03_Multiwfn计算Mayer键级 - Yiwei666/01_python_script GitHub Wiki

1. 关键词

Mayer键级分析
创建cp2k输入文件
Mulliken电荷布居分析
ELF分析

1. 实空间函数分析

(1)电子密度
(2)电子密度的梯度
(3)电子密度的拉普拉斯函数
(4)轨道波函数。轨道可以是正则分子轨道、定域化轨道、自然轨道、NTO、NBO、NHO、NAO等，取决于输入文件类型
(5)电子自旋密度或自旋极化参数
(6)电子的哈密顿动能密度K(r)
(7)电子的拉格朗日动能密度G(r)
(8)由原子核产生的静电势。如果用.chg文件（记录了原子电荷数值）作为输入文件，则对应的是原子电荷产生的静电势
(9)电子定域化函数(Electron localization function, ELF)。包括Becke和Tsirelson各自提出的形式。开壳层体系的Becke的ELF所用的具体形式是由笔者导出的，见《电子定域化函数的含义与函数形式》（物理化学学报,27,2786-2792）
(10)定域化轨道指示函数(Localized orbital locator,LOL)。包括Becke和Tsirelson各自提出的形式。关于ELF、LOL和电子密度拉普拉斯函数的简介可参见《电子定域性的图形分析》（http://sobereva.com/63）
(11)局部信息熵
(12)总静电势(ESP)
(13)约化密度梯度(RDG)
(14)Promolecular近似下的RDG
(15)Sign(lambda2)*rho（电子密度Hessian矩阵第二大本征值的符号乘以电子密度）
(16)Promolecular近似下的Sign(lambda2)*rho
(17)电子的交换穴、相关穴、相关因子
(18)平均局部离子化能(ALIE)
(19)源函数(Source function)
(20)电子离域范围函数(EDR)
(21)轨道重叠距离函数D(r)
(22)独立梯度模型(IGM）的δg函数

2. 周期性波函数分析（P50）

Viewing orbitals (main function 0)
Calculate properties at a point (main function 1)
Topology analysis (main function 2)
Plotting curve map for real space functions (main function 3) 3), including promolecular and deformation properties
Plotting plane map for real space functions (main function 4) 4), including promolecular and deformation properties
Calculating grid data and plotting isosurface map for real space functions (main function 5), including promolecular and deformation properties. Note that in the case of nonorthogonal cell, isosurface map cannot be correctly plotted in Multiwfn, however you can export the grid data as cube file and then visualize it in VMD and VESTA
Hirshfeld charge, CM5 charge, 1.2*CM5 charge, Mulliken population, Löwdin population, various modified Mulliken populations, PEOE charge, EEM charge (in main function 7), and AIM charge (via basin analysis module)
Mulliken, Stout-Politzer and SCPA orbital composition analyses, including showing fragment contributions (subfunctions 1~6 in main function 8)
Mayer bond order, multicenter bond order, Wiberg bond order, Mulliken bond order and its decomposition analysis, orbital occupancy-perturbed Mayer bond order (in main function 9)
Plotting TDOS TDOS, PDOS, OPDOS, LDOS and MO-PDOS (main function 10)
Orbital localization by Pipek Mezey method (main function 19)
Visualization analyses of weak interactions (IGMH, IRI, RDG, DORI)
Electronic excitation analyses: Electron hole analysis (hole and electron distributions, transition density and transition dipole moment density density, various indices that irrelevant to centroids), NTO analysis, generate natural orbitals of specific excited states, "Check, modify and export configuration coefficients of an excitation", print major MO transitions in all excited states

