AOMix | AOMix-FO | FAQ | SWizard


Developments and software modifications in the AOMix programs

Stanford University

Development of the AOMix suite of programs (see the AOMix manual for a complete description) is a continuous project. It started in 1997 at York University (Toronto, Canada). In 2002, it moved to Stanford / Mountain View (California) and, in 2006, back to Ontario, Canada. I am glad that many people around the world found the software very useful and helpful for their research.

Development of additional software features (or features tuned for a specific user or a project) is possible on a contract basis. Please contact the author.

AOMix, Revision 6.90: Support for DFTB+ version 1.3 output files is added.

AOMix, Revision 6.87: Support for ORCA 3.0 output files (for calculations with more than 1000 orbitals) is added.

AOMix, Revision 6.86: Support for printing the summary of electronic transitions (using the x->y format with % contributions in parentheses) to AOMix output files is added (similar functionality existed in the SWizard software):

  Summary of calculated electronic transitions:
 
  #    nm  1000 cm-1   eV     f     Assignment (excitations with contrib. greater than 10.0%)
  1 1597.7    6.26   0.776  0.0005  113->121B(39.4%) 114->121B(33.6%) 112->121B(11.5%)  
  2 1338.9    7.47   0.926  0.0002  111->121B(22.3%) 114->121B(16.8%) 112->121B(11.8%) 106->121B(10.7%)  
  3  744.2   13.44   1.666  0.0002  120->121B(36.4%)  
  4  696.5   14.36   1.780  0.0042  120->121B(18.4%) 114->122B(18.1%) 113->122B(10.8%)  
  5  642.4   15.57   1.930  0.0194  121->122(24.9%) 120->121B(19.9%)  
  6  624.9   16.00   1.984  0.0067  119->121B(58.5%) 120->121B(13.8%)  
  7  593.2   16.86   2.090  0.0017  117->121B(17.4%) 119->121B(17.3%) 118->122(14.5%) 115->122(13.6%)  
  8  586.8   17.04   2.113  0.0011  121->122(32.8%) 117->121B(18.6%)  
  9  569.3   17.57   2.178  0.0014  120->122(27.4%) 115->122(15.9%)  
 10  558.2   17.91   2.221  0.0015  118->121B(38.8%) 120->122(22.0%)  
 11  555.0   18.02   2.234  0.0023  118->121B(32.0%) 120->122(27.2%) 117->121B(14.8%)  
 12  519.0   19.27   2.389  0.0014  119->122(15.5%)  
...

AOMix, Revision 6.85: Support for ORCA 3.0 output files (for calculations with less than 1000 orbitals) is added. Support for Jaguar output files has been extended to deal with calculations containing more than 1000 orbitals. A format issue with processing GAMESS output files for calculations with more than 100 atoms has been addressed.

AOMix, Revision 6.82: Printing of two-center attribute files for easy visualization with UCSF Chimera is expanded to include close-contact interatomic distances. AOMix can be used for processing Firefly (version 8) and Turbomole 6.5 output files. Support for the older versions of Turbomole has been removed.

AOMix, Revision 6.81: AOMix can be used for calculation of charge transfer integrals T(i,j) for the analysis of electron transfer (ET) in molecules (see doi: 10.1021/ja037027d, 10.1063/1.1615476, 10.1021/ja054257e, 10.1016/j.cplett.2009.12.048, 10.1007/s00894-010-0865-7). The output example is shown below:

