AIMAll
(Version 17.11.14)

Copyright © by Todd A. Keith
1997-2017 (aim@tkgristmill.com)

Frequently Asked Questions About AIMAll



General FAQs

Wavefunction FAQs

Property FAQs

Error and Warning FAQs

AIMQB FAQs

AIMStudio FAQs



Does AIMAll have any visualization capabilities?

Yes, AIMAll has a visualization component called AIMStudio that allows all results from AIMAll calculations to be interactively visualized in 3D windows and in customizable tables.  Screenshots from AIMStudio are available here.  A list of visualization-related features is available here.


Does AIMAll have a manual?

A basic operating manual, with tutorials, is provided in html format.  It is accessible via the Help menu of AIMStudio.  The help page for AIMQB is available here.  AIMStudio is designed to be intuitively easy to use and status bar help and / or tooltip help is available throughout AIMStudio.  Also, see the README file, these FAQs and the list of References.  Note that the primary numerical result files from AIMAll calculations, the .sum files, are written to be self-describing.


Does AIMAll have an official mailing list, message board, user forum, etc.?

Not at this time, but this is something that is being investigated.  In any event, users are encouraged to contact Todd A. Keith at aim@tkgristmill.com with questions, comments, suggestions or problems related to AIMAll.


Does AIMAll impose any limits on the size of the wavefunction, i.e., the number of nuclei, MOs or primitive functions?

No limits are imposed on computational functionality for either the AIMAll Standard operating mode or the AIMAll Professional operating mode.  Visualization-related functionality and shared memory multi-processor support is limited to 12 atoms or less and 400 primitives or less for the AIMAll Standard operating mode.  No limits are imposed on visualization-related functionality or shared memory multi-processor support with the AIMAll Professional operating mode.


Can AIM wavefunctions derived from calculations using Spherical Harmonic / Pure (in other words 5D, 7F, 9G, 11H instead of 6D, 10F, 15G, 21H) Gaussian basis sets be used?

Yes, as long as the Pure Gaussian basis set has been properly converted to the equivalent Cartesian Gaussian basis set when the AIM wavefunction is created.  This conversion is done automatically by AIM wavefunction writers.  The definition (which is used for historical reasons rather than logical ones) of the Cartesian Gaussian primitive type numbers appearing in both traditional AIM .wfn files and extended AIM .wfx files is given here.


Can wavefunctions derived from Semi-Empirical calculations be used?

No.


Can wavefunctions derived from calculations using Effective Core Potentials (ECPs) be used?

Yes, as long as the wavefunctions are AIM Extended Wavefunction files (.wfx files) that include additional core density function data to represent the electron density of the ECP-modeled core electrons.  More information can be found here.  Note that Gaussian 09 B.01 and later support writing .wfx files and automatically writes <Number of Core Electrons> and <Additional Electron Density Function (EDF)> data sections to the .wfx file when the wavefunction is based on an ECP calculation.

In the absence of core electron densities, numerous spurious electron density critical points appear that complicate QTAIM analyses.  For an atom for which a "small-core" or "medium-core" ECP was used, the spurious electron density critical points are typically confined to the core region and they can, in principle, just be ignored.  In practice, it is better to model the missing core electron density and eliminate the spurious critical points.  For an atom for which a "large-core" ECP was used, spurious electron density critical points typically occur even in the valence regions and the topology of the electron density is changed throughout the neighborhood of the atom and QTAIM analyses become meaningless.  In such cases, one has no choice but to model the missing core electron density.

The .wfx files written by Gaussian B.01 and later for ECP-based wavefunctions automatically include, as needed, atomic core electron densities derived from all-electron, relativistic calculations of free atoms.

