文/Sobereva @北京科音 2019-May-21
随着程序的进步，手册也在不断地扩充、完善，为此花费了极大的精力，3.5版手册是522页，而3.6正式版的手册已达717页。由于手册已经很庞大，为了让新用户可以快速从中找到做自己需要的分析对应的章节，特意在可执行文件包里增加了quick start文档，用户可以迅速从中查到自己要做的分析在哪一节有详细介绍、在哪一节有具体例子。还专门撰写了《Multiwfn FAQ》（http://sobereva.com/452），汇总了所有Multiwfn用户常见问题。
• 支持了core-valence bifurcation (CVB)指数，对于研究氢键很有帮助，见《使用Multiwfn计算CVB指数考察氢键强度》（http://sobereva.com/461）
• 支持了在ACS Omega, 3, 18370 (2018)新提出的基于信息理论定义的芳香性指数，见手册3.18.11节
• 球对称平均的ELF和LOL现已可以计算，这可以用于做J. Comput. Chem., 38, 2258 (2017)和J. Phys. Chem. C, 123, 4407 (2019)中提出的DFT泛函的ELF调控、LOL调控。见3.100.4节
• 支持了刘述斌教授在J. Chem. Phys., 126, 244103 (2007)中提出的能量分解方法，见3.24.2节的介绍和4.21.2节的例子
• 结合VMD已可以绘制漂亮的填色Hirshfeld/Becke表面图，对于研究弱相互作用，特别是晶体分子中的弱相互作用极其有用，见《使用Multiwfn结合VMD绘制Hirshfeld surface图分析分子晶体中的弱相互作用》（https://www.bilibili.com/video/av35738671/）
• 支持了对ORCA常见类型任务产生输入文件的功能，详见《Multiwfn已经可以产生ORCA中最常用计算级别的输入文件》（http://bbs.keinsci.com/thread-13109-1-1.html）。一个实际应用例子见《Simulating UV-Vis and ECD spectra using ORCA and Multiwfn》（http://sobereva.com/485）
- A very powerful and easy-to-use RESP module is added into main function 7 (Population analysis). It can calculate the well-known ElectroStatic Potential (RESP) charge proposed in J. Phys. Chem., 97, 10269 (1993), and can also calculate ESP fitting charges under various customized conditions such as atomic equivalence constraint and fragment charge constraint. Multiple conformation is fully supported. See Section 3.9.16 for detailed introduction and Section 4.7.7 for examples. This module should be able to bring a revolution in the field of RESP charge derivation.
- Energy decomposition analysis based on UFF/AMBER/GAFF molecular forcefield is supported as subfunction 1 of main function 21. See corresponding introduction in Section 3.24.1 and examples in Section 4.21.1 of the manual.
- A new parameter "cubegenpath" is introduced into settings.ini file. If the parameter is set to actual path of cubegen utility of Gaussian package and the input file is .fch/fchk type, for most analyses of electrostatic potential (ESP), such as plotting plane map of ESP, molecular surface analysis of ESP, the ESP data will be calculated using cubegen instead of internal code of Multiwfn, the overall computational time will be significantly reduced, especially for large systems (since speed of calculating ESP by cubegen is evidently faster than current version of Multiwfn). See Section 5.7 of manual for detail.
- If .chg file is used as input file, now it can be converted to .pqr file using subfunction 2 of main function 100. The .pqr file can be directly loaded into VMD. This feature is very useful if you want to vividly exhibit atomic properties (e.g. atomic charges, atomic spin populations, condensed Fukui function) calculated by Multiwfn by means of coloring atoms. See Section 4.A.10 of the manual for illustration.
- Subfunction 21 of main function 100 is extended, now it can easily calculate molecular length/width/height and diameter. See Section 4.200.21 of the manual for example.
- Raman optical activity (ROA) spectrum now can be plotted via main function 11 based on Gaussian output file, see Section 3.13 for detail and Section 4.11.7 for example.
- Almost all kinds of kinetic energy density (more than twenty) have been supported by Multiwfn as user-defined function 1200. See corresponding part of Section 2.7 of the manual for detail.
- Option -3 is added to MK and CHELPG charges calculation module, by using it, it is able to examine electrostatic potential reproducibility of given atomic charges around the whole system or around specific region, see Section 4.7.8 for example.