 
 === Overlap and charge transfer integrals (see 10.1021/ja037027d, 10.1021/ja054257e) ===
 --- Fragment 1 ---   --- Fragment 2 --                T=S*C*E*C-1      1/2*Sij*
        Site energy         Site energy  Overlap    T(j,i)    T(i,j)  *(Tii+Tjj)
   FO     T(i,i) eV     FO    T(j,j) eV  S(i,j)       eV        eV         eV
 HOFO- 4   -522.449  HOFO- 4   -669.764  0.0000     0.0095     0.0096     0.0116
 HOFO- 4   -522.449  HOFO- 3    -30.324  0.0005    -0.2030    -0.2070    -0.1310
 HOFO- 4   -522.449  HOFO- 2    -12.900  0.0043    -2.1695    -2.1748    -1.1521
 HOFO- 4   -522.449  HOFO- 1     -9.052  0.0000    -0.0118    -0.0082    -0.0066
 HOFO- 4   -522.449  HOFO- 0     -9.054  0.0000     0.0193     0.0160     0.0100
 HOFO- 4   -522.449  LUFO+ 0     -1.049  0.0304   -15.7455   -15.7485    -7.9468
 HOFO- 4   -522.449  LUFO+ 1     21.089 -0.0221    11.5548    11.5531     5.5290
 HOFO- 4   -522.449  LUFO+ 2     29.949 -0.0131     6.8204     6.8254     3.2216
 HOFO- 4   -522.449  LUFO+ 3     33.064  0.0000    -0.0219    -0.0228    -0.0116
 HOFO- 4   -522.449  LUFO+ 4     33.060 -0.0001     0.0368     0.0342     0.0193
 HOFO- 4   -522.449  LUFO+ 5     39.257 -0.0181     9.4433     9.4443     4.3652
 HOFO- 4   -522.449  LUFO+ 6     50.204  0.0000     0.0019     0.0040    -0.0029
 HOFO- 4   -522.449  LUFO+ 7     50.202  0.0000     0.0007     0.0015    -0.0033
 HOFO- 4   -522.449  LUFO+ 8     51.902  0.0000     0.0011     0.0014     0.0005
 HOFO- 4   -522.449  LUFO+ 9     51.901  0.0000    -0.0022    -0.0008     0.0002
 HOFO- 4   -522.449  LUFO+10     70.486 -0.0008     0.4367     0.4352     0.1864
 HOFO- 4   -522.449  LUFO+11     99.830 -0.0144     7.5542     7.5527     3.0513
...
 HOFO- 1    -11.721  HOFO- 4   -669.764 -0.0002     0.1062     0.1022     0.0662
 HOFO- 1    -11.721  HOFO- 3    -30.324  0.0071    -0.2769    -0.2767    -0.1497
 HOFO- 1    -11.721  HOFO- 2    -12.900  0.0307    -0.7934    -0.7934    -0.3783
 HOFO- 1    -11.721  HOFO- 1     -9.052 -0.0034     0.0873     0.0873     0.0348
 HOFO- 1    -11.721  HOFO- 0     -9.054  0.0045    -0.1147    -0.1147    -0.0470
 HOFO- 1    -11.721  LUFO+ 0     -1.049  0.1204    -2.0880    -2.0880    -0.7690
 HOFO- 1    -11.721  LUFO+ 1     21.089 -0.0390     0.1727     0.1726    -0.1826
 HOFO- 1    -11.721  LUFO+ 2     29.949 -0.0429     0.5628     0.5626    -0.3908
 HOFO- 1    -11.721  LUFO+ 3     33.064 -0.0045     0.0664     0.0665    -0.0484
 HOFO- 1    -11.721  LUFO+ 4     33.060  0.0087    -0.1368    -0.1368     0.0923
 HOFO- 1    -11.721  LUFO+ 5     39.257 -0.0683     0.8707     0.8706    -0.9407
 HOFO- 1    -11.721  LUFO+ 6     50.204 -0.0022     0.0555     0.0552    -0.0420
 HOFO- 1    -11.721  LUFO+ 7     50.202 -0.0021     0.0501     0.0504    -0.0409
 HOFO- 1    -11.721  LUFO+ 8     51.902  0.0011    -0.0287    -0.0289     0.0229
 HOFO- 1    -11.721  LUFO+ 9     51.901  0.0003    -0.0075    -0.0075     0.0052
 HOFO- 1    -11.721  LUFO+10     70.486  0.0318    -0.5424    -0.5424     0.9351
 HOFO- 1    -11.721  LUFO+11     99.830 -0.0442     0.5278     0.5275    -1.9454
 HOFO- 0     -9.877  HOFO- 4   -669.764 -0.0006     0.4203     0.4187     0.2027
 HOFO- 0     -9.877  HOFO- 3    -30.324 -0.0456     1.6160     1.6161     0.9160
 HOFO- 0     -9.877  HOFO- 2    -12.900 -0.1010     2.2962     2.2962     1.1499
 HOFO- 0     -9.877  HOFO- 1     -9.052 -0.0068     0.1853     0.1853     0.0647
 HOFO- 0     -9.877  HOFO- 0     -9.054  0.0100    -0.2684    -0.2684    -0.0943
 HOFO- 0     -9.877  LUFO+ 0     -1.049 -0.2980     3.9987     3.9985     1.6282
 HOFO- 0     -9.877  LUFO+ 1     21.089  0.0851     0.1560     0.1560     0.4769
 HOFO- 0     -9.877  LUFO+ 2     29.949  0.0813    -0.6681    -0.6682     0.8164
 HOFO- 0     -9.877  LUFO+ 3     33.064 -0.0105     0.1650     0.1648    -0.1219
 HOFO- 0     -9.877  LUFO+ 4     33.060  0.0182    -0.2918    -0.2918     0.2114