But for an atom for which a "small-core" or "medium-core" ECP was used, it is usually sufficient to model the core electron density using a simple tight electron density function to restore the strong electron density maximum at the nucleus and eliminate the spurious critical points.  If you do not already have atomic core densities in your wavefunction, you can add the following data section to the bottom of .wfx file for each atom that used a "small-core" or "medium-core" ECP:

<Additional Electron Density Function (EDF)>
<Number of EDF Primitives>
1
</Number of EDF Primitives>
<EDF Primitive Centers>
ICent
</EDF Primitive Centers>
<EDF Primitive Types>
1
</EDF Primitive Types>
<EDF Primitive Exponents>
12.56637061436
</EDF Primitive Exponents>
<EDF Primitive Coefficients>
Coeff
</EDF Primitive Coefficients>
</Additional Electron Density Function (EDF)>

where ICent is the number of the atom and Coeff is 8 times the number of ECP-modeled core electrons of the atom.  This data section represents a single S-type Gaussian function with exponent 12.56637061436 (4 times pi) that is centered on the ICent atom and that is multiplied by the number Coeff.  The integral of this function over all of space gives the number of ECP-modeled core electrons of the ICent atom.  For example, if the third atom of your molecule used a 60-electron ECP, then ICent=3 and Coeff=8*60=480.0 and the corresponding EDF data section would be:

<Additional Electron Density Function (EDF)>
<Number of EDF Primitives>
1
</Number of EDF Primitives>
<EDF Primitive Centers>
3
</EDF Primitive Centers>
<EDF Primitive Types>
1
</EDF Primitive Types>
<EDF Primitive Exponents>
12.56637061436
</EDF Primitive Exponents>
<EDF Primitive Coefficients>
480.0
</EDF Primitive Coefficients>
</Additional Electron Density Function (EDF)>

If you have more than one atom that used an ECP, then the model core electron density data sections can be combined into one.  For example, if the second, third and fifth atoms of your molecule used a 46-electron ECP, a 18-electron ECP and a 60-electron ECP respectively then the corresponding combined EDF data section would be:

<Additional Electron Density Function (EDF)>
<Number of EDF Primitives>
3
</Number of EDF Primitives>
<EDF Primitive Centers>
2 3 5
</EDF Primitive Centers>
<EDF Primitive Types>
1 1 1
</EDF Primitive Types>
<EDF Primitive Exponents>
12.56637061436 12.56637061436 12.56637061436
</EDF Primitive Exponents>
<EDF Primitive Coefficients>
368.0 144.0 480.0
</EDF Primitive Coefficients>
</Additional Electron Density Function (EDF)>


Can wavefunctions derived from calculations using typical Kohn-Sham DFT (KS-DFT) methods be used?

Yes, and the use of KS-DFT wavefunctions for the calculation and interpretation of most QTAIM properties is similar to that for Hartree-Fock wavefunctions, with decent KS-DFT methods hopefully being more accurate.  For calculation of atomic DFT-based exchange-correlation energies and additive IQA atomic energies, the only KS-DFT methods currently supported are LSDA and B3LYP and M062X.  The underlying DFT model of a .wfx wavefunction file must be specified in the .wfx file using the <Model> tag ( see here ) in order for the corresponding exchange-correlation energies to be appropriately calculated.  For more information about atomic energy calculations, see here.


What platforms does AIMAll run on?

AIMAll is available for Windows, Mac OS X and Linux.  System Requirements are given here.


Does AIMAll support use of multiple processors / cores?

Yes, support for optionally running AIMExt and AIMInt jobs using multiple processors (shared memory only) is available (AIMAll Professional required for non-small wavefunctions).  Support for optionally running multiple AIMInt jobs simultaneously (i.e., calculating more than one atom at a time) using multiple processors is also available (AIMAll Professional required for non-small wavefunctions).  Multiprocessor options are specifiable via the "Processors" and "Atoms at a Time" fields of the AIMQB dialog or via the "-nproc" and "-naat" command-line arguments to AIMQB.  Note that the most effective use of multiple processors for small wavefunctions is to calculate more than one atom at a time (e.g., -nproc=3 -naat=3).  For large wavefunctions, using more than one processor per atomic calculation becomes effective (e.g., -nproc=3 -naat=1).  More information about multiprocessing can be found here and here.


How does one calculate atomic magnetic response properties with AIMAll?

Calculation of atomic contributions to magnetizability tensors and NMR shielding tensors requires the selection of either CSGTB, IGAIM or GIAO in the "Magnetic Response Properties" combobox in AIMQB, as well as the use of a CSGT magnetic wavefunction file or a GIAO magnetic wavefunction file.