- Biorthogonalization between alpha and beta orbitals is supported as subfunction 12 of main function 100. For UHF or UKS wavefunction, after applying this transformation, alpha orbitals will be almost perfectly paired with beta orbitals, so that you no longer need to separately discuss two set of spin orbitals, this makes analysis of orbitals much easier. See Section 3.100.12 for introduction and 4.100.12 of example.
- The aromaticity index defined based on information-theoretic quantities in ACS Omega, 3, 18370 (2018) has been supported as subfunction 12 of main function 15. See Section 3.18.11 for detail.
- The core-valence bifurcation (CVB) index, which is a useful quantity of distinguishing strength and classifying H-bonds, now is supported as subfunction 1 of main function 200, see Section 3.200.1 for introduction and example.
- In main function 19, center position of localized molecular orbitals (LMOs) can be given and directly visualized, see updated Section 4.19.1 for example. In addition, dipole moment of LMOs and bond polarity now can be studied, see Section 4.19.4 for example. Introduction of related theories have been added to Section 3.22.
- The spherically symmetric average ELF and LOL now can be calculated by subfunction 4 of main function 100, see Section 3.100.4 for detail. These quantites are key ingredient of the ELF-tuning and LOL-tuning, which were proposed in J. Comput. Chem., 38, 2258 (2017) and J. Phys. Chem. C, 123, 4407 (2019), respectively.
- A "quick start" document has been added into binary package, it should be particularly useful for new Multiwfn users, since via this they can quickly find needed information for performing common analyses.
- The energy decomposition method proposed by Shubin Liu in J. Chem. Phys., 126, 244103 (2007) has been supported as subfunction 2 of main function 21. Please check Section 3.24.2 for introduction and Section 4.21.2 for example.
- The density-of-states (DOS) plotting module now has a special interface aiming for easily plotting photoelectron spectrum (PES) based on (generalized) koopmans theorem, see Section 3.12.4 for introduction and Section 4.10.4 for example.
- Subfunction 22 of main function 100 has been significantly extended, now it can automatically detect pi orbitals based on localized molecular orbitals for both planar and non-planar systems; moreover, pi composition of any kind of orbitals can be evaluated. This feature makes separate study of sigma and pi electrons extremely easy for any system. See Section 3.100.22 of the manual for detail and Section 4.100.22 for illustrative application.
- Subfunction 16 has been added to main function 100, it can automatically calculate all important quantities defined in the framework of conceptual density functional theory via minimal steps (including Fukui function and dual descriptor as well as their condensed form, Mulliken electronegativity, hardness, electrophilicity and nucleophilicity index, softness, local softness, relative electrophilicity and nucleophilicity, etc.)
UPDATES ABOUT ELECTRON EXCITATION ANALYSIS MODULE
- Hole-electron analysis module has been significantly rewritten. Definition of some indices have been changed and the result will be different to older version. This module now supports a new definition for measuring overlap between hole and electron, it is named as Sr, while the old one is named as Sm. Basis function, atom and fragment contribution to hole and electron distribution now can be directly printed. In addition, atom and fragment contribution can be vividly plotted as heat map. See Section 3.21.1 for introduction and Section 4.18.1 for example.
- The Λ (Lambda) index proposed in J. Chem. Phys., 128, 044118 (2008) has been supported as subfunction 14 of main function 18, it has been prevalently employed in literatures to determine type of electron excitations. See Section 3.21.14 for introduction.
- By newly added subfunction 13 of main function 18, natural orbitals for a batch of selected excited states can be generated and exported to .molden file. See Section 3.21.13 for detail and Section 4.18.13 for example.
- The transition density matrix plotting function (subfunction 2 of main function 18) now can plot fragment based TDM map. In addition, this function now can automatically generate TDM between ground state and selected excited state and thus becomes much easier to use. See Section 3.21.2 for introduction and Section 4.18.2 for example.
- The function of generating transition density matrix (TDM) has been moved to subfunction 9 of main function 18. At the meantime, this function now supports generating TDM between two selected excited states.
- Definition of some quantites outputted by subfunction 3 of main function 18 (Analyze charge-transfer based on density difference grid data) has been modified to make the result more meaningful, see Section 3.21.3 for detail.
- Delta_r index now can be calculated for a batch of excited states at one time (subfunction 4 of main function 18).
- Speed of calculating transition electric dipole moment between excited states (subfunction 5 of main function 18) has been remarkably improved.