键级分析（9），

2. Multiwfn 软件目录

主页：  

 0 Show molecular structure and view orbitals  
 1 Output all properties at a point       2 Topology analysis   
 3 Output and plot specific property in a line  
 4 Output and plot specific property in a plane   
 5 Output and plot specific property within a spatial region (calc. grid data)   
 6 Check & modify wavefunction   
 7 Population analysis and calculation of atomic charges   
 8 Orbital composition analysis           9 Bond order analysis   
 10 Plot total DOS, partial DOS, OPDOS, local DOS and photoelectron spectrum   
 11 Plot IR/Raman/UV-Vis/ECD/VCD/ROA/NMR spectrum   
 12 Quantitative analysis of molecular surface   
 13 Process grid data (No grid data is presented currently)   
 14 Adaptive natural density partitioning (AdNDP) analysis   
 15 Fuzzy atomic space analysis   
 16 Charge decomposition analysis (CDA) and plot orbital interaction diagram   
 17 Basin analysis                       18 Electron excitation analysis   
 19 Orbital localization analysis        20 Visual study of weak interaction   
 21 Energy decomposition analysis        22 Conceptual DFT (CDFT) analysis   
 23 ETS-NOCV analysis                    24 (Hyper)polarizability analysis   
 25 Electron delocalization and aromaticity analyses   
 100 Other functions (Part 1)            200 Other functions (Part 2)   
 300 Other functions (Part 3)

1. Mayer键级分析

9 Bond order analysis

9  （9 --> 1）

            ================ Bond order analysis ===============
 -1 Define fragment 1 and 2 for options 1,3,4,7,8,10 (to be defined)
 0 Return
 1 Mayer bond order analysis
 2 Multicenter bond order analysis
 -2 Multicenter bond order analysis in NAO basis
 3 Wiberg bond order analysis in Lowdin orthogonalized basis
 4 Mulliken bond order (Mulliken overlap population) analysis
 5 Decompose Mulliken bond order between two atoms to orbital contributions
 6 Orbital occupancy-perturbed Mayer bond order
 7 Fuzzy bond order analysis (FBO)
 8 Laplacian bond order (LBO)
 9 Decompose Wiberg bond order in NAO basis as atomic orbital pair contribution
 10 Intrinsic bond strength index (IBSI)
 11 AV1245 index (approximate multicenter bond order for large rings) and AVmin

Mayer键级分析脚本

01_Mayer键级分析脚本.txt 脚本内容如下，在cmd命令行中需要指出 .molden 文件的绝对路径

//  cmd 命令行：Multiwfn C:\Users\sun78\Desktop\cp2k_model\56_SiTiB-E\410-OT-200atoms\modify-SiTiB410-MOS-1_0.molden < 01_Mayer键级分析脚本.txt > 键级分析_out.txt
9 // Bond order analysis 
1 // Mayer bond order analysis
y // If outputting bond order matrix to bndmat.txt in current folder? (y/n)
0 // Return
q // "q": Exit program gracefully

运行脚本方法：打开cmd命令行窗口，执行 Multiwfn C:\Users\sun78\Desktop\cp2k_model\56_SiTiB-E\410-OT-200atoms\modify-SiTiB410-MOS-1_0.molden < 01_Mayer键级分析脚本.txt > 键级分析_out.txt 命令即可，在脚本中 // 代表注释
运行脚本得到：bndmat.txt存储了键级信息，键级分析_out.txt 存储了终端输出日志信息

2. 创建cp2k输入文件

100 Other functions (Part 1)

100  （100 --> 2，快捷键输入 cp2k）

               ============ Other functions (Part 1) ============
 0 Return
 1 Draw scatter graph between two functions and generate their cube files
 2 Export various files (mwfn/pdb/xyz/wfn/wfx/molden/fch/47/mkl...) or generate input file of quantum chemistry programs
 3 Calculate molecular van der Waals Volume
 4 Integrate a function in whole space
 5 Show overlap integral between alpha and beta orbitals
 6 Monitor SCF convergence process of Gaussian
 8 Generate Gaussian input file with initial guess from fragment wavefunctions
 9 Evaluate interatomic connectivity and atomic coordination number
 11 Calculate overlap and centroid distance between two orbitals
 12 Biorthogonalization between alpha and beta orbitals
 13 Calculate HOMA and Bird aromaticity index
 14 Calculate LOLIPOP (LOL Integrated Pi Over Plane)
 15 Calculate intermolecular orbital overlap
 17 Generate Fock/KS matrix based on orbital energies and coefficients
 18 Yoshizawa's electron transport route analysis
 19 Generate new wavefunction by combining fragment wavefunctions
 20 Calculate Hellmann-Feynman forces
 21 Calculate properties based on geometry information for specific atoms
 22 Detect pi orbitals, set occupation numbers and calculate pi composition
 23 Fit function distribution to atomic value
 24 Obtain NICS_ZZ value for non-planar or tilted system