 HOFO- 0     -9.877  LUFO+ 5     39.257  0.1018    -0.9284    -0.9286     1.4949
 HOFO- 0     -9.877  LUFO+ 6     50.204 -0.0069     0.1722     0.1725    -0.1384
 HOFO- 0     -9.877  LUFO+ 7     50.202 -0.0075     0.1868     0.1866    -0.1521
 HOFO- 0     -9.877  LUFO+ 8     51.902  0.0015    -0.0325    -0.0323     0.0324
 HOFO- 0     -9.877  LUFO+ 9     51.901  0.0004    -0.0081    -0.0080     0.0075
 HOFO- 0     -9.877  LUFO+10     70.486 -0.0435     0.7474     0.7469    -1.3185
 HOFO- 0     -9.877  LUFO+11     99.830  0.0570    -0.4940    -0.4939     2.5652
 LUFO+ 0      0.632  HOFO- 4   -669.764 -0.0019     1.3097     1.3106     0.6405
 LUFO+ 0      0.632  HOFO- 3    -30.324 -0.0452     1.4480     1.4477     0.6713
 LUFO+ 0      0.632  HOFO- 2    -12.900 -0.0658     0.8659     0.8658     0.4034
 LUFO+ 0      0.632  HOFO- 1     -9.052 -0.0121     0.2290     0.2290     0.0511
 LUFO+ 0      0.632  HOFO- 0     -9.054  0.0187    -0.3518    -0.3517    -0.0787
 LUFO+ 0      0.632  LUFO+ 0     -1.049 -0.2245     0.3149     0.3148     0.0469
 LUFO+ 0      0.632  LUFO+ 1     21.089  0.1278     0.3969     0.3969     1.3882
 LUFO+ 0      0.632  LUFO+ 2     29.949  0.0569     0.2374     0.2374     0.8705
 LUFO+ 0      0.632  LUFO+ 3     33.064 -0.0181     0.0267     0.0266    -0.3046
 LUFO+ 0      0.632  LUFO+ 4     33.060  0.0296    -0.0467    -0.0468     0.4982
 LUFO+ 0      0.632  LUFO+ 5     39.257  0.0520     0.1207     0.1207     1.0364
 LUFO+ 0      0.632  LUFO+ 6     50.204 -0.0077     0.0487     0.0488    -0.1961
 LUFO+ 0      0.632  LUFO+ 7     50.202 -0.0089     0.0567     0.0568    -0.2250
 LUFO+ 0      0.632  LUFO+ 8     51.902  0.0022     0.0008     0.0006     0.0565
 LUFO+ 0      0.632  LUFO+ 9     51.901  0.0001     0.0040     0.0039     0.0018
 LUFO+ 0      0.632  LUFO+10     70.486  0.0237     0.2003     0.2008     0.8439
 LUFO+ 0      0.632  LUFO+11     99.830  0.0401     0.1721     0.1719     2.0147
 LUFO+ 1      2.991  HOFO- 4   -669.764 -0.0001     0.0957     0.0970     0.0481
 LUFO+ 1      2.991  HOFO- 3    -30.324 -0.0020     0.0640     0.0641     0.0278
 LUFO+ 1      2.991  HOFO- 2    -12.900 -0.0009     0.0061     0.0062     0.0047
 LUFO+ 1      2.991  HOFO- 1     -9.052  0.0153    -0.2985    -0.2986    -0.0463
 LUFO+ 1      2.991  HOFO- 0     -9.054  0.0133    -0.2544    -0.2543    -0.0402
 LUFO+ 1      2.991  LUFO+ 0     -1.049 -0.0018    -0.0223    -0.0223    -0.0018
 LUFO+ 1      2.991  LUFO+ 1     21.089  0.0020     0.0063     0.0062     0.0247
 LUFO+ 1      2.991  LUFO+ 2     29.949 -0.0011     0.0103     0.0101    -0.0179
 LUFO+ 1      2.991  LUFO+ 3     33.064 -0.0295     0.0817     0.0817    -0.5310
 LUFO+ 1      2.991  LUFO+ 4     33.060 -0.0130     0.0474     0.0474    -0.2338
 LUFO+ 1      2.991  LUFO+ 5     39.257 -0.0025    -0.0065    -0.0067    -0.0531
 LUFO+ 1      2.991  LUFO+ 6     50.204  0.0074    -0.0761    -0.0758     0.1977
 LUFO+ 1      2.991  LUFO+ 7     50.202 -0.0082     0.0774     0.0776    -0.2190
 LUFO+ 1      2.991  LUFO+ 8     51.902  0.0028    -0.0303    -0.0304     0.0765
 LUFO+ 1      2.991  LUFO+ 9     51.901 -0.0087     0.0957     0.0954    -0.2379
 LUFO+ 1      2.991  LUFO+10     70.486  0.0019     0.0154     0.0153     0.0709
 LUFO+ 1      2.991  LUFO+11     99.830 -0.0015     0.0007     0.0006    -0.0782
...
 LUFO+13     94.692  LUFO+ 8     51.902 -0.0011     0.0208     0.0208    -0.0843
 LUFO+13     94.692  LUFO+ 9     51.901 -0.0005     0.0062     0.0062    -0.0330
 LUFO+13     94.692  LUFO+10     70.486  0.0201     1.5544     1.5545     1.6564
 LUFO+13     94.692  LUFO+11     99.830  0.0167     1.1537     1.1537     1.6226
 ===============================================================================
 Data were printed for the following fragment orbitals:
 Fragment 1: orbitals    1 to   19
 Fragment 2: orbitals    1 to   17
 ===============================================================================

