Manual Dev

• !!!!!!!!!! ALL USERS MUST READ !!!!!!!!!!
• Linux and Mac OS USERS MUST READ
• About the manual
• 1 Overview
• 2 General information
  • 2.1 Install
    • 2.1.1 Windows version
    • 2.1.2 Linux version
    • 2.1.3 Mac OS version
  • 2.2 Using Multiwfn
  • 2.3 The files of Multiwfn
  • 2.4 Parallel implementation
  • 2.5 Input files and wavefunction types
  • 2.6 Real space functions
  • 2.7 User defined real space function
  • 2.8 Graphic formats and image size
• 3 Functions
  • 3.2 Showing molecular structure and viewing orbitals / isosurfaces (0)
  • 3.3 Outputting all properties at a point (1)
  • 3.4 Outputting and plotting specific property in a line (3)
  • 3.5 Outputting and plotting specific property in a plane (4)
    • 3.5.1 Graph types
    • 3.5.2 Setting up grid, plane and plotting region
    • 3.5.3 Options in post-process interface
    • 3.5.4 Setting up contour lines
    • 3.5.5 Plot critical points, paths and interbasin paths on plane graph
  • 3.6 Outputting and plotting specific property within a spatial region (5)
  • 3.7 Custom operation, promolecular and deformation properties (subfunction 0, -1, -2 in main function 3, 4, 5)
    • 3.7.1 Custom operation for multiple wavefunctions (0)
    • 3.7.2 Promolecular and deformation properties (-1, -2)
    • 3.7.3 Generation of atomic wavefunctions
    • 3.7.4 Sphericalization of atom wavefunction
  • 3.8 Checking & Modifying wavefunction (6)
  • 3.9 Population analysis and atomic charges (7)
    • 3.9.1 Hirshfeld population (1)
    • 3.9.2 Voronoi deformation density (VDD) population (2)
    • 3.9.3 Mulliken atom & basis function population analysis (5)
    • 3.9.4 Löwdin population (6)
    • 3.9.5 Modified Mulliken population defined by Ros & Schuit (SCPA) (7)
    • 3.9.6 Modified Mulliken population defined by Stout & Politzer (8)
    • 3.9.7 Modified Mulliken population defined by Bickelhaupt (9)
    • 3.9.8 Becke atomic charge with atomic dipole moment correction (10)
    • 3.9.9 Atomic dipole moment corrected Hirshfeld charges (ADCH, 11)
    • 3.9.10 CHELPG (Charges from electrostatic potentials using a grid based method, 12)
    • 3.9.11 Merz-Kollmann charge (13)
    • 3.9.12 AIM charge (14)
    • 3.9.13 Hirshfeld-I population (15)
    • 3.9.14 CM5 charge (16)
    • 3.9.15 Electronegativity Equalization Method (EEM) (17)
  • 3.10 Orbital composition analysis (8)
    • 3.10.1 Output basis function, shell and atom composition in a specific orbital by Mulliken, Stout-Politzer and SCPA approaches (1, 2, 3)
    • 3.10.2 Define fragment 1 and 2 (-1, -2)
    • 3.10.3 Output composition of fragment 1 and inter-fragment composition by Mulliken, Stout-Politzer and SCPA approaches (4, 5, 6)
    • 3.10.4 Orbital composition analysis by natural atomic orbital approach (7)
    • 3.10.5 Calculate atom and fragment contributions by Hirshfeld or Hirshfeld-I method (8,10)
    • 3.10.6 Calculate atom and fragment contributions by Becke method (9)
    • 3.10.7 Evaluate oxidation state by LOBA method
  • 3.11 Bond order analysis (9)
    • 3.11.1 Mayer bond order analysis (1)
    • 3.11.2 Multi-center bond order analysis (2, -2, -3)
    • 3.11.3 Wiberg bond order analysis in Löwdin orthogonalized basis (3)
    • 3.11.4 Mulliken bond order analysis (4) and decomposition (5)
    • 3.11.5 Orbital occupancy-perturbed Mayer bond order (6)
    • 3.11.6 Fuzzy bond order (7)
    • 3.11.7 Laplacian bond order (8)
    • 3.11.8 Decompose Wiberg bond order in NAO basis as atomic orbital pair contributions (9)
  • 3.12 Plotting total, partial, and overlap population density-of-states (10)
    • 3.12.1 Theory
    • 3.12.2 Input file
    • 3.12.3 Options for plotting DOS
    • 3.12.4 Local DOS
  • 3.13 Plotting IR/Raman/UV-Vis/ECD/VCD spectrum (11)
    • 3.13.1 Theory
    • 3.13.2 Input file
    • 3.13.3 Usage and options
