Software for Quantum Chemistry, Electron Population Analysis (Mulliken, Lowdin, CDA)


	Developments and software modifications in the AOMix programs

Development of the AOMix suite of programs is a continuous project. It started in 1997 at York University (Toronto). Then, moved to Stanford, California and, in 2006, to Ottawa, Ontario. I am glad that many people around the world found the software very useful and helpful for their research and data processing.

If you are interested to see some additional features in it, please contact the author (Serge Gorelsky). The development of the AOMix programs and their additional features will depend on programming time and high enough general interest and funding. Sponsorships and donations are welcome.

IN PREPARATION:

Connecting the ADF density functional package (Scientific Computing & Modelling NV) with AOMix-CDA: the work is in progress to provide direct connectivity between ADF 2007 and the AOMix-CDA program. AOMix-CDA will be available for all computer platforms and operating systems that are supported by ADF: UNIX, Linux, MAC OS, and Windows XP (see the complete list).

AOMix-CDA, Revision 2.20: calculation of Green function matrix elements, G_ij(E) ,for molecular systems containing 3 fragments (the donor site, the bridge and the acceptor site).

IN TESTING:

a new Linux and MS Windows version of AOMix. This version will have additional improvements and allow a fully NON-INTERACTIVE and batch-list execution, so that you will be able to process 10s/100s/1000s of output files at a time by running a script file (instead of a single output file per execution).

Your input about how to organize file and data processing in the new version is welcome. The development of the AOMix programs and their additional features will depend on programming time and high enough general interest or funding.

COMPLETED:

AOMix-L, Revision 1.70: the (automatic) analysis of bonding/antibonding character of the frontier orbitals (6 HOMOs and 6 LUMOs). This feature is to be documented in the AOMix manual.

AOMix-S, Revision 2.38: printing of the gross S-,P-,D-,(etc.) orbital populations of atoms/fragments is added to the AOMix-S output:

ATOM ====== ALPHA- and BETA-SPIN GROSS POPULATIONS ====== A: - s - - p - - d - B: - s - - p - - d - 1C 1.6193 1.5337 0.0202 1.5846 1.2321 0.0196 2C 1.6193 1.5337 0.0202 1.5846 1.2321 0.0196 3C 1.5781 1.3793 0.0197 1.6065 1.5036 0.0166 4C 1.6193 1.5337 0.0202 1.5846 1.2321 0.0196 5C 1.6193 1.5337 0.0202 1.5846 1.2321 0.0196 6C 1.5781 1.3793 0.0197 1.6065 1.5036 0.0166 7H 0.3758 0.0118 0.0000 0.3904 0.0109 0.0000 8H 0.3758 0.0118 0.0000 0.3904 0.0109 0.0000 9H 0.3899 0.0114 0.0000 0.3864 0.0116 0.0000 10H 0.3758 0.0118 0.0000 0.3904 0.0109 0.0000 11H 0.3758 0.0118 0.0000 0.3904 0.0109 0.0000 12H 0.3899 0.0114 0.0000 0.3864 0.0116 0.0000

AOMix-L, Revision 1.67: the analysis of four-center orbital interactions is added. This feature can be activated or turned off by using the 4-CENTER keyword.

AOMix-L, Revision 1.64: printing of three-center bond order indices (for example, see [Ref.]) is expanded for molecular systems with more than 100 fragments.

AOMix-L, Revision 1.62: printing of two-center attribute files (PseudoBond attributes) for visualization in UCSF Chimera is enabled:

The Mayer bond orders for the C-C and C-H bonds in the anthracene molecule (C₁₄H₁₀)

AOMix-CDA, Revision 2.12: the program has been modified to simplify the preparation of (Initial wave function = a sum of fragment wave functions) input files for Gaussian.

AOMix-CDA, Revision 2.11: the new keyword (CORE) is added to simplify the construction of orbital interaction diagrams.

AOMix-S, Revision 2.35: the CUBE keyword is extended. This keyword instructs the AOMix-S program to create two scripts (one for UNIX, one for MS Windows) for cube file generation for the cubegen utility in the Gaussian package. Please refer to the AOMix manual for details.

AOMix-CDA, Revision 2.09: energy decomposition analysis (Morokuma's EDA, for Gaussian calculations only)

AOMix-prep: Turbomole output files can be processed for AOMix-L,S calculations.