AOMix, Revision 6.80e: AOMix can be used for processing TD-DFT calculations from Gaussian to generate UV-Vis absorption spectra.

AOMix, Revision 6.80: AOMix can be used for processing ADF and Q-Chem output files under the 64-bit Windows OS environment. The new version also allows processing of Turbomole output files from calculations with more than 10000 basis functions.

AOMix, Revision 6.70: AOMix can be used for processing Jaguar 7.x- output files under the 64-bit Windows OS environment. Support for the older versions of Jaguar has been removed. Few other improvements.

AOMix, Revision 6.60b: AOMix can be used for a detailed analysis of the atomic orbital overlap matrix:

 
 THE ANALYSIS OF THE ATOMIC ORBITALS OVERLAP INTEGRALS BETWEEN THE FRAGMENTS
                     Maximum    The sum of   The sum of absolute
                     overlap     overlap     values of overlap
   A     B   d(A-B)  integral   integrals    integrals
 ----- ----- ------  --------   ----------   -------------------
   1N    2N   1.109    0.599      2.518        7.319

For each pair of atoms (fragments), AOMix will pick the maximum values of atomic orbital overlap integrals, add together atomic orbital overlap integrals and print the corresponding total values.

AOMix, Revision 6.60: AOMix can be used to calculate orbital contributions to Mayer bond orders via orbital occupancy-perturbed bond orders (J. Chem. Theory Comput. 2012, 8, 908914 DOI: 10.1021/ct3000124).

========  EVALUATION OF BONDING CHARACTER OF THE FRONTIER ORBITALS  ========
==========  VIA ORBITAL OCCUPANCY PERTURBED MAYER BOND ORDERS  =============
 