A CSGT magnetic wavefunction file in traditional AIM format (.wfn) can be produced by Gaussian using the keywords: nmr=csgt iop(10/21=1,99/6=200) output=wfn

A CSGT magnetic wavefunction file in extended format (.wfx) can be produced by Gaussian 09 Revision B.01 and later using the keywords: nmr=csgt output=(wfx,csgt)

The keyword "CSGT" (without the quotes) must be manually added to the end of the 2nd line (after NUCLEI) of a CSGT magnetic wavefunction file in traditional AIM format so that AIMAll knows it is CSGT wavefunction file.

CSGT magnetic wavefunctions can be used for both the CSGTB and the IGAIM methods of calculating atomic magnetic response properties in AIMAll.  The CSGTB method in AIMAll is the same to the CSGT method implemented in Gaussian.  The IGAIM method in AIMAll (which uses QTAIM atoms) is different than the IGAIM method in Gaussian and produces slightly different total results for smaller basis sets.

A GIAO magnetic wavefunction file in traditional AIM format (.wfn) can be produced by Gaussian using the keywords: nmr=giao iop(10/21=1,99/6=300)

A GIAO magnetic wavefunction file in extended format (.wfx) can be produced by Gaussian 09 Revision B.01 and later using the keywords: nmr=giao output=(wfx,giao)

The keyword "GIAO" (without the quotes) must be manually added to the end of the 2nd line (after NUCLEI) of a GIAO wavefunction file in traditional AIM format so that AIMAll knows it is GIAO wavefunction file.

A GIAO magnetic wavefunction file in either extended AIM format (.wfx) or traditional AIM format (.wfn) can also be automatically produced by AIMQB by opening a Gaussian formatted checkpoint file resulting from an nmr=giao calculation.


What does a message in a sum file about a "significant" or "potentially significant" integration error mean?

Ideally, calculated atomic L(A) values should be zero and the sum of any calculated atomic property over all atoms in a molecule should of course equal the known molecular value.  In practice, there will always be some numerical integration errors, usually related to the complexity of atomic surfaces.

A "Warning!  Significant ... integration error ..." message will be written to the sum file if any of the following occurs:

A "Note.  Potentially significant ... integration error ..." message will be written to the sum file if any of the following occurs:

The threshold values of 0.01 au for "Significant" and 0.002 au for "Potentially significant" integration errors are reasonable, but may be too conservative or not conservative enough depending on one's purposes.

Note that it is possible (but not likely) that a calculated atomic L(A) value can be fortuituously small in magnitude due to a cancellation of errors.

Users are always advised to monitor themselves the sums of calculated atomic properties as well as the individual calculated L(A) values, and be prepared to recalculate "problem atoms" using higher quadrature and / or a different atomic integration algorithm, if necessary.


How can dipole polarizability tensors of atoms in molecules be calculated using AIMAll?

The components of a molecular dipole polarizability tensor can be calculated as the set of first derivatives of the molecular dipole moment components with respect to the components of an applied electric field, the derivatives being evaluated at the zero-field point. The same is true of an atom in a molecule. To calculate the atomic dipole derivatives it is necessary to use numerical differentation since the atomic surfaces (being defined by the electron density distribution) are dependent on the electric field.  A spreadsheet might be helpful.

The basic steps are:

  1. Do a regular, zero-field ab initio calculation of the molecule of interest and generate a corresponding wavefunction file, say molecule_0.wfn.
  2. Run AIMAll on molecule_0.wfn to produce molecule_0.sum, which will contains all of the atomic dipole moments of the molecule at the zero-field point.
  3. Do another ab initio calculation of the molecule at the same geometry, level of theory and basis, but in the presence of a small (say 0.0025 au) electric field applied along the +X axis and generate a corresponding wavefunction file, say molecule_0025_x.wfn.
  4. Run AIMAll on molecule_0025_x.wfn to produce molecule_0025_x.sum, which will contain all of the atomic dipole moments of the molecule in the presence of the applied electric field.
  5. For each atom in the molecule, calculate the XX, YX and ZX components of the atomic polarizability tensor as the change in the X, Y and Z components of the atomic dipole moment divided by the change in the applied electric field along the X-axis, i.e. 0.0025 au.
  6. Repeat steps 3-5, but with the applied electric field along the +Y axis, to calculate XY, YY and ZY elements of the atomic polarizability tensors.
  7. Repeat steps 3-5, but with the applied electric field along the +Z axis, to calculate XZ, YZ and ZZ elements of the atomic polarizability tensors.