- In the function "Calculate interfragment charge transfer in electron excitation via IFCT method" (subfunction 8 of main function 18), a batch of fragments now can be simultaneously defined and the result between all fragments are outputted together. Notice that the equation used in this function in older version is incorrect, this problem has been fixed. See Section 3.21.8 for introduction of this method and Section 4.18.8 for example.
- The function "Generate transition density matrix" has been moved to subfunction 9 of main function 18 from hole-electron analysis module. At the meantime, speed of this function was significantly improved.
- The function "Decompose transition electric dipole moment as molecular orbital pairs contribution" has been moved to subfunction 10 of main function 18 from hole-electron analysis module. At the meantime, speed of this function was significantly improved, and the terms can be sorted and outputted according to contribution to transition dipole moment.
- The function "Decompose transition dipole moment as basis function and atom contributions" has been moved to subfunction 11 of main function 18 from hole-electron analysis module.
- The function "Check, modify and export configuration coefficients of an excitation" has been moved to subfunction -1 of main function 18 from hole-electron analysis module. In addition, this function now can export user-modified configuration coefficients to an external file, which can then be directly used as input file for all subfunctions in main function 18.
- Output files of TDDFT task of Firefly and GAMESS-US programs are fully supported as input file for all kinds of electron excitation analyses, see beginning of Section 3.21.
- Option 4 is added to subfunction 5 of main function 18. This option is able to calculate dipole moment for all excited state at once.
- Generating transition density and transition dipole moment density between two excited states is available now, see Section 184.108.40.206 for example.
Numerous improvements and changes have been made for main function 18, they are summarized as follows. At the meantime, the corresponding sections of the manual have been significantly rewritten.
IMPROVEMENTS AND CHANGES
- Calculation speed of charge decomposition analysis for large systems has been significantly improved.
- Section 4.A.13 has been added to manual, it describes how to very easily plot pretty ESP colored molecular vdW surface map as well as penetration map of monomer vdW surface in VMD program based on output file of Multiwfn.
- Section 4.2.5 has been added to the manual, it describes how to very easily plot pretty AIM critical points and topology paths in VMD program based on output file of Multiwfn.
- In the MK and CHELPG module, if option 6 as been chosen once, then after calculation, fitting points with exact ESP value or absolute difference between the exact ESP and the ESP evaluated by atomic charges can be exported to .pqr file, which can be directly render in VMD. The example in Section 4.7.8 utilized this feature.
- Algorithm detail of ADCH atomic charge has been changed, see Section 3.9.9 of the manual for detail. If the system has local planar (or almost planar) regions, the ADCH charges in these regions obtained via the new version may be different to those obtained via older versions. The result produced by the new version should be more reasonable. Similarly, the result of atomic dipole moment corrected Becke charges is also different to the older versions.
- .pqr file is supported as input file. For Multiwfn, the information provided by .pqr and .chg is the same, namely atom information as well as atomic charges, see Section 2.5 of the manual.
- Output file of Firefly has been experimentally supported. After changing the suffix of output file of Firefly to .gms, the file can be directly loaded into Multiwfn to provide wavefunction information.
- Molden input file produced by NWChem has been formally supported. See beginning of Chapter 4 of the manual on how to properly generated it.
- Option 8 is added to post-process menu of main function 4 for most kinds of plane maps. Using this option, chemical bonds can be drawn on the graph as straight lines.
- When using Independent Gradient Model (IGM) anaylsis, if your input file contains wavefunction information, the program will let you choose the kind of the sign(lambda2)rho to be used, the first one is that based on actual electron density, the second one is that based on promolecular density.
- Section 4.7.6 is added to the manual, in which I discussed how to easily determine correspondence between basis functions and atomic orbitals via Mulliken population analysis.
- Section 4.4.9 is added to the manual to illustrate how to plot LOL-pi map for porphyrin to reveal favorable electron delocalization path.
- Section 4.2.4 is added to the manual to illustrate how to decompose properties at a critical point or given point as orbital contributions.
- Interface of Mulliken population analysis (MPA) is improved, meantime Section 4.7.0 is added to the manual to illustrate the use of MPA.
- When outputting vtx.pdb in post-process menu of quantitative molecular surface analysis, for electrostatic potential analysis, if value at any surface vertex exceeded recording limit of B-factor field of .pdb file, eV will be used instead of kcal/mol.