 A = anti-bonding character; B = bonding character
 
 Mayer bond orders B(AB) after addition of an electron to alpha-spin UMO
 - Fragments -   GS   LUMO    LUMO+1  LUMO+2  LUMO+3  LUMO+4  LUMO+5
    1V     2C   0.36  0.40    0.42    0.37    0.37    0.36    0.37   
    1V     3C   0.37  0.40    0.37    0.38    0.36    0.37    0.28   
    1V     4C   0.36  0.36    0.34    0.41    0.36    0.35    0.32   
    1V     5C   0.37  0.36    0.37    0.45    0.37    0.36    0.35   
    1V     6C   0.37  0.38    0.41    0.43    0.37    0.36    0.34   
    1V    12C   0.46  0.50    0.56    0.44    0.46    0.46    0.47   
    1V    13C   0.44  0.48    0.52    0.43    0.43    0.44    0.45   
    1V    14C   0.46  0.59 B  0.45    0.46    0.44    0.46    0.41   
    1V    18C   0.34  0.34    0.34    0.36    0.32    0.34    0.33   
    1V    20C   0.35  0.34    0.34    0.38    0.33    0.35    0.34   
    1V    26V   0.94  0.95    1.01    0.79 A  1.15 B  0.99    1.02   
    2C     3C   1.23  1.20    1.21    1.23    1.21    1.23    1.22   
    2C     4C   1.21  1.17    1.21    1.21    1.20    1.21    1.21   
    2C     8H   0.96  0.96    0.96    0.96    0.96    0.96    0.96   
    3C     6C   1.21  1.19    1.20    1.19    1.20    1.21    1.24   
    3C     7H   0.95  0.95    0.95    0.95    0.95    0.95    0.95   
    4C     5C   1.22  1.23    1.22    1.14    1.22    1.22    1.24   
    4C    11H   0.93  0.93    0.93    0.93    0.92    0.93    0.93   
    5C     6C   1.22  1.21    1.23    1.16    1.22    1.22    1.21   
...
 
 Mayer bond orders B(AB) after removal of an electron from alpha-spin OMO
 - Fragments -   GS   HOMO    HOMO-1  HOMO-2  HOMO-3  HOMO-4  HOMO-5
    1V     2C   0.36  0.37    0.36    0.37    0.37    0.37    0.31   
    1V     3C   0.37  0.37    0.37    0.37    0.37    0.31    0.37   
    1V     4C   0.36  0.35    0.35    0.36    0.36    0.30    0.34   
    1V     5C   0.37  0.37    0.37    0.37    0.37    0.34    0.34   
    1V     6C   0.37  0.36    0.37    0.37    0.37    0.36    0.31   
    1V    12C   0.46  0.43    0.46    0.46    0.38    0.46    0.47   
    1V    13C   0.44  0.41    0.44    0.44    0.36    0.44    0.45   
    1V    14C   0.46  0.47    0.46    0.46    0.46    0.47    0.46   
    1V    18C   0.34  0.34    0.34    0.33    0.34    0.34    0.34   
    1V    20C   0.35  0.34    0.35    0.34    0.35    0.35    0.36   
    1V    26V   0.94  0.78 B  0.92    0.73 B  0.99    1.01    0.95   
    2C     3C   1.23  1.23    1.23    1.23    1.23    1.22    1.15   
    2C     4C   1.21  1.21    1.21    1.21    1.21    1.21    1.10 B 
    2C     8H   0.96  0.96    0.96    0.96    0.96    0.96    0.95   
    3C     6C   1.21  1.21    1.21    1.20    1.21    1.11    1.28   
    3C     7H   0.95  0.95    0.95    0.95    0.95    0.94    0.95   
    4C     5C   1.22  1.23    1.22    1.22    1.22    1.10 B  1.32 A 
    4C    11H   0.93  0.93    0.93    0.93    0.93    0.92    0.93   
    5C     6C   1.22  1.23    1.22    1.22    1.22    1.31    1.07 B 
...

AOMix, Revision 6.55: AOMix can be used to calculate empirical dispersion corrections (Edisp) to the Kohn-Sham energy using the Grimme 2006 method (J. Comput. Chem. 2006, 27, 17871799).

DFT-D Correction (S. Grimme, J.Comput.Chem. 2006, vol 27, 1787-1799)
====================================================================
PBE value:
Dispersion correction to the SCF energy is   -18.5 kJ/mol
                                              -4.41 kcal/mol
====================================================================

Calculation of the dispection correction will be activated if the keyword GUESS=CARDS is activated in the AOMix execution parameter file (aomixpar.txt).

