be clustered. In CSR systems such situations are inevitable, and considerable overlapping is always present. In this paper, a GS scheme is proposed that takes into account the most significant eigenvalues of covariance matrices in the clustering process. In this way the previously mentioned problem is addressed, as will be explained later. The main idea is to place mixtures in several groups based on the eigenvalues of their covariance matrices. The goal is for every group to contain only those mixtures with the most of their significantly high eigenvalues in some predefined range. After the grouping of the mixtures is applied, baseline VQ based Gaussian mixture clustering is performed on every group of mixtures separately. Owing to this, in any particular cluster it is likely that a large majority of mixtures will have either dominantly larger or dominantly smaller eigenvalues of their covariance matrices. The frequency of clusters that contain both kinds of mixtures is thus severely reduced. For a particular input vector,