Consider repeating the above steps with the the applied electric field along the -X, -Y and -Z axes.

Consider repeating the above steps with smaller (say 0.001 au) and larger (say 0.005 au) field strengths.


Can AIMQB be run from a command-line interface?

Yes.  For example, to run AIMQB using the default options and the wavefunction file oxirane.wfn (assumed to be in the current directory), enter the following at a command prompt:

Windows:  c:\aimall\aimqb -nogui oxirane.wfn

Mac OS X:  /AIMAll/AIMQB.app/Contents/MacOS/aimqb -nogui oxirane.wfn

Linux:  /usr/local/AIMAll/aimqb.ish -nogui oxirane.wfn

All of the option controls in the AIMQB dialog have corresponding command-line arguments.

More information about the AIMQB command-line interface can be found here


How does one make objects semi-transparent in a 3D Window in AIMStudio?

Any type of object (including text) can be made semi-transparent in a 3D window of AIMStudio by using the "Alpha channel" field in the corresponding Color Dialog for the object type.  Alpha channel values can range from 255 (opaque) to 0 (invisible).  Most object types are opaque by default.


How can one get smoother lines/paths/curves/text in AIMStudio?

Anti-Aliasing may (depending on the quality of your computer's graphics card) improve the appearance (smoothness) of paths and points (and possibly text).  Anti-Aliasing is on by default but can be turned off via the "View->Anti-Aliasing" menu items.  Anti-Aliasing may not work well with some low-end graphics systems.  In many cases, anti-aliasing support for the graphics system can be adjusted using the graphics system's "Control Panel" GUI.  Alternatively, you can check the "View->Tubular Lines, Curves and Paths" menu item, which will draw lines, paths and curves using cylinder segments instead of rasterized line segments.  Drawing lines, paths and curves using cylinder segments may look good both on screen and in pictures (including those of High resolution) but can be expensive.


How does one zoom the objects in and out in a 3D Window in AIMStudio?

Any of the following can be used to zoom:
How does one rotate the objects in a 3D Window in AIMStudio?

Any of the following can be used to rotate:
How does one move (translate) the objects left/right/up/down in a 3D Window in AIMStudio?

Any of the following can be used to translate:
How can I get values of the electron density, the Laplacian of the electron density and other functions at any point in space I choose, not just critical points?

Run the program AIMExt and use Main Menu option (5), "Properties at Input Coordinates".  The data of interest will be in the .extout file.


How can I locate and characterize critical points of the virial field or other functions?

All critical points of the electron density are always calculated automatically when running AIMQB.  Critical points of the Laplacian of the electron density can optionally be calculated automatically, for some or all atoms, when running AIMQB.  For functions other the electron density and the Laplacian of the electron density (e.g., the virial field), run the program AIMExt directly and answer the question "What is the Primary function you want to analyze?" accordingly.  Then use the Main Menu options such as (6) to search for critical points of the Primary function.  The data of interest will be in the .extout file.


Can I hide individual atoms, bond paths, BCPs, etc. in an AIMStudio 3D window?

Yes.  Right-clicking on any nuclear, BCP, RCP, CCP, NNACP, Ghost or other object sphere will push up a context menu with various options (at the top of the menu) specific to that object.  One of the these options will be "Cloak Object".  Cloaking an object will hide it (the more general term "Cloak" is used instead of "Hide" to allow for possible different representations of "Cloaking" in the future).  Cloaking a BCP will also cloak its bond path and its IAS EV paths.  Cloaking an RCP will also cloak its RCP-to-BCP paths.  Note that a cloaked object cannot be decloaked by right-clicking on it (because it is not there anymore), but all cloaked objects can be decloaked via the "View->Decloak All" menu item.  Cloaking is especially useful for contour maps and other 2D plots in non-planar molecules, where you may only want to show those atoms, bond paths, etc. in the plotting plane.


Is there any way to have AIMAll sort and / or filter all of the numerical data it produces?

Yes.  AIMStudio now provides customizable Atom Tables, BCP Tables, RCP tables, CCP tables, etc. which interact with the corresponding 3D windows and allow the user to view, sort, copy and print property data in a variety of ways.