AOMix, Revision 6.54: the automatic s,p,d,f,g-orbital contribution breakdown when possible (AOMix-MPA-atom.txt):

  Alpha MO:      41      42      43      44      45      46      47      48      49      50
              HOMO-8  HOMO-7  HOMO-6  HOMO-5  HOMO-4  HOMO-3  HOMO-2  HOMO-1    HOMO    LUMO 
 Energy(eV):  -14.18  -14.08  -13.49  -13.48  -13.32  -13.18  -12.56  -10.02   -9.88   -8.42 
   Symmetry:    na      na      na      na      na      na      na      na      na      na   
============================================================================================ 
ATOM#   1Dy:   70.55   32.62   84.42   96.21   15.62    7.12    7.68   65.31   37.31   29.03
 s orbitals:    0.03    0.03    0.30    0.73    0.38    0.13    0.16   62.53   25.08   15.72
 p orbitals:    0.02    0.01    0.00   -0.01    0.07    2.11    2.79   -4.41   -1.85   -0.88
 d orbitals:    0.32    0.46    0.01    0.06    0.21    3.91    4.62    6.96   13.62   13.66
 f orbitals:   70.15   32.05   84.10   95.42   14.92    0.89    0.04    0.27    0.46    0.51
 g orbitals:    0.04    0.07    0.01    0.00    0.05    0.08    0.07   -0.04    0.00    0.01
-------------------------------------------------------------------------------------------- 
ATOM#   2C :    3.28    5.00    1.36    0.98    6.32    6.48   16.10    4.89   14.64    3.07
 s orbitals:   -0.10    0.12   -0.01    0.04    0.24    0.00    0.05    1.16   -0.22    0.10
 p orbitals:    3.30    4.68    1.34    0.94    5.97    6.38   15.97    3.69   14.79    2.68
 d orbitals:    0.09    0.20    0.03    0.01    0.11    0.10    0.07    0.04    0.07    0.29
-------------------------------------------------------------------------------------------- 

A new functionality: AOMix can now be used to generate a new initial guess for a calculation in which an electron is removed from any of the occupied orbitals of the closed shell molecule and this set of orbitals is used to create a new Gaussian input file:

Creating a new electronic state from an existing closed-shell calculation

The AOMix keyword that activates and controls this functionality is REMOVE-ELECTRON. This keyword should be included in the aomixpar.txt file. An example of the usage:

REMOVE-ELECTRON 123

Here AOMix will remove an electron from molecular orbital 123.

AOMix, Revision 6.53: AOMix supports Q-Chem 4 output files.

AOMix, Revision 6.52b: The analysis of the overlap integrals between alpha- and beta-spin MOs is extended to be in more user-friendly form (see the example below). There are cases of interest where it is relevant to evaluate the overlap integrals between alpha- and beta-spin MOs. These overlap integrals are useful for evaluating the matching degree of corresponding spin orbital pairs, as can be see from the following section of the AOMix output (AOMix-atom.txt):

============= Matching Alpha- and Beta-Spin Molecular Orbitals =============
 Alpha MO     Closely matching beta-spin MO (overlap integral between the two)
    1 Occ.     1 Occ.  (1.00)
    2 Occ.     2 Occ.  (1.00)
    3 Occ.     3 Occ.  (1.00)
    4 Occ.     4 Occ.  (1.00)

   89 Occ.    89 Occ.  (0.85)
   90 Occ.    90       (0.83)
   91         91       (1.00)

In the above example, it can be seen that alpha-HOMO (alpha spin-orbital 90) is closely related to beta-LUMO (the overlap integral between the two spin-orbitals is 0.83), while alpha-LUMO (alpha spin-orbital 91) is identical to beta-LUMO+1 (the overlap integral is 1.00).

AOMix, Revision 6.52: Processing of Density Functional based Tight Binding with a lot of extensions (DFTB+) output files.

AOMix, Revision 6.51: The CDA keyword has been replaced by the FO keyword. This change is a reflection of the fact that charge decomposition analysis (CDA) is only one of the features of the fragment orbital calculations in AOMix.

AOMix, Revision 6.50: AOMix (with Gaussian) can be used to evaluate contributions Eorb(a,b) to the fragment interaction energy Eint from individual donor-acceptor orbital pairs. This feature (the original idea came during the one-day trip to Caltech in August 2006) has been tested for both closed- and open-shell species. See the AOMix manual for details. The manuscript with the full description and examples is in preparation.

AOMix, Revision 6.46: AOMix now allows construction of orbitals interaction plots for systems with more than 2 fragments.

AOMix, Revision 6.46: MS Windows 64-bit OS compatible version of AOMix.