AOMix-CDA, Revision 2.08: with the FO OVERLAP keyword, the LCFO-MO output for non-ZDO calculations is expanded to include overlap integrals and overlap populations between the contributing FO pairs of the two fragments for each MO in the output:

--- ALPHA-SPIN ORBITALS --- Mol. Orbital Compositions in terms of dominant FO contributions Overlap integrals S and overlap populations,OP=2c*c*S ========================================================================= ... LUMO+1[#13, 3.161 eV]= Fr 1: 7.1%L+2 3.0%H-1 1.9%L+1 Fr 2: 46.7%L+0 S(-0.32 0.24 0.09 ) OP(0.07 -0.10 -0.01 ) 40.0%L+1 S(0.09 -0.06 0.32 ) OP(0.02 -0.02 0.04 ) LUMO+0[#12, 3.161 eV]= Fr 1: 7.1%L+1 3.0%H-0 1.9%L+2 Fr 2: 46.7%L+1 S(0.32 0.24 0.09 ) OP(0.07 -0.10 -0.01 ) 40.0%L+0 S(0.09 0.06 -0.32 ) OP(0.02 -0.02 0.04 ) HOMO-0[#11, -12.718 eV]= Fr 1: 94.9%H-0 Fr 2: 3.6%L+1 S(0.24 ) OP(0.05 ) 1.4%H-1 S(0.06 ) OP(-0.02 ) HOMO-1[#10, -12.718 eV]= Fr 1: 94.9%H-1 Fr 2: 3.6%L+0 S(0.24 ) OP(0.05 ) 1.4%H-2 S(0.06 ) OP(-0.02 )

In the above example, the HOMO of the complex (orbital #12 with the energy of -12.718 eV) is a mixture of 94.9% HOMO of Fragment 1 and 3.6% LUMO+1 and 1.4% HOMO-1 of Fragment 2. The overlap integral between the HOMO of Fragment 1 and LUMO+1 of Fragment 2 is 0.24 and the overlap population for this fragment orbital pair is 0.05 for this molecular orbital of the complex. The overlap integral between the HOMO of Fragment 1 and HOMO-1 of Fragment 2 is 0.06 and the overlap population for this fragment orbital pair is -0.02.

AOMix-CDA, Revision 2.07: the new keyword (CLEANUP) is added. This keyword instructs AOMix-CDA.exe to delete all AOMix temporary files after execution.

AOMix-L, Revision 1.61: the new keyword (AOMIX-S TO-FOLLOW) is added. This keyword instructs AOMix-L to:

start AOMix-S.exe after the AOMix-L execution and
delete all AOMix temporary files after execution.

AOMix-L, Revision 1.57: the LOWDIN population analysis keyword has been modified. The new default is to apply LPA to all AOMix-L calculations in which the number of orbitals is 500 or less and to skip it for larger (>500 orbitals) MO calculations.

AOMix-S, Revision 2.31: the OP-CONTRIBUTIONS keyword is added. This keyword instructs the AOMix-S program to print AO contributions (2*C_a*C_b*S_ab absolute values that are greater than 0.01) to the overlap populations between two fragments. For example:
Alpha MO 7, OP contributions > 0.01: 5 17 Ca= 0.2832 Cb= 0.2742 Sab=-0.2372 2*Ca*Cb*Sab= -0.037 5 20 Ca= 0.2832 Cb= -0.4442 Sab=-0.3048 2*Ca*Cb*Sab= 0.077 5 21 Ca= 0.2832 Cb= 0.6196 Sab=-0.1509 2*Ca*Cb*Sab= -0.053 9 17 Ca= 0.1484 Cb= 0.2742 Sab=-0.6042 2*Ca*Cb*Sab= -0.049 9 20 Ca= 0.1484 Cb= -0.4442 Sab=-0.2327 2*Ca*Cb*Sab= 0.031 9 21 Ca= 0.1484 Cb= 0.6196 Sab=-0.5103 2*Ca*Cb*Sab= -0.094
These data can be helpful in the analysis of molecular orbital calculations.

AOMix-CDA, Revision 2.03: printing of a table of changes in atomic orbital populations in the whole molecule relative to non-interacting fragments is added. See this example.

AOMix, Revision 6.29: with AOMix-CDA, Revision 2.02: setting up wave function calculations for molecular systems using converged wave functions of molecular fragments as an initial guess (any spin states). This option is very useful for generation of the correct guess wave function for broken symmetry calculations and open-shell low-spin states in which unpaired electrons are antiferromagnetically coupled. Please refer to APPENDIX II of the AOMix manual for details.