    • 3.13.4 Plotting multiple files and weighted spectrum
  • 3.14 Topology analysis (2)
    • 3.14.1 Theory
    • 3.14.2 Search critical points
    • 3.14.3 Generate paths
    • 3.14.4 Generate interbasin surfaces
    • 3.14.5 Visualize, analyze, modify and export results
    • 3.14.6 Calculate the aromaticity indices based on topology properties of electron density
  • 3.15 Quantitative analysis of molecular surface (12)
    • 3.15.1 Theory
    • 3.15.2 Numerical algorithm
    • 3.15.3 Parameters and options
    • 3.15.4 Options at post-process stage
    • 3.15.5 Special topic: Hirshfeld and Becke surface analyses
  • 3.16 Process grid data (13)
    • 3.16.0 Visualize isosurface of present grid data (-2)
    • 3.16.1 Output present grid data to Gaussian cube file (0)
    • 3.16.2 Output all data points with value and coordinate (1)
    • 3.16.3 Output data points in a XY/YZ/XZ plane (2, 3, 4)
    • 3.16.4 Output average data of XY/YZ/XZ planes in a range of Z/X/Y (5,6,7)
    • 3.16.5 Output data points in a plane defined three atom indices or three points (8,9)
    • 3.16.6 Output data points in specified value range (10)
    • 3.16.7 Grid data calculation (11)
    • 3.16.8 Map values of a cube file to specified isosurface of present grid data (12)
    • 3.16.9 Set value of the grid points that far away from / close to some atoms (13)
    • 3.16.10 Set value of the grid points outside overlap region of two fragments (14)
    • 3.16.11 If data value is within certain range, set it to a specified value (15)
    • 3.16.12 Scale data range (16)
    • 3.16.13 Show statistic data of the points in specific spatial and value range (17)
    • 3.16.14 Calculate and plot integral curve in X/Y/Z direction (18)
  • 3.17 Adaptive natural density partitioning (AdNDP) analysis (14)
    • 3.17.1 Theory
    • 3.17.2 Input file
    • 3.17.3 Options
  • 3.18 Fuzzy atomic space analysis (15)
    • 3.18.0 Basic concepts
    • 3.18.1 Integration of a real space function in fuzzy atomic spaces (1)
    • 3.18.2 Integration of a real space function in overlap spaces (8)
    • 3.18.3 Calculate atomic multipole moments (2)
    • 3.18.4 Calculate atomic overlap matrix (3)
    • 3.18.5 Calculate localization and delocalization index (4)
    • 3.18.6 Calculate PDI (5)
    • 3.18.7 Calculate FLU and FLU-π (6,7)
    • 3.18.8 Calculate condensed linear response kernel (9)
    • 3.18.9 Calculate para linear response index (10)
    • 3.18.10 Calculate multi-center delocalization index (11)
  • 3.19 Charge decomposition analysis and plotting orbital interaction diagram (16)
    • 3.19.1 Theory
    • 3.19.2 Input file
    • 3.19.3 Usage
  • 3.20 Basin analysis (17)
    • 3.20.1 Theory
    • 3.20.2 Numerical aspects
    • 3.20.3 Usage
  • 3.21 Electron excitation analysis (18)
    • 3.21.1 Analyze and visualize hole-electron distribution, transition dipole moment and transition density (1)
      • 3.21.1.1 Theory
      • 3.21.1.2 Input file
      • 3.21.1.3 Functions
    • 3.21.2 Plot transition density matrix as color-filled map (2)
    • 3.21.3 Analyze charge-transfer based on density difference grid data (3)
    • 3.21.4 Calculate (r index to measure charge-transfer length (4)
    • 3.21.5 Calculate transition dipole moments between all excited states (5)
    • 3.21.6 Generate natural transition orbitals (NTOs) (6)
    • 3.21.7 Calculate ghost-hunter index (7)
    • 3.21.8 Calculate interfragment charge transfer in electronic excitation (8)
  • 3.100 Other functions part 1 (100)
    • 3.100.1 Draw scatter graph between two functions and generate their cube files
    • 3.100.2 Export .pdb, .xyz, .wfn, .wfx, .molden, .fch, NBO .47 or input file of mainstream quantum chemistry codes
    • 3.100.3 Calculate molecular van der Waals volume
    • 3.100.4 Integrate a function in whole space
    • 3.100.5 Show overlap integral between alpha and beta orbitals