AOMix, Revision 6.46: AOMix supports Turbomole 6 output files that were generated by using the t2aomix script in Turbomole:

[AOMix Format]
[Title]
                                                                                
[SCF Energy / Hartree]
  -.13148671657790E+04
[Atoms] AU
 o     1    8 0.21549252131700E+00 0.59614303698830E+01 -.28174749460510E+01
 o     2    8 0.22572784880900E+00 0.64422644598460E+01 0.19523633277080E+01
 s     3   16 0.14931988896300E+00 0.47294490923450E+01 -.27550234799100E+00
 c     4    6 -.25486991117690E+01 0.27494069690320E+01 -.99793941652000E-01
 c     5    6 -.23143557694950E+01 0.16888497094600E+00 0.45155649775000E-01
 n     6    7 -.22486500430000E-01 -.11016716519160E+01 0.84259037373000E-01
...

Support for older versions of Turbomole has been removed from AOMix.

AOMix, Revision 6.45: AOMix allows a generation of initial guesses of the wave functions for GAMESS(US) calculations from GAMESS fragment wave functions. Please refer to APPENDIX II in the AOMix manual for details.

AOMix, Revision 6.44: AOMix supports Gaussian 09 and Spartan output files.

AOMix, Revision 6.44: The analysis of 5- and 6-center orbital interactions is added. This feature can be activated or de-activated by using the MULTI-CENTER keyword:

 The analysis of the 3-center orbital interactions:
 
   A     B     C    3-center bond orders with B(ABC) > 0.01
 ----- ----- -----  ---------------------------------------
   1C    3C    9C   B(ABC)=  0.017
   1C    5C    7C   B(ABC)=  0.017
   1C    5C    9C   B(ABC)=  0.017
   3C    5C    7C   B(ABC)=  0.017 
   3C    7C    9C   B(ABC)=  0.017
 
 Sum of (P*S)(P*S)(P*S)/4 :     35.9996 [OK]

 The analysis of the 4-center orbital interactions:
  
   A     B     C     D    4-CENTER bond order index (value > 0.01)
 ----- ----- ----- -----  ----------------------------------------
   1C    3C    7C    9C   B(ABCD)=  0.028
   3C    5C    7C    9C   B(ABCD)=  0.024
 
 The analysis of the 5-center orbital interactions:
 
   A     B     C     D     E   5-CENTER bond order index (value > 0.01)
 ----- ----- ----- ----- ----- ----------------------------------------
   1C    3C    5C    7C    9C   B(ABCDE)=  0.018
 
 The analysis of the 6-center orbital interactions:
 
   A     B     C     D     E     F   6-CENTER bond order index (value > 0.001)
 ----- ----- ----- ----- ----- ----- -----------------------------------------
 all B(ABCDEF) < 0.001; no 6-center interactions.
 

AOMix, Revision 6.43: AOMix supports Q-Chem 3.2 output files. Support for older versions of Q-Chem has been removed.

AOMix, Revision 6.42: AOMix processes NPA-derived populations (Gaussian calculations only) to calculate NPA-derived atomic spin density. The NPA-derived spin densities and charges are printed to UCSF Chimera attribute files for easy visualization.

AOMix, Revision 6.40: AOMix-S, AOMix-L and AOMix-FO codes are integrated into the AOMix program. This version allows a fully NON-INTERACTIVE execution of regular and CDA/EDA jobs. Bond orders and total overlap populations (TOPs) are printed in a more convinient format:

 2-CENTER BOND ORDERS BETWEEN FRAGMENTS, B(AB) and its components,
 2(PA*S)(PA*S) and 2(PB*S)(PB*S), and TOTAL OVERLAP POPULATIONS (TOPs)
 