- Content of Section 4.12.7 of the manual has been replaced, now it corresponds to a newly added example, namely illustrating how to predict density of molecular crystal based on result of quantitative molecular surface analysis
- Section 4.17.1 of the manual is extended to illustrate how to carry out AIM basin analysis for the systems containing pseudoatoms (non-nuclear attractors of electron density)
- After integrating specific domain in domain analysis module (subfunction 14 of main function 200), minimum and maximum X/Y/Z of points belonging to the domain, as well as span distance in X/Y/Z will be outputted. In addition, option 11 is added to post-process menu, which is used to export boundary grids of specific domain to a .pdb file, so that you can easily use such as VMD program to measure size of the domain. These updates are quite useful for characterizing molecular cavity (see Section 220.127.116.11 of the manual)
- In the interface of defining fragments for plotting PDOS and OPDOS, the fragments now can be directly defined according to angular moment of atomic orbital. Meantime, the DOS plotting example in Section 4.10 has been extended to reflect this improvement
- Subfunction 28 is added to wavefunction modification module (main function 6), it is used to modify orbital energies. This function is useful when you want to rectify the orbital energies using a given relationship (e.g. J. Am. Chem. Soc., 121, 3414 (1999)) before plotting density-of-states (DOS) map.
- Section 4.A.7 has been added to the manual to show how to study polarizability and hyperpolarizability densities by Multiwfn. This method is important for studying local contribution to (hyper)polarizability.
- Section 4.9.5 has been added to the manual to illustrate the usefulness of decomposition analysis of Mulliken bond order.
- The atomic radii used in MK and CHELPG charge fitting now can be set via option 10 in corresponding interface. The default radii of Na, Mg, Al, Si used in MK fitting have been modified (the older ones are not quite reasonable).
- Options 7 and 8 are added to post-process menu of IGM module. They are used to set delta_g and delta_g_inter where sign(lambda2)rho is out of specific range. Obviously, by these options you can screen unwanted regions from isosurface map of delta_g and delta_g_inter map.
- "imodlayout" in settings.ini now can be set to 2, the layout of all GUI will be very suitable for 1024*768 resolution.
- The option "2 Delete some CPs" in subfunction -4 of topology analysis module has been significantly extended, now it can also delete CPs according to type and distance to a given molecular fragment.
- Using the newly added option "10 Set the atoms to be considered in searching modes 2, 3, 4, 5" in subfunction -1 of topology analysis module, one can only search CPs in a given molecular region.
- Subfunction 9 of main function 100 now can evaluate and print index for measuring interatomic connectivity.
- When calculating AdNDP and LMO orbital energies, Fock matrix now can be directly loaded from $FOCK field of NBO .47 file.
- Generation of path in topology analysis module has been parallelized, the speed is improved significantly!
- New parameter "plotwinsize3D" has been added to settings.ini, it controls the size of the plotting region for 3D objects in GUI
- The .fchk files generated by PSI4 since 1.2 have been formally supported, and the way of analyzing CCSD(T) wavefunction generated by PSI4 has been changed, see Section 4.A.8 for detail.
- When showing orbital list in console window via "Orbital info." option of main function 0, for beta orbitals, now the index counted from the first beta orbital is also shown.
- Main function 11 now is able to plot spin-orbit coupling corrected (SOC) UV-Vis and ECD spectra based on SOC-TDDFT calculation of ORCA 4.1. See Section 3.13.2 of detail and Section 4.11.6 for example.
- In main function 1, when you request Multiwfn to print properties at nuclear position of an atom, the electrostatic potential without contribution of nuclear charge of this atom now is simultaneously printed (this quantity at hydrogen site is useful in pKa studies, because it measures binding strength between this proton and rest of the system). Due to this update, the procedure of the example in Section 4.1.2, which introduces how to predict intermolecular interaction energy based on ESP at nuclear position, has been significantly simplified.
- Thickness of lines/curves/axes/texts in spectrum plotting module (main function 11) now can be set by the newly added option 22.
- The molden input file generated by Grimme's xtb code has been supported.
- In the GUI windows showing 3D objects, now one can zoom in and zoom out the perspective by rotating mouse wheel on the drawing region.
- In the GUI of showing structure and orbitals (main function 0), the "Other settings" in the menu bar has been extended significantly. Its options now is able to choose atomic label type, atomic label color, set lighting and select predefined drawing style (CPK, vdW, line)
- In the GUI of topology analysis, label color of critical points and atoms now can be set via "Set label color" in the menu bar.