    • 3.100.6 Monitor SCF convergence process of Gaussian
    • 3.100.7 Generate Gaussian input file with initial guess from converged wavefunction
    • 3.100.8 Generate Gaussian input file with initial guess from fragment wavefunctions
    • 3.100.9 Evaluate coordination number for all atoms
    • 3.100.11 Calculate overlap and centroid distance between two orbitals
    • 3.100.13 Calculate HOMA and Bird aromaticity index
    • 3.100.14 Calculate LOLIPOP (LOL Integrated Pi Over Plane)
    • 3.100.15 Calculate intermolecular orbital overlap
    • 3.100.18 Yoshizawa's electron transport route analysis
    • 3.100.19 Generate promolecular .wfn file from fragment wavefunctions
    • 3.100.20 Calculate Hellmann-Feynman forces
    • 3.100.21 Calculate properties based on geometry information for specific atoms
    • 3.100.22 Detect π orbitals and set occupation numbers
    • 3.100.23 Fit function distribution to atomic value
    • 3.100.24 Obtain NICS_ZZ for non-planar system
    • 3.100.25 Calculate area and perimeter for a ring
  • 3.200 Other functions part 2 (200)
    • 3.200.1 Weak interaction analysis for fluctuation environment by RDG method
    • 3.200.2 Calculate atomic and bond dipole moments in Hilbert space
    • 3.200.3 Generate cube file for multiple orbital wavefunctions
    • 3.200.4 Generate iso-chemical shielding surfaces (ICSS) and related quantities
    • 3.200.5 Plot radial distribution function for a real space function
    • 3.200.6 Analyze correspondence between orbitals in two wavefunctions
    • 3.200.7 Parse output of (hyper)polarizability task of Gaussian
    • 3.200.8 Calculate (hyper)polarizability by sum-over-states (SOS) method
    • 3.200.9 Calculate average bond length and average coordinate number
    • 3.200.10 Output various kinds of integral between orbitals
    • 3.200.11 Calculate center, the first and second moments of a real space function
    • 3.200.12 Calculate energy index (EI) or bond polarity index (BPI)
    • 3.200.13 Pipek-Mezey orbital localization
    • 3.200.14 Perform integration within isosurfaces of a real space function
    • 3.200.15 Calculate electron correlation index
    • 3.200.16 Generate natural orbitals based on the density matrix in .fch/.fchk file
• 4 Tutorials and Examples
  • Prologue and generation of input files
  • 4.0 View orbitals and structure
    • 4.0.1 Viewing molecular orbitals of monofluoroethane
    • 4.0.2 Viewing natural bond orbitals (NBO) of ethanol
  • 4.1 Calculate properties at a point
    • 4.1.1 Show all properties of triplet water at a given point
    • 4.1.2 Calculate ESP at nuclear positions to evaluate interaction strength of H2O∙∙∙HF
  • 4.2 Topology analysis
    • 4.2.1 Atoms in molecules (AIM) and aromaticity analysis for 2-pyridoxine 2-aminopyridine
    • 4.2.2 LOL topology analysis for acetic acid
    • 4.2.3 Plot electron density ellipticity along bond path
  • 4.3 Plot properties in a line
    • 4.3.1 Plot the spin density curve of triplet formamide along carbon and oxygen atoms
    • 4.3.2 Study Fermi hole and Coulomb hole of H2
    • 4.3.3 Study interatomic interaction via PAEM-MO method
  • 4.4 Plot properties in a plane
    • 4.4.1 Color-filled map of electron density of hydrogen cyanide
    • 4.4.2 Shaded surface map with projection of localized orbital locator in a plane of monofluoroethane
    • 4.4.3 Contour map of electron density Laplacian of uracil without contributions from some atoms
    • 4.4.4 Contour map of electrostatic potential of chlorine trifluoride
    • 4.4.5 Contour map of two orbital wavefunctions
    • 4.4.6 Gradient+contour map with topology paths of electron density of hydrogen peroxide
    • 4.4.7 Deformation map of electron density of acetyl chloride
  • 4.5 Generate grid data and view isosurface
    • 4.5.1 Electron localization function of chlorine trifluoride
