AIMAll
(Version 11.12.19)

Copyright © by Todd A. Keith
1997-2011 (aim@tkgristmill.com)

Richard F.W. Bader
1931-2012

README for AIMAll (Version 11.12.19)

About AIMAll:

AIMAll is a software package for performing quantitative and visual QTAIM (Quantum Theory of Atoms in Molecules) analyses of molecular systems - starting from molecular wavefunction data.

Two of AIMAll's components (AIMExt and AIMInt) are very heavily modified and extended derivatives of two programs (Extreme and ProaimV) from the AIMPAC package that was developed and maintained by members of Richard F.W. Bader's research group.

TAK was fortunate enough to be one of those members from 1991-1993.

Continued interest in QTAIM and its practical implementation eventually led to the development of AIMAll, which has been a spare-time effort for several years.

The initial goal for AIMAll was to make a QTAIM package that was:

Once this goal was reasonably close to being achieved, work on AIMAll accelerated, including extensive work on a visualization component (AIMStudio) and shared memory multi-processor support for AIMAll calculations.  Visualization and shared memory multi-processor support have recently been added to the AIMAll package.  These features require an AIMAll Professional license in order to be used with non-small wavefunctions.

AIMAll is actively developed to address any issues which may arise, to expand upon existing features and algorithms and to implement new features and algorithms.

AIMAll is available for Windows, Mac OS X and Linux.


Contact:
License Agreement:

Downloading, installing or using "AIMAll (Version 11.12.19)" requires and constitutes acknowledgement of and agreement to the following:
  1. "AIMAll (Version 11.12.19)" is provided by Todd A. Keith (Doing Business As "TK Gristmill Software") "AS-IS", without any expressed or implied warranties of any kind.
     
  2. Todd A. Keith (TAK) disclaims all implied warranties including, but not limited to, implied warranties of merchantability and fitness for a particular purpose.
     
  3. Neither "AIMAll (Version 11.12.19)" nor any of its components may be sold, redistributed, repackaged, bundled, copied, modified, disassembled or reverse engineered in any form, either in whole or in part, without the explicit, written consent of TAK.
     
  4. While TAK believes "AIMAll (Version 11.12.19)" to be useful, TAK makes no guarantees of any kind about the fitness of "AIMAll (Version 11.12.19)" for any purpose, its compatibility with or effect on any computer hardware or software, or the reliability or accuracy of any results it produces.
     
  5. In no event shall TAK be held liable for any damages of any kind arising directly or indirectly from the download, installation or use of "AIMAll (Version 11.12.19)".
     
  6. "AIMAll (Version 11.12.19)" operates either in AIMAll Professional mode or AIMAll Standard mode depending upon the presence of a valid aimallpro.lic file in the main AIMAll directory.
     
  7. The AIMAll Standard operating mode is the default mode.  It does not require an aimallpro.lic file and is free of charge, though registration is requested.   The AIMAll Standard operating mode imposes a limit on the size of the molecular wavefunction data that can be used for running multi-processor calculations, for generating visualization-related data files (*.*viz) by AIMQB, AIMExt, AIMInt and AIMSum, and displaying them with AIMStudio.  This limit is 12 or fewer atoms and 400 or fewer primitive basis functions.  Depending on the evolution of AIMAll, future versions of AIMAll may impose other limits on the AIMAll Standard operating mode.
     
  8. The AIMAll Professional operating mode does not impose any multi-processor limits, visualization limits or other limits on the size of the molecular wavefunction data.  A valid aimallpro.lic file must be present in the main AIMAll directory in order for AIMAll to operate in AIMAll Professional mode.  An aimallpro.lic file is specific to a single computer.  An aimallpro.lic file must be purchased as part of an AIMAll Professional License Pack.  An aimallpro.lic file is permanently valid on the corresponding computer for any version of AIMAll released within at least one year from the time that the aimallpro.lic file is issued.
     
Support and Feedback:

Please report any problems, questions, comments or suggestions only to:  aim@tkgristmill.com


Citation:

If results from "AIMAll (Version 11.12.19)" are used in publications or for other reasons, please use the following citation:

     AIMAll (Version 11.12.19), Todd A. Keith, TK Gristmill Software, Overland Park KS, USA, 2011 (aim.tkgristmill.com)


Contents (Windows):

Contents (Mac OS X):

The contents of the Mac OS X version of AIMAll is similar to Windows except that the application executables are wrapped in bundles (e.g., AIMQB.app) that are used to launch the applications via the Finder and the non-system shared libraries that the AIMAll executables depend on are contained in the Frameworks folder.  The executables in each bundle are located in the the Contents/MacOS subdirectory (e.g., AIMQB.app/Contents/MacOS/aimqb).  To run an AIMAll application from the command line, you can use the executable path.  When running AIMExt, AIMInt and AIMSum directly (instead of indirectly via AIMQB), it is recommended to launch them from AIMStudio or from the command line rather than from the Finder.  AIMStudio and AIMQB are typically launched from the Finder, though command-line usage of AIMQB is sometimes useful.