AOMix-S, Revision 2.28: the ENERGYRANGE keyword is added. This keyword instructs the AOMix-S program to use a user-defined energy range for DOS calculations (instead of the default program values). Please refer to the AOMix manual for details.

AOMix-L, Revision 1.56: AOMix-L can be used to recover the initial guess from the converged wave function. See Appendix I of the AOMix manual for details. This option is very useful for large molecule calculations if the corresponding checkpoint file was lost.

AOMix-CDA, Revision 2.01: the program output is extended to include (if needed) the full LCFO-MO matrix.

AOMix-CDA, Revision 2.00: the program can be used for orbital relaxation analysis for molecular systems. The new functionality derives from the ability of the program to analyze MO compositions of molecule/ion X in terms of MOs of the other, reference state of X. So, for example, you can obtain MO compositions of cation X⁺ and/or anion X^- in terms of MOs of the neutral molecule X to identify the redox active orbitals. For more details, check the following publication:

Extended Charge Decomposition Analysis and Its Application for the Investigation of Electronic Relaxation
S. I. Gorelsky, E. I. Solomon
Theor. Chem. Acc., 2007, Online First, [PDF]

AOMix-S, Revision 2.26: the CUBE keyword is added. This keyword instructs the AOMix-S program to create a script for cube file generation for the cubegen utility in the Gaussian package. Please refer to the AOMix manual for details.

AOMix-S, Revision 2.24: the SPDF keyword is expanded to include more print options for the orbital composition analysis in terms of s-, p-, d-, and f-atomic orbitals. Please refer to the AOMix manual for details.

AOMix-S and AOMix-L modules:

The wave function verification procedure is extended.

AOMix-L writes two UCSF Chimera attribute files. The first file (with atomic attributes) allows easy visualization of atom-based properties:

atomic MPA- and LPA-derived charges of atoms/fragments,
MPA- and LPA-derived spin densities of atoms/fragments,

total and free valence indices of atoms/fragments.

Atomic valence indices in the anthracene molecule (C₁₄H₁₀)

The second file (with the two-atom attributes) allows easy visualization of pseudo-bond-based properties:

Lowdin and Wiberg bond orders,
Mayer bond orders and its components.

If each atom is a fragment, AOMix-S generates a UCSF Chimera attribute file. This file allows easy visualization of atomic contributions to the frontier orbitals (10 HOMOs and 10 LUMOs).

AOMix 6.25 and all AOMix-x modules: the additional information is recorded in AOMix-x output files to help a user in identifying a molecule and details of an original calculation, such as:
Molecule: C6H12Cl2N4Ru(1+,2)
Details: #P B3LYP/LANL2DZ 5D Test SCF=Tight Guess=Check Geom=Check Pop=Full IOp(3/33=1) 
AOMix-S, Revision 2.21: an extra option has been added for presenting density-of-states plot data: line DOS plots.

AOMix-S, Revision 2.19: automatic printing of MO compositions in terms of s,p,d,f,(etc) orbital contributions for each atom/fragment (in addition to the MO gross compositions).

AOMix-S, Revision 2.17: printing of net MO compositions (in addition to the MO gross compositions) in AOMix-S output files is available.

AOMix-L, Revision 1.45: evaluation of atomic (or fragment) total and free valence indices is added; bond-order contributions from orbitals of a given symmetry type (irreducible representation) is printed in a more convinient format.

AOMix-S, Revision 2.16: a user can define non-default weighting coefficients in DOS calculations using the pseudo-Voigt function; MMPA calculations are made easier to run in AOMix-S.

AOMix-L, Revision 1.39: the AOMix-L output has been extented to include the calculation of symmetry components of Mayer bond orders.

AOMix-CDA, Revision 1.90: charge decomposition analysis scheme has been extended to extract polarization and pure charge transfer contributions, the MO-FO output has been extended.

AOMix, Revision 6.13: Support for Q-Chem output files is added.

AOMix-CDA, Revision 1.85: Support for molecular orbital symmetry is added. A user can now easily sort molecular orbital interactions between orbitals of different symmetry.

AOMix, Revision 5.80: MO compositions and overlap populations are written in a new data format.

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All contents copyright � 1997-2008 S. I. Gorelsky
Last updated: April 2008