    • 4.5.2 Laplacian of electron density of 1,3-butadiene
    • 4.5.3 Calculate ELF-α and ELF-π to study aromaticity of benzene
    • 4.5.4 Use Fukui function and dual descriptor to study favorable site for electrophilic attack of phenol
    • 4.5.5 Plot difference map of electron density to study electron transfer of imidazole coordinated magnesium porphyrin
    • 4.5.6 Study electron delocalization range function EDR(r;d) of anionic water dimer
    • 4.5.7 Study orbital overlap distance function D(r) of thioformic acid
  • 4.6 Modify wavefunction
    • 4.6.1 Delete certain Gauss functions
    • 4.6.2 Remove contributions from certain orbitals to real space functions
    • 4.6.3 Translate and duplicate graphene primitive cell wavefunction to periodic system
  • 4.7 Population analysis and atomic charge calculation
    • 4.7.1 Calculate Hirshfeld and CHELPG charges for chlorine trifluoride
    • 4.7.2 Calculate and compare ADCH charges with Hirshfeld charges for acetamide
    • 4.7.3 Calculate condensed Fukui function and condensed dual descriptor
    • 4.7.4 Illustration of computing Hirshfeld-I charges
    • 4.7.5 Calculating EEM charges for ethanol-water cluster
  • 4.8 Molecular orbital composition analysis
    • 4.8.1 Analyze acetamide by Mulliken method
    • 4.8.2 Analysis on water by natural atomic orbital method
    • 4.8.3 Analyze acetamide by Hirshfeld and Becke method
    • 4.8.4 Calculate oxidation state by LOBA method
  • 4.9 Bond order analysis
    • 4.9.1 Mayer bond order and fuzzy bond order analysis on acetamide
    • 4.9.2 Three-center bond order analysis on Li6 cluster
    • 4.9.3 Calculate Laplacian bond order (LBO)
    • 4.9.4 Decomposition analysis of Wiberg bond order in NAO basis for formaldehyde
  • 4.10 Plot density of states (DOS)
    • 4.10.1 Plot total, partial and overlap DOS for N-phenylpyrrole
    • 4.10.2 Plot local DOS for butadiene
  • 4.11 Plot spectrums
    • 4.11.1 Plot infrared spectrum for NH3BF3
    • 4.11.2 Plot UV-Vis spectrum and the contributions from individual transitions for acetic acid
    • 4.11.3 Plot electronic circular dichroism spectrum for asparagine
    • 4.11.4 Plot conformational weighted spectrum for plumericin
    • 4.11.5 Plot Raman spectrum for 2-methyloxirane based on Raman intensity
    • 4.11.6 Simultanously plot multiple systems
  • 4.12 Quantitative analysis of molecular surface
    • 4.12.1 Electrostatic potential analysis on phenol molecular surface
    • 4.12.2 Average local ionization energy analysis on phenol molecular surface
    • 4.12.3 Local molecular surface analysis for acrolein
    • 4.12.4 Fukui function distribution on local molecular surface of phenol
    • 4.12.5 Becke surface analysis on guanine-cytosine base pair
    • 4.12.6 Hirshfeld surface analysis and fingerprint plot analysis on urea crystal
    • 4.12.7 Two tricks to reduce computational time in ESP analysis on vdW surface
    • 4.12.8 Quantitative analysis of orbital overlap distance function D(r) on thioformic acid molecular surface
  • 4.13 Process grid data
    • 4.13.1 Extract data points in a plane
    • 4.13.2 Perform mathematical operation on grid data
    • 4.13.3 Scaling numerical range of grid data
    • 4.13.4 Screen isosurfaces in local regions
      • 4.13.4.1 Screen isosurfaces inside or outside a region
      • 4.13.4.2 Screen isosurfaces outside overlap region of two fragments
    • 4.13.5 Acquire barycenter of a molecular orbital
    • 4.13.6 Plot charge displacement curve
    • 4.13.7 Evaluation of electron density overlap
  • 4.14 Adaptive natural density partitioning (AdNDP) analysis
    • 4.14.1 Analyze Li5+ cluster
    • 4.14.2 Analyze B11- cluster
    • 4.14.3 Analyze phenanthrene
  • 4.15 Fuzzy atomic space analysis
    • 4.15.1 Study delocalization index of benzene
    • 4.15.2 Study aromaticity of phenanthrene by PDI, FLU, FLU-π and PLR