- Section 4.A.11 is added to the manual, this section presents an overview of all methods supported by Multiwfn that can be used to discuss chemical bonds.
- .gjf is now supported as input file, it can provide atomic coordinate information to Multiwfn.
- Magnitude of electric field is added as the 103th user-defined function.
- .mol2 is supported as input file.
- .chk file can be directly loaded as long as you have set "formchkpath" in settings.ini to actual path of formchk executable file in Gaussian package.
- Section 4.11.8 is added to the manual, it describes how to extremely easily plot spectrum for a batch of files via shell script
- For unrestricted wavefunction, now one can plot various kinds of DOS maps for alpha and beta spin simultaneously. The spin can be chosen via option 6 in DOS plotting interface.
- cube file with non-rectangle grid now can be loaded, however, in this case only the grid data calculation function in main function 13 could be normally used.
- In the AdNDP module, the option used to export cube files has been improved.
- The rarely used subfunction 7 of main function 100 is removed. Instead, when user export Gaussian .gjf using the subfunction 2 of main function 100 and meantime wavefunction is presented, the wavefunction can be written into the .gjf as initial guess.
- The interface of outputting ORCA input file (option 12 of subfunction 2 of main function 100) now is able to specify commonly used level and type of task.
- The function for calculating intermolecular orbital overlap integral is no longer limited for Gaussian users, see updated Section 3.100.15 of manual for detail.
- The default integration grid for computing orbital composition via Hirshfeld/Hirshfeld-I/Becke has been slightly changed to make result evidently more accurate for orbitals showing Rydberg character
- In the orbital localization module (main function 19), now Hirshfeld is employed as the default method to automatically compute composition of the resulting LMOs, it is more robust than the Mulliken+SCPA method used in earlier verison and compatible with diffuse functions.
- The method of calculating orbital composition for LOBA analysis has been changed to Hirshfeld, which is more robust than the SCPA method used in earlier version.
- In the DOS plotting module (main function 10), Hirshfeld and Becke methods have been supported for calculating orbital compositions, which are more robust than the Mulliken/SCPA method used in earlier version and compatible with diffuse functions. See Part 6 of Section 4.10.1 for example.
- More options have been added to the post-process menu of DOS plotting module to make it more flexible, and many improvements have been made to make graphical effect better.
- A section 4.A.14 has been added to manual, it introduces a way of very easily rendering cube files produced by Multiwfn as state-of-the-art isosurface map via VMD script.
- Option 13 has been added to post-process menu of quantitative molecular surface analysis module. Via this new option one can easily plot pretty color-mapped Hirshfeld/Becke surface isosurface via VMD program to illustrate intermolecular interactions, see updated Section 4.12.6 for example.
- Overband and combination band of IR, VCD and Raman spectra now can be plotted by main function 11 based on output file of corresponding Gaussian anharmonic tasks.
- Option -1 has been added to the plotting plane definition interface of main function 4. By this option you can set translation and rotation of the plotting plane. This point has been mentioned in Section 3.5.2 of the manual, a practical instance of using this option was posted on http://bbs.keinsci.com/thread-11037-1-1.html.
- Subfunction 8 is added to option -5 of topology analysis module, it is used to only retain bond paths (and corresponding BCPs) connecting two fragments but remove all other bond paths, so that one can more easily study interfragment interactions via AIM method. See Section 4.2.6 for illustration this option.
- Fixed a fatal bug in the calculation of beta, gamma and delta via sum-over-states (SOS) method. This bug was introduced since version 3.5.
- Due to some bugs in EDFlib library, (3,+3) rather than (3,-3) type of AIM critical points are located at nuclear position for some elements when pseudopotential is employed. This problem has been fixed via updating EDFlib.
- When drawing spectra for multiple systems based on .dat file outputted by Grimme's sTDA program, Multiwfn crashes. This problem has been fixed.
- When custom operation involves "+" operator, the program doesn't work. This problem has been fixed, thanks jimkress for reporting.
- GAMESS-US output file cannot be loaded properly when pseudopotential is used, this problem has been solved, thanks PedroS for reporting.
- The sign of Coulomb attractive energy (exciton binding energy) outputted by hole-electron analysis module has been inverted, now this quantity is always positive to in line with literature convention.
Local DOS map for beta part of unrestricted wavefunction is incorrect, this problem has been fixed.