What are the units of length, energy, the electron density, etc. given in the .sum files, the .mgp files, the .extout files and other AIMAll result files?

Length units throughout AIMAll are atomic units (bohr).  Energy units throughout AIMAll are atomic units (Hartree).  Electron density units throughout AIMAll are atomic units (e/bohr^3).  As stated near the top of every .sum file, all output data from (and input data to) AIMAll is in atomic units unless stated otherwise.


Does AIMAll support Ghost centers?

Yes.  In the wavefunction file, ghost centers should be presented as extra nuclei (increment the value for the number of nuclei by the number of ghosts added) with charge 0.0, atomic number 0 and should have unique names beginning with Bq (e.g., Bq17).  If you have done a counterpoise calculation, for example, then it will be necessary to include the counterpoise (Ghost) centers and corresponding primitive function data in the wavefunction file.  But ghost centers with no basis functions can also be added to the wavefunction file for the purpose of having AIMAll calculate local and atomic contributions to properties (e.g., ESP, Electrostatic Force, "NICS" NMR shielding, Source Functions, Fermi hole, etc.) at target or reference points defined by the user, in addition to the default set of target or reference points that includes the real nuclei and possibly the electron density CPs.


What does the AIMQB error message "Invalid traditional wfn file!  Normalization check failed.  Could be due to an orientation inconsistency." mean?

Some versions of g03 may write traditional AIM .wfn files with an inconsistency between the nuclear coordinate orientation and the orientation that the MO coefficients correspond to, i.e., the nuclear coordinates are written in the input orientation while the written MO coefficients correspond to the Gaussian standard orientation - unless the Gaussian keyword NOSYMM is specified.  This issue is usually caught by AIMQB, which performs a normalization check on traditional AIM .wfn files.  To avoid this and other issues with traditional AIM .wfn files, it is strongly recommended to open Gaussian formatted checkpoint files (.fch or .fchk files) with AIMQB instead and then use the corresponding .wfx files for all AIMAll calculations.  Opening formatted checkpoint files with AIMQB and then using the .wfx files with the AIMAll programs is beneficial in several other ways as well.

There are other reasons that this message might appear.  For example, at least some versions of GAMESS and Firefly write incorrect .wfn files when the basis set includes contracted F shells.  And at least some versions of Turbomole sometimes write .wfn files with MOs that are not sufficiently orthonormal.


What does the AIMQB error message "Invalid .wfx file!  Normalization check failed." mean?

g09 C.01 may sometimes write invalid .wfx files for post-scf methods (e.g., MP2, CCSD, etc.), invalid because at least some of the natural orbitals and / or their occupancies are incorrect.  This issue can be avoided by updating to Gaussian 09, Revision D.01 or later.  To workaround this issue one can open the Gaussian formatted checkpoint files (.fch or .fchk files) with AIMQB instead and then use the corresponding .wfx files for all AIMAll calculations.


Does AIMExt calculate and print the Cremer and Kraka energy density H(r)?

The Cremer and Kraka energy density H(r) = G(r) + V(r) is equivalent to -K(r), i.e., minus the Hamiltonian form of the electron kinetic energy density.  K(r) is calculated by AIMExt at critical points of the electron density (such as BCPs) and this data is available in the .sum file, the .sumviz file, the .mgp file and the .mgpviz file.  Like all other CP properties, the K(r) values can be viewed in AIMStudio in table form and / or in the 3D windows.  Like the electron density, the Laplacian of the electron density, etc., the function K(r) can itself be topologically analyzed using AIMExt.  Contour maps, relief maps and isosurfaces of K(r) can be displayed using AIMStudio.


Does AIMAll calculate atomic electronic spin populations?

Yes.  The atomic populations N_alpha(A), N_beta(A), N_total(A) and N_spin = N_alpha(A) - N_beta(A) are printed near the end of the atomic integration result files (.int files) along with other atomic electronic spin properties such the electronic spin kinetic energies, electronic spin moments, etc. The atomic spin populations are also tabulated at the end of the .sum files and .sumviz files and are viewable in AIMStudio 3D windows and Atom Tables.  A picture of atomic electronic spin values N_spin(A) in phenoxy radical are shown here.