  • 4.16 Charge decomposition analysis and plotting orbital interaction diagram
    • 4.16.1 Close-shell interaction case: COBH3
    • 4.16.2 Open-shell interaction case: CH3NH2
    • 4.16.3 More than two-fragments case: Pt(NH3)2Cl2
  • 4.17 Basin analysis
    • 4.17.1 AIM basin analysis for HCN
    • 4.17.2 ELF basin analysis for acetylene
    • 4.17.3 Electrostatic potential basin analysis for H2O
    • 4.17.4 Basin analysis of electron density difference for H2O
    • 4.17.5 Calculate source function in AIM basins
    • 4.17.6 Local region basin analysis for polyyne
    • 4.17.7 Evaluate atomic contribution to population of ELF basins
  • 4.18 Electron excitation analysis
    • 4.18.1 Analyze hole-electron distribution, transition density, transition dipole moment, charge-transfer and so on for N-phenylpyrrole
    • 4.18.2 Plot transition density matrix of large-size conjugated molecule as color-filled map
    • 4.18.3 Analyze charge-transfer during electron excitation based on electron density difference
    • 4.18.4 Generate and analyze natural transition orbitals (NTOs)
    • 4.18.5 Plot transition dipole moment vector contributed by molecular fragments as arrows
    • 4.18.6 Calculate interfragment charge transfer during electronic excitation for 4-nitroaniline
  • 4.100 Other functions, Part 1
    • 4.100.1 Visual study of weak interaction by RDG (NCI) and DORI method
    • 4.100.4 Calculate kinetic energy and nuclear attraction potential energy of phosgene by numerical integration
    • 4.100.8 Perform simple energy decomposition by using combined fragment wavefunctions
    • 4.100.13 Calculate HOMA and Bird aromaticity index for phenanthrene
    • 4.100.14 Calculate LOLIPOP for phenanthrene
    • 4.100.15 Calculate intermolecular orbital overlap integral of DB-TTF
    • 4.100.18 Yoshizawa's electron transmission route analysis for phenanthrene
    • 4.100.19 ELF analysis on the promolecular wavefunction combined from fragment wavefunctions
    • 4.100.22 Analyze ( electron character of non-planar system: cycloheptatriene
  • 4.200 Other functions, Part 2
    • 4.200.1 Visually studying weak interaction in molecular dynamics simulation by aRDG method
    • 4.200.4 Study iso-chemical shielding surface (ICSS) and magnetic shielding distribution for benzene
    • 4.200.5 Plot radial distribution function of electron density
    • 4.200.8 Calculate polarizability and hyperpolarizability for NH3 via sum-over-states (SOS) method
    • 4.200.12 Calculate energy index (EI) and bond polarity index (BPI)
    • 4.200.13 Localizing molecular orbital of 1,3-butadiene by Pipek-Mezey method
    • 4.200.14 Integrate real space function within reduced density gradient (RDG) isosurfaces to study weak interaction
  • 4.A Special topics and advanced tutorials
    • 4.A.1 Study variation of electronic structure along IRC path
    • 4.A.2 Calculate spin population
    • 4.A.3 Study aromaticity
    • 4.A.4 Predict reactive sites
    • 4.A.5 Study weak interactions
    • 4.A.6 Calculate odd electron density and local electron correlation function
    • 4.A.7 Plot (hyper)polarizability density
    • 4.A.8 Analyze higher level of wavefunction than CCSD
• 5 Skills
  • 5.1 Make Multiwfn support more quantum chemistry programs
  • 5.2 Running Multiwfn in silent mode
  • 5.3 Running Multiwfn in batch mode (for Windows)
  • 5.4 Copy outputs from command-line window to clipboard
  • 5.5 Make command-line window capable to record more outputs
  • 5.6 Rapidly load a file into Multiwfn
• Appendix
  • 1 Setting up environment variable for Gaussian in Windows
  • 2 The routines for evaluating real space functions
  • 3 Detail of built-in atomic densities
  • 4 Details about supplying inner-core electron density for the wavefunctions involving pseudopotential
  • 5 Check sanity of wavefunction
  • 6 Special functions