               Wiberg     Mayer bond orders(>0.01)  Overlap populations
   A     B   (P*S)(P*S)    B(AB)  B(alpha) B(beta)  TOP(alpha) TOP(beta)
 ----- ----- ----------   ------- -------- -------  ---------  -------- 
   1Cu   2N     0.299      0.299   0.149   0.150       0.104    0.104
   1Cu   3N     0.011      0.011   0.005   0.005      -0.004   -0.004
   1Cu   4N     0.518      0.545   0.243   0.303       0.189    0.235
   1Cu   6N     0.518      0.545   0.243   0.303       0.189    0.235
   1Cu   8C     0.020      0.020   0.010   0.010      -0.009   -0.008
   1Cu  10C     0.010      0.011   0.005   0.005       0.012    0.012
   1Cu  11C     0.032      0.033   0.015   0.018      -0.017   -0.016
   1Cu  13C     0.019      0.020   0.009   0.011       0.020    0.022
   1Cu  14C     0.032      0.033   0.015   0.018      -0.017   -0.016
   1Cu  16C     0.019      0.020   0.009   0.011       0.020    0.022
   1Cu  28S     0.936      1.073   0.378   0.695       0.291    0.373
   1Cu  29C     0.081      0.083   0.039   0.044       0.020    0.018
   1Cu  30C     0.008      0.018   0.000   0.018       0.006    0.006
   1Cu  32C     0.008      0.019   0.000   0.019       0.001    0.001
   1Cu  39F     0.014      0.015   0.006   0.009       0.000    0.000
   2N    3N     1.048      1.048   0.524   0.524       0.160    0.161
   2N    5N     0.010      0.010   0.005   0.005       0.012    0.012
   2N    7N     0.010      0.010   0.005   0.005       0.012    0.012
   2N    8C     1.570      1.570   0.785   0.784       0.513    0.513
   2N   10C     0.128      0.128   0.064   0.064      -0.065   -0.065
   2N   27H     0.016      0.016   0.008   0.008       0.009    0.009
   3N    4N     0.010      0.010   0.005   0.005       0.012    0.011
   3N    6N     0.010      0.010   0.005   0.005       0.012    0.011
   3N    8C     0.092      0.092   0.046   0.046      -0.044   -0.045
   3N   10C     1.347      1.347   0.674   0.673       0.404    0.402
   3N   17B     0.874      0.874   0.437   0.437       0.356    0.356
   3N   23H     0.013      0.013   0.006   0.006       0.010    0.010
   4N    5N     1.034      1.034   0.516   0.519       0.145    0.160
   4N    7N     0.012      0.012   0.006   0.006       0.016    0.013
...

Regular AOMix calculations with a default fragment specification (atoms / orbitals) are executed by the following command:

AOMix.exe output-file-to-be-processed

See the picture below as an example.

AOMix execution in the WinNC file manager

Regular AOMix calculations with non-default fragments (such as a user-defined list of atoms/orbitals) are executed by the following command:

AOMix.exe output-file-to-be-processed fragment-list-file

such as

AOMix.exe BH3CO.log fragments.dat

For FO calculations, the command line is:

AOMix.exe output-file FO

output-file is the name of the output file which contains results of MO calculation for the whole molecule. For example,

AOMix.exe BH3CO.log FO

For FO calculations, do not enter the names of fragment files (FRAGM1.LOG, FRAGM2.LOG, etc.) The possible number of fragments in FO calculations has been increased to 4000. FO calculations are followed by DOS calculations for the same fragments.

AOMix: 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: printing of the gross s-, p-, d-,(etc.) orbital populations of atoms/fragments is added to the AOMix 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: the analysis of four-center orbital interactions is added. This feature can be activated or de-activated by using the MULTI-CENTER keyword.

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

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

Mayer bond orders in the anthracene molecule

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

AOMix-FO: the new keyword (CORE) is added to simplify the construction of orbital interaction diagrams.

AOMix: the CUBE keyword is extended. This keyword instructs the AOMix 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-FO: energy decomposition analysis (Morokuma-Ziegler EDA, for Gaussian calculations only)

. AOMix allows to evaluate the following two terms of EDA: Esteric and Eorb:

Eint = Esteric + Eorb

Esteric is the sum of two components, the electrostatic interaction energy between the fragments with the frozen electronic distributions and Pauli repulsion.

 Electronic energy (a.u.)
 ===================== E(SCF) ===========================
  Whole molecule     -82.611817 
                     -82.535557 from CARDS, E(orb)=  -47.9 kcal mol-1
Sum of fragments     -82.552583 
   Fragment    1     -56.184287 
   Fragment    2     -26.368297 
 
 Interaction energy between the fragments (without the BSSE correction)
 ----------------------------------------------------------------------
 Delta E(SCF)=    -1.612 eV,    -37.17 kcal mol-1

AOMix: Turbomole output files can be processed for AOMix calculations.

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

AOMix: the OP-CONTRIBUTIONS keyword is added. This keyword instructs AOMix to print AO contributions (2*Ca*Cb*Sab 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-FO: 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 with the