2
 0 Return
                 Export system to various formats of files:
 1 Output current structure to .pdb file
 2 Output current structure to .xyz file
 3 Output current structure and atomic charges to .chg file
 4 Output current wavefunction as .wfx file
 5 Output current wavefunction as .wfn file
 6 Output current wavefunction as Molden input file (.molden)
 7 Output current wavefunction as .fch file
 8 Output current wavefunction as .47 file
 9 Output current wavefunction as old Molekel input file (.mkl)
 31 Output current structure to .cml file
 32 Output current wavefunction as .mwfn file
 33 Output current structure and cell information as .cif file
              Generate input file of quantum chemistry codes:
 10 Gaussian
 11 GAMESS-US
 12 ORCA         13 NWChem       14 MOPAC
 15 PSI4         16 MRCC         17 CFOUR
 18 Molpro       19 Dalton       20 Molcas
 21 Q-Chem
 25 CP2K         26 Quantum ESPRESSO      27 VASP (POSCAR)

25
 Hint: You can also input "cp2k" in the main menu to enter this function


 Note: Please mention Multiwfn and cite original paper of Multiwfn if you benefits from this function in your study, thank you!

 Input path for generating CP2K input file, e.g. C:\ltwd.inp
 If press ENTER button directly, will export to modify_SiP460-MOS-1_0.inp

 Generating KIND information...

 -11 Enter the interface for geometry operations
 -10 Return
 -9 Other settings
 -7 Set direction(s) of applying periodic boundary condition, current: XYZ
 -4 Calculate atomic charges, current: None
 -3 Set exporting cube file, current: None
 -2 Toggle exporting .molden file for Multiwfn, current: No
 -1 Choose task, current: Energy
  0 Generate input file now!
  1 Choose theoretical method, current: PBE
  2 Choose basis set and pseudopotential, current: DZVP-MOLOPT-SR-GTH
  3 Set dispersion correction, current: None
  4 Switching between diagonalization and OT, current: Diagonalization
  5 Set density matrix mixing, current: Broyden mixing
  6 Toggle smearing electron occupation, current: No
  7 Toggle using self-consistent continuum solvation (SCCS), current: No
  8 Set k-points, current: GAMMA only
 15 Toggle calculating excited states via TDDFT, current: No
-4
 Printing which kind of atomic charge?
 0 None
 1 Mulliken
 2 Lowdin
 3 Hirshfeld
 4 Hirshfeld-I
 5 Voronoi
 6 RESP
 7 REPEAT

3. Mulliken电荷布居分析

7 Population analysis and calculation of atomic charges

7

      ============== Population analysis and atomic charges ==============
 -2 Calculate interaction energy between fragments based on atomic charges
 -1 Define fragment
 0 Return
 1 Hirshfeld atomic charge
 2 Voronoi deformation density (VDD) atom population
 5 Mulliken atom & basis function population analysis
 6 Lowdin atom & basis function population analysis
 7 Modified Mulliken atom population defined by Ros & Schuit (SCPA)
 8 Modified Mulliken atom population defined by Stout & Politzer
 9 Modified Mulliken atom population defined by Bickelhaupt
 10 Becke atomic charge with atomic dipole moment correction
 11 Atomic dipole corrected Hirshfeld atomic charge (ADCH) (recommended)
 12 CHELPG ESP fitting atomic charge
 13 Merz-Kollmann (MK) ESP fitting atomic charge
 14 AIM atomic charge
 15 Hirshfeld-I atomic charge
 16 CM5 atomic charge    -16 Generate 1.2*CM5 atomic charge
 17 Electronegativity Equalization Method (EEM) atomic charge
 18 Restrained ElectroStatic Potential (RESP) atomic charge
 19 Gasteiger (PEOE) charge
5

               ---------- Mulliken population analysis ----------
 -1 Choose output destination, current: Screen
 0 Return
 1 Output Mulliken population and atomic charges
 2 Output gross atomic population matrix and decompose it
 3 Output gross basis function population matrix and decompose it
 4 Output orbital contributions to atomic populations to atmpopdcp.txt

