Gennbo Helper

After a string of blogs on visualization of NBO orbitals in Jmol, today I am going to introduce new application:

Gennbo Helper

Gennbo Helper is java-based application which offers a simple way of generating:

•  Keylists and the corresponding keywords for standalone program GENNBO5/6 (processing of existing archive files (FILE47))
•  Keylists and the corresponding keywords for ESS-linked or "embedded" NBO modules
•  Input files with nbo keywords for two ESS/NBO programs, namely Gaussian09 and PC-GAMESS/Firefly

Gennbo Helper assists with syntax of NBO keylists and keywords and formats them for input into standalone Gennbo program.

The main reason behind Gennbo Helper was to "script" repetitive tasks behind preparation of .47 archive files, running the stand-alone GENNBO module, and consistently writing properly formatted ESS input files.

Fig. 1 Gennbo Helper GUI.

Being written in Java7 code, this application requires having the latest version of Java installed on your computer. Gennbo Helper was developed and tested in java environment of Windows 7 and Linux systems. Installation is rather simple. Files from GennboHelper.zip archive can be placed into any disk/directory on your system.

Without any doubts, efficient use of Gennbo Helper assumes familiarity with NBO concepts and programs developed by Frank Weinhold at the University of Wisconsin. Reference section below lists key resources, which are invaluable for better understanding of chemical phenomena predicted by NBO analysis.

Since this application makes direct use of standalone NBO6w program, having NBO6w installed on your computer will fully utilize capabilities of Gennbo Helper. For details and availability of NBO programs, visit the NBO6 website.

Gennbo Helper works with local NBO6 gennbo executable to process .47 archive files. Alternatively, modified .47 file can be used as input for the older Gennbo5W program.

Brief Overview:

Gennbo Helper graphical user interface (Fig. 1) consists of three main areas:

1) File input (top area)
2) Options (middle section)
3) Output (bottom area)

Archive file .47 is loaded first at the top by clicking "1. Browse dir" button. Filename and extension is parsed into different text fields and optional suffix can be added.

Fig. 2 Basic keywords tab

Middle panel is subdivided into three tabs for different tasks. On the Basic keywords panel, options are selected by checking the corresponding check boxes, levels, atom lists, and drop-down menus (Fig. 2). In the middle part of Options is a group of control keywords. By selecting Plot or Archive keyword will always set FILE keyword on as well. Clicking button "3. Create/Append input" generates string of NBO keywords in the output area below (in blue). Typical flow includes clicking "Write *47" and "Run Gennbo6" buttons. String of formatted NBO keywords is inserted into .47 archive file and processed by nbo6 modules. Alternatively, older GENNBO5W can be used to load and run modified .47 file manually.

On the Keylists tab (Fig. 3), user can create two main keylists with their specific keywords. Those are $CHOOSE and $DELETE. The former list can be used with standalone GENNBO application, the latter list with ESS-linked nbo6 modules or with ESS program having nbo routines included. While NEDA and NCS keywords are not necessarily parts of $DEL list, they were added into this group as they also require nbo modules being either internal or linked to ESS program. If format of keylist is incorrect, warning message will appear asking you to correct formatting. Hovering mouse over any field will display tip on format or the keyword.

Fig. 3 Keylists

ESS Input tab (Fig. 4) allows generating basic input files for two ESS programs, Gaussian 09 and GAMESS/FIREFLY. Molecular geometries can either be pasted in or loaded from Examples drop-down menu. From this tab, input file with instructions to generate the necessary .47 archive file can be created and directly used with the two ESS programs mentioned above. Pull-down menus and check boxes offer selection of computational method, examples of molecular geometries, symmetry, and other options to be added into input files. After all the necessary parameters are entered, click on buttons 4.-5.-6. “Create NBO input” button has the same function as button “3. Create/Append input”. It populates the output area with NBO keywords. “Save NBO param” will copy all keylists and keywords from the nbo output area and “Generate Input” button will create new .inp or .gjf file for use in FF or G09, respectively.

Checking the new checkbox “Run” and clicking button 6. will generate windows batch file “gaussrun.bat” in the directory set by clicking button 2. If Gaussian program is installed in C:/G09W, the job will start immediately. This option was added for a greater convenience of Windows users and won’t work on other systems. All options except of running Gaussian (&Run) work also under Linux OS.

Fig. 4 ESS Input tab

In case that GAMESS/Firefly option was checked, button "6. Generate Input" will also create initialization batch file filename_RUN.bat in the directory of Firefly executable. To launch Firefly job, just double-click the .bat file.

In the Input and Output areas, there are two drop-down menus with nbo keyword presets and user settings. NBO keywords that are generated by user (or just typed in) can be saved (and re-used) in three different User settings.

Batch Input tab (Fig. 5) allows GENNBO processing of multiple .47 files from one directory. Running a batch of .47 files is independent of other settings in the app.

Prerequisites:
In order to process .47 files by GENNBO6 modules, a helper jvgennbo.bat file has to be present in the main NBO6 directory (here c:/nbo6w). The file is part of the download. Since it is Windows file, the Batch processing is limited to Window users.

1. First set the NBO6 (GENNBO) directory using the button “2. Load Dir”.
2. Load .47 files by clicking the “Load Files” button (1.) and by control-selecting multiple files in that directory. Selected files will appear in the Batch list area.
3. Write NBO keywords and lists into $NBO $END section of the .47 files. By clicking the “Write Batch” button, keywords in the NBO keyword and keylist area will be inserted into all .47 files. Successful insertion of keywords will be indicated in the Notification area at the bottom of the window.
Optionally, if .47 files already have $NBO section populated, skip the “Write Batch” step. Clicking the “Write Batch” button (2.) with no keywords in the Keyword and keylist area, default keyword PRINT=0 will be used.
4. By pressing “Run batch” button (3.) a loop feeding each .47 file into GENNBO modules will be launched. Progress monitor bar will indicate status of the processing and current file being process by GENNBO modules will be shown in the text field left of the progress bar. Upon completion, a message window will pop up.

Fig. 5 Batch List tab

Download:

The latest version of GennboHelper.zip file (ver 1.32 on April 2015) can be downloaded from NBO Scripts and Handy Applications website. Gennbo Helper manual, README file, and accessory files are included.

Video Tutorial:

References:

• NBO6 manual
• F. Weinhold, “Natural bond orbital analysis: A critical overview of relationships to alternative bonding perspectives,” J. Comput. Chem. (2012).
• F. Weinhold and C. R. Landis, Valency and Bonding: A Natural Bond Orbital Donor-Acceptor Perspective (Cambridge U. Press, 2004), 760pp.
• F. Weinhold and C. R. Landis, Discovering Chemistry with Natural Bond Orbitals (Wiley-VCH, 2012), 319pp.
• References at NBO6 Website.