Contents (Linux):

The contents of the Linux version of AIMAll is similar to Windows except that the application executables are contained in the "bin" subdirectory and the non-system shared libraries that the AIMAll executables depend on are contained in the "lib" subdirectory.  "Wrapper" scripts (e.g., aimqb.ish) for setting up the environment for and running the AIMAll executables are provided in the main AIMAll directory.  Icons for the AIMAll applications are provided in the "icons" subdirectory.  Using the provided wrapper scripts and the icons, users can easily take care of setting up the AIMAll applications for quick launching from most Linux desktops.


Overview of How AIMAll Typically Works:
Example 1:  Typical Usage
  1. Launch AIMQB (Windows: aimqb.exe; Mac OS X Finder: AIMQB.app; Linux terminal: aimqb.ish).
     
  2. Click the "Browse" button and select the file C:\AIMAll\test\cyclopropanone\cyclopropanone.wfn
     
  3. Click the "OK" button in the AIMQB dialog to start the calculation.
     
  4. Wait for a minute or so, until the AIMQB log window says "Job Completed".
     
  5. In AIMStudio, select the File menu item "Open in Text Viewer" to look at the file cyclopropanone.sum.
     
  6. Note that the magnitude of each atom's L value is acceptably small (the L value is ideally zero) and that the difference between the sum of atomic properties and the corresponding molecular value is small.  For example, the atomic charges sum to 0.00003 compared to the molecular charge of zero, and the sum of scaled atomic kinetic energies is -190.77444 compared to the total molecular energy of -190.77440.
     
  7. In AIMStudio, select the File menu item "Open in New Window" and select the cyclopropanone.sumviz file to display the molecular graph derived from cyclopropanone.wfn as well as other data such as electron density critical point properties and atomic properties.  Atomic properties such as the atomic charges can be viewed in the "Atoms Table" by selecting "Table" from the "Atoms" menu.  Atomic property values can also be displayed in the 3D window next to the nuclear spheres by selecting one of the "Atoms->Properties->..." menu items.

Dealing With Problem Atoms:

For AIMAll, much time and effort has been spent on improving the robustness of the default "Proaim" Basin Integration method (compared to its original implementation in AIMPAC) since this method is the most efficient.   Development work on further improvement of the "Proaim" algorithm continues, with the goal of making it even more robust.

It is highly recommended that the default "Proaim" Basin Integration method and the default Basin Quadrature parameters always be tried first since they usually work quite well for most atoms and are relatively fast.

In the event that integration results for one or more atoms are not sufficiently accurate (or are unavailable) using the default integration options, you can rerun AIMQB for just those problem atoms, using different integration options along with the "Atoms to Calculate" fields near the bottom of the AIMQB dialog.

For molecules with very diffuse charge distributions, such as some anions or excited states, increasing the maximum atomic integration radius may be necessary to obtain good accuracy, independent of the basin integration method and basin quadrature parameters.  The following assumes that the maximum atomic integration radius has been set sufficiently large.

If an atom has a "potentially significant" but not "significant" or serious integration error, simply increasing the "Outer Ang" Basin Quadrature to "Very High" or "Sky High" while still using the "Proaim" Basin Integration method might help, and is not too expensive.

The "IAS Mesh" options are specific to the "Proaim" method and control the maximum allowed spacing between adjacent interatomic surface (IAS) paths and hence the fineness of the IAS triangulation and the accuracy of the intersections of the basin integration rays with the IASs.  The default "Fine IAS Mesh" is usually quite sufficient for accurate atomic integrations but the "Very Fine" or "Super Fine" IAS Meshes in conjunction with large quadratures may sometimes be useful for very accurate atomic integrations.

Using the "Promega (1st-Order)" basin integration method is usually a good choice for atoms whose integration results are significantly in error (or are unavailable due to a failure to connect a BCP to an RCP) using the default "Proaim" method.  Note, however, that the "Promega (1st-Order)" method is significantly more expensive than the "Proaim" method.

The method of last resort is usually the "Sculpt" method, which is very expensive but will always work when other methods fail to deliver acceptable accuracy.  The non-default "Extended Capture" option can be used to significantly speed up the "Sculpt" method, at the slight risk of causing the method to fail.

The "Promega (3rd-Order)" method is similar to the "Promega (1st-Order)" method except that up to 3 intersections of the integrations rays with the atomic surfaces are searched for.  While the "Promega (3rd-Order)" is at least as accurate and sometimes more accurate than the "Promega (1st-Order)" method, it is also much slower.

Once a rerun of AIMQB for just the specified problem atoms is done, the .sum file and possibly .sumviz will automatically be properly upated to include the results for the newly calculated atoms.


Example 2:  Recalculation of Problem Atom(s) Using Higher Angular Quadrature Outside of Beta Sphere
  1. Launch AIMQB.
     
  2. Select the file C:\AIMAll\test\n4c2_c2h\n4c2_c2h.wfx
     
  3. Click the "OK" button.
     
  4. Wait for a couple of minutes, until the AIMQB log window says "Job Completed".
     
  5. In AIMStudio, select the File menu item "Open in Text Viewer" to look at the file n4c2_c2h.sum.
     
  6. Note the warnings about the potentially significant integration error for the N3 and N4 nitrogen atoms and the potentially significant cumulative integration error.  These errors are not severe, but can likely be reduced.  Inspection of the n4c2_c2h_n3.int and n4c2_c2h_n4.int files does not indicate a failure of the "Proaim" algorithm to trace and triangulate the interatomic surfaces, so the "Proaim" integration accuracy can probably be improved simply by increasing the "Outer Ang" angular quadrature level.
     
  7. Close the file n4c2_c2h.sum and launch AIMQB again.
     
  8. Select the file C:\AIMAll\test\n4c2_c2h\n4c2_c2h.wfx again.
     
  9. Select "Sky High" from the left-most Basin Quadrature combobox.
     
  10. Select "Connectivity and Integration of Listed Atoms" from the "Atoms to Calculate" combobox.
     
  11. Enter "3 4" (without the quotes) in the line editor to the right of the "Atoms to Calculate" combobox.
     
  12. Click the "OK" button.
     
  13. Wait for a few minutes, until the recalculation of the atom N3 and N4 atoms is completed, the updating of the n4c2_c2h.sum file is done and the AIMQB log window says "Job Completed".
     
  14. Look at the file n4c2_c2h.sum again and note that the magnitude of the N3 and N4 atoms' L values are much smaller and the sums of atomic properties are also now in better agreement with the corresponding molecular values.
     
  15. If you haven't already done so, launch AIMStudio and open the file n4c2_c2h.sumviz to display the molecular graph and other data such as critical point properties and atomic properties.

Example 3:  Recalculation of Problem Atom(s) Using "Promega"
  1. Launch AIMQB.
     
  2. Select the file C:\AIMAll\test\triazine_crownh+\triazine_crownh+.wfx
     
  3. Click the "OK" button.
     
  4. Wait for a couple of minutes, until the AIMQB log window says "Job Completed".
     
  5. In AIMStudio, select the File menu item "Open in Text Viewer" to look at the file triazine_crownh+.sum.
     
  6. In the .sum file, note the "data not available" statements for the N2, N8, N9 and H10 atoms. Inspection of the triazine_crownh+_n2.int, triazine_crownh+_n8.int, triazine_crownh+_n9.int and triazine_crownh+_h10.int files reveals the failure of the "Proaim" algorithm to connect a BCP to an RCP (a necessary step for the "Proaim" algorithm when RCPs are present in an atomic surface) so a different basin integration algorithm is needed for the N2, N8, N9 and H10 atoms. This is is also visually obvious by inspection of the Ring Paths after opening the triazine_crownh+.sumviz file with AIMStudio.  The reason for the failure is the extreme flatness of the electron density between the BCPs and RCPs connecting the proton to the ring.
     
  7. Close the file triazine_crownh+.sum and launch AIMQB again.
     
  8. Select the file C:\AIMAll\test\triazine_crownh+.sum\triazine_crownh+.sum again.
     
  9. Select "Promega (1st-Order)" from the Basin Integration Method combobox.
     
  10. Select "Connectivity and Integration of Listed Atoms" from the "Atoms to Calculate" combobox.
     
  11. Enter "2 8 9 10" (without the quotes) in the line editor to the right of the "Atoms to Calculate" combobox.
     
  12. Click the "OK" button.
     
  13. Wait for several minutes (the "Promega" method is inherently slower than the "Proaim" method) until the recalculation of N2, N8, N9 and H10 atoms is completed, the updating of the triazine_crownh+.sum file is done and the AIMQB log window says "Job Completed".
     
  14. Look at the file triazine_crownh+.sum again and note that results for all atoms are now present and the magnitude of the L value for each of the atoms (including the N2, N8, N9 and H10 atoms) is acceptably small and the sums of atomic properties are also in pretty good agreement with the corresponding molecular values.
     
  15. Look at the file triazine_crownh+.sum (and / or triazine_crownh+.sumviz with AIMStudio) again and note that results for all atoms are now present and the magnitude of the L value for each of the atoms (including the N2, N8, N9 and H10 atoms) is acceptably small and the sums of atomic properties are also in pretty good agreement with the corresponding molecular values.

Main File Types:
Wavefunction Files:

The primary input data for all of the AIMAll programs except AIMStudio is an AIM "Wavefunction" file.

AIM Wavefunction files can be generated by g09, g03, GAMESS and possibly other ab-initio quantum chemistry packages.  Consult the documentation for your ab-initio quantum chemistry package to see how this is done.


Formatted Checkpoint Files:

For convenience, aimqb.exe can open a g09 or g03 fchkfile and automatically generate a corresponding wfnfile or wfxfile, which will have the same base name.  For g03, this is the recommended procedure to ensure consistency between the data in the wavefunction file and what AIMAll expects.


System Requirements for "AIMAll (Version 11.12.19)":
Some Limitations of "AIMAll (Version 11.12.19)":
References:
Copyright © 1997-2011 by Todd A. Keith