4. ELF电子局域化分析

绘图可以参考手册 4.4 Output and plot various properties in a plane

4      // Output and plot specific property in a plane   
9      // Electron Localization Function (ELF)
5      // Shaded surface map with projection
Enter  //  You can press ENTER button directly to use recommended value
4      // Define by three atoms
94,219,142  // Input index of three atoms, e.g. 3,6,7
Return      // GUI界面Return按钮
-8          // Change length unit of the graph to Angstrom
0           // Save the graph to a graphical file in current folder
-5          // Return to main menu

4 Output and plot specific property in a plane

4 

 -10 Return to main menu
 -2 Obtain deformation property
 -1 Obtain promolecule property
 0 Set custom operation
             ----------- Available real space functions -----------
 1 Electron density                 2 Gradient norm of electron density
 3 Laplacian of electron density    4 Value of orbital wavefunction
 5 Electron spin density
 6 Hamiltonian kinetic energy density K(r)
 7 Lagrangian kinetic energy density G(r)
 8 Electrostatic potential from nuclear charges
 9 Electron Localization Function (ELF)
 10 Localized orbital locator (LOL)
 11 Local information entropy
 12 Total electrostatic potential (ESP)
 13 Reduced density gradient (RDG)       14 RDG with promolecular approximation
 15 Sign(lambda2)*rho      16 Sign(lambda2)*rho with promolecular approximation
 17 Correlation hole for alpha, ref. point:   0.00000   0.00000   0.00000
 18 Average local ionization energy (ALIE)
 19 Source function, mode: 1, ref. point:   0.00000   0.00000   0.00000
 20 Electron delocal. range func. EDR(r;d)  21 Orbital overlap dist. func. D(r)
 22 Delta-g (promolecular approximation)    23 Delta-g (Hirshfeld partition)
 24 Interaction region indicator (IRI)    25 van der Waals potential (probe=C )
 100 User-defined function (iuserfunc=    0), see Section 2.7 of manual

9
 -10 Return to main menu
 Draw which kind of map?
 1 Color-filled map (with/without contour lines)
 2 Contour line map
 3 Relief map
 4 Shaded surface map
 5 Shaded surface map with projection
 6 Gradient lines map with/without contour lines
 7 Vector field map with/without contour lines

5
  -10 Return to main menu
 How many grids in the two dimensions, respectively?
 (100,100 is recommended)
 Hint: You can press ENTER button directly to use recommended value

Enter
  -10 Return to main menu
 Please define the plane to be plotted
 1: XY plane   2: XZ plane   3: YZ plane
 4: Define by three atoms    5: Define by three given points
 6: Input origin and translation vector (For expert users)
 7: Parallel to a bond and meantime normal to a plane defined by three atoms
 0: Set extension distance for plane type 1~5, current:  4.5000 Bohr
 -1: Set translation and rotation of the map for plane types 4 and 5

4
 Input index of three atoms, e.g. 3,6,7


92,198,208
 X/Y/Z of origin of the plane:   26.74921  16.26161  32.08804 Bohr
 X/Y/Z of end of the plane:       3.10191  18.35527  10.39724 Bohr
 X/Y/Z of translation vector 1: -0.11670 -0.14073 -0.05058 Bohr, Norm:  0.18969
 X/Y/Z of translation vector 2: -0.12216  0.16187 -0.16852 Bohr, Norm:  0.26368

 Calculating plane data, please wait...
 Note: All exponential functions exp(x) with x< -20.000 will be ignored
 Progress: [##################################################]  100.00 %     /

 Calculation took up wall clock time        16 s

 The minimum of data:  6.382567386005174E-010
 The maximum of data:  0.922958915338141

          -------- Post-processing menu of plotting plane map --------
 -9 Only plot the data around certain atoms
 -8 Change length unit of the graph to Angstrom
 -7 Multiply the current data by a factor
 -6 Export the current plane data to plane.txt in current folder
 -5 Return to main menu
 -4 Save (load) all plotting settings to (from) an external file
 -3 Change other plotting settings
 -2 Set label intervals in X, Y and color scale axes, current:  2.683  3.729    0.100000
 -1 Show the graph again
 0 Save the graph to a graphical file in current folder
 1 Set color scale range for filling color
 2 Toggle drawing mesh on the surface, current: ON
 3 Set color transition, current: Rainbow & white/black for out-of-limit data


0
 Graph have been saved as png format with "dislin" prefix in current directory