Does AIMAll calculate atomic contributions to NICS ("Nucleus Independent Chemical Shielding")?

Yes, as long as you have an appropriate wavefunction from which to calculate atomic magnetic response properties.  To calculate NICS shielding tensors and their atomic contributions, just add coordinates for the "Ghost nuclei" to the wavefunction file for each point at which you want NICS contributions to be calculated.  For each ghost nucleus, make sure to add an appropriate nuclear name (must begin with Bq, e.g., Bq13), atomic number (0) and charge (0.0) and make sure to increase the value for the number of nuclei by the number of ghost nuclei added.


How can I get the distance between a BCP and an RCP, a nucleus and a BCP, etc.?  Can I get angle and dihedral angle data for the critical points I am interested in?

For nuclei (NACPs) connected by a bond path, the distance between the nuclei (NACPs) and the distances from the nuclei (NACPs) to their shared bond critical point are written to the .mgp, .mgpviz, .sum and .sumviz files and can be displayed in AIMStudio as BCP Length Properties.  Bond path angles and corresponding geometric bond angles are also written to these files.  Distances, angles and dihedral angles involving any primary point objects (i.e., Nuclei, BCPs, RCPs, CCPs, NNACPs, Laplacian of Rho CPs and Ghosts) can be obtained from AIMStudio by selecting (clicking on) the object spheres in the 3D window and showing the distance tables, angle tables and dihedral tables for Selected objects via the "Tools->Selection Tables..." menu item.


How do I install and use the Linux version of AIMAll?

For concreteness, the following assumes AIMAll will be installed in your home directory.  AIMAll can, of course, be installed in any directory to which you (the installer) have write permission or can obtain write permission (via sudo, for example).  For general, multi-user purposes, installing AIMAll in /usr/local is usually a good choice if you (the installer) have or can obtain write permission to /usr/local.

To install AIMAll:
  1. Download a gzipped tarball of AIMAll for Linux from here, e.g., aimall_10_12_11_linux_64bit.tar.gz, and move it to your home directory.
  2. Open or switch to a terminal window
  3. cd ~
  4. gunzip aimall_10_12_11_linux_64bit.tar.gz
  5. tar xvf aimall_10_12_11_linux_64bit.tar
  6. Note that the AIMAll directory path is ~/AIMAll (e.g., /home/todd/AIMAll)
Note:  If your Linux system uses a non-English locale/language, you may need to uncomment the "#export LANG=en_US" line in each of the 6 .ish wrapper scripts (e.g., aimqb.ish) in order for AIMAll to function properly.

To launch AIMQB in GUI mode from a terminal window:
  1. Open or switch to a terminal window
  2. ~/AIMAll/aimqb.ish
To launch AIMQB in command-line mode from a terminal window and immediately run a job (e.g., on one of the AIMAll test wavefunction files):
  1. Open or switch to a terminal window
  2. cd ~/AIMAll/test/cyclopropanone
  3. ~/AIMAll/aimqb.ish -nogui cyclopropanone.wfn

More information about the AIMQB command-line interface can be found here

To launch AIMStudio from a terminal window:
  1. Open or switch to a terminal window
  2. ~/AIMAll/aimstudio.ish
Note that including the directory path of the aimqb.ish and aimstudio.ish scripts in the PATH environment variable should be considered for routine command-line usage of AIMQB and AIMStudio (to avoid having to specify a full path for aimqb.ish and aimstudio.ish every time).

Alternatively, adding aimqb() and aimstudio() bash functions to your .bashrc file can be considered to simplify the running of aimqb.ish and aimstudio.ish:

# Bash function for command-line launching of AIMQB on Linux, to be added to .bashrc file
aimqb() {
  /home/todd/AIMAll/aimqb.ish $*
}

# Bash function for command-line launching of AIMStudio on Linux, to be added to .bashrc file
aimstudio() {
  /home/todd/AIMAll/aimstudio.ish $*
}

To create a launchable AIMQB icon on your Ubuntu desktop (the procedure for most other Linux desktops is similar):
  1. Right-click on the desktop and select "Create Launcher"
  2. Specify the ~/AIMAll/aimqb.ish file as the Application
  3. Choose the ~/AIMAll/icons/aimqb.png file (or the ~/AIMAll/manual/images/aimqb.png file) for the Application icon.
  4. Double-click on the AIMQB icon to launch AIMQB
  5. Drag-and-drop a wavefunction file onto the AIMQB icon to launch AIMQB with the specified wavefunction file.
To create a launchable AIMStudio icon on your Ubuntu desktop (the procedure for most other Linux desktops is similar):
  1. Right-click on the desktop and select "Create Launcher"
  2. Choose the ~/AIMAll/aimstudio.ish file as the Application
  3. Choose the ~/AIMAll/icons/aimstudio.png file (or the ~/AIMAll/manual/images/aimstudio.png file) as the Application icon.
  4. Double-click on the AIMStudio icon to launch AIMStudio.
  5. Drag-and-drop a .sumviz file or other AIMAll .*viz file onto the AIMStudio icon to launch AIMStudio and display the data from the file in AIMStudio.
  6. If AIMStudio is already open, drag-and-drop a .sumviz file or other AIMAll .*viz onto the AIMStudio main window to display the data from the file in a new 3D window.  Secondary AIMAll .*viz files can be dropped onto an existing AIMStudio 3D window to display the data in that window.
To create a launchable AIMQB icon or AIMStudio icon on your Ubuntu taskbar, right click on the taskbar and select "Add to Panel" and then "Custom Application Launcher" and then follow the same procedure as for the desktop icons.


When running AIMQB in non-GUI mode, how do I prevent calculation progress from being displayed in the terminal window?

By default, some calculation progress is written to standard output when AIMQB is run in command-line mode.  The AIMQB command-line argument -scp=false will prevent all calculation progress from being written to standard output while -scp=true will result in detailed calculation progress being written to standard output.

But, instead of using -scp=false, simply redirecting the standard output (and stderr) to a log file is probably a better choice, since then the calculation progress information is there if you want it:

/home/todd/AIMAll/aimqb.ish -nogui dma.wfx >& dma.qblog &


Do I have to re-register for each new version of AIMAll?

No.


How do I update AIMAll to the latest version?

Just download and install the latest version.  At any time, you can download the latest AIMAll package of interest from here (using the same login information that was sent to you after you registered) and install it over your currently installed version.  For AIMAll Professional users, the AIMAll Professional license file (aimallpro.lic) will remain in place and valid.


I have a bunch of wavefunctions I want to run AIMQB calculations on, one after the other, over the next day/week/month/etc.  How can I do that most easily?

The AIMQB Dialog (GUI) mode now supports easily running calculations on multiple wavefunction in "batch mode".  More information can be found here.

For running a series of AIMQB calculations in AIMQB command-line (non-GUI) mode, the calculations should be set up and run using a script (e.g., a .bat batch file on Windows or a BASH script file on Mac or Linux) that consecutively runs AIMQB on each of the wavefunctions of interest.  For example, here is a very simple script for Linux for running AIMQB (using different options for demonstration purposes) on 5 molecules, one at a time.

#!/bin/sh

aimqb=/home/todd/AIMAll/aimqb.ish

cd molecule1
$aimqb -nogui molecule1.wfx

cd ../molecule2
$aimqb -nogui molecule2.wfn >& molecule2.qblog

cd ../molecule3
$aimqb -nogui -nproc=2 -boaq=veryhigh molecule3.wfn

cd ../molecule4
$aimqb -nogui -encomp=2 molecule4.fchk

cd ../molecule5
$aimqb -nogui -source=1 molecule5.wfx >& molecule5.qblog


Why are some bond paths dashed in AIMStudio 3D windows?

When the electron density at a BCP is below the "Weak CP Threshold" value, all paths that originate (bond paths) and terminate (RCP-to-BCP Paths, IAS EV Paths and IAS Paths) at the BCP are drawn dashed instead of solid.  Similarly, when the electron density at an RCP is below the "Weak CP Threshold", its RCP attractor paths are drawn dashed.  And when the electron density at a nuclear or non-nuclear attractor is below this threshold, all of its basin paths are drawn as dashed.  This threshold value is 0.025 a.u. by default but can be changed using the "View->Weak CP Threshold..." menu item.

The "Non-CP Threshold" is similar, except that instead of dashed paths, the paths (and the CPs) are hidden.  The default for the "Non_CP Threshold" is 0, which means that nothing is hidden by default.  This can be changed via the "View->Non-CP Threshold..." menu item but you will be warned if you do so.


Do wavefunction files derived from the ADF package work with AIMAll?

Not at this time.  ADF uses Slater basis functions.  Currently, only Gaussian basis functions are supported.


Does AIMAll calculate Source functions?

Yes.  Atomic sources of the electron density at each electron density critical point and at each nucleus can be calculated by checking "Atomic Sources" in the AIMQB dialog or by using the argument -source=1 when running AIMQB from the command-line interface.  The results are printed near the bottom of the .sum and .sumviz files.  Atomic sources of the electron density at points other than critical points and nuclei can be calculated by including the additional points as Ghosts in the wavefunction file.


Does AIMAll calculate and display the topological properties of the Laplacian of the electron density like it does for the electron density?

Yes, the ability to automatically calculate, characterize and interactively visualize critical points and atomic graph paths of the Laplacian of the electron density and their properties, for some or all atoms, has recently been added to AIMAll.  More information can be found here.


Does AIMAll calculate the so-called "Electron Localization Function (ELF)" of Becke, Edgecombe and Savin?

Not at this time.


Can I display Molecular Orbitals (MOs) in AIMStudio?

Yes, contour maps, relief maps, isosurfaces and isosurface mapping of any occupied molecular orbital in the wavefunction can be displayed in AIMStudio.  In addition, AIMExt supports the full topological analysis of any occupied MO in the wavefunction file.


Can I display spin densities in AIMStudio?

Yes.  The Alpha electron density, Beta electron density and their difference, the Alpha-Beta spin density, can be displayed in AIMStudio as contour maps, relief maps, isosurfaces or as a mapped function on the isosurface of another function.    A picture of spin density isosurfaces along with atomic electronic spin populations N_spin(A) in phenoxy radical is shown here.


Can I get the individual MO populations for an atom in a molecule using AIMAll?

Yes, you can get the atomic MO populations from the Atomic Overlap Matrix (which is in the MO basis) section of the individual atomic integration (.int) files.  The Atomic Overlap Matrix (AOM) is printed in lower triangular form (with row line wraparound every 6 elements).  It is important to remember that the AOM given in the .int file does not include the MO occupancies.  A diagonal element of the Atomic Overlap Matrix multiplied by the corresponding MO occupancy gives the atomic population for that MO, i.e., that MO's contribution to the total electron population of the atom.


When displaying Contour maps in a 3D window, how am I supposed to know what the Contour values are? Can I display the Contour values alongside the Contours?

The ability to display Contour value labels on Contours has recently been added to AIMStudio.  To display a Contour value label at any point on a Contour, just click there.  Clicking an existing Contour value label will remove it.  As many labels as desired can be shown for any number of Contours.  It was decided that this approach is almost always preferable to an "Automatic" placement of labels.  Automatic placement of Contour labels is, in general, difficult to do in a consistently useful and visually appealing manner and will almost always not be what the user ultimately wants.  Display options for Contour value labels (font, color, etc.) are given on the "Contours->Text" submenu.


Can I display spectrograms of functions in AIMStudio?

Yes.  A spectrogram is basically a Relief Map colored by value.  When loading a .g2dviz file (a grid of function values in a plane), check "Make Relief Map" in the "Maps of 2D Grid Data" dialog.  After the Relief Map is displayed, check the "Show Color by Value" item in the "Relief Maps->Color by Value" menu if it is not already checked and adjust the "Range and Coloring" settings as necessary.  For a 2D spectrogram, specify 0 for the "Maximum Height" when creating the Relief Map.


Where are basin path visualization files (.basviz files), interatomic surface visualization files (.iasviz files) and atomic Laplacian of rho criticial point visualization files (.agpviz files) located?

Since .basviz files, .iasviz files and .agpviz files are atom-specific, they will be located in the wfname_atomicfiles subdirectory of the directory containing their corresponding wavefunction file.  For a wavefunction file named abc.wfx, for example, any corresponding .basviz files (if calculated), .iasviz files (if calculated) and .agpviz files (if calculated) will be written to the abc_atomicfiles subdirectory of the directory containing abc.wfx.



Copyright © 1997-2017 by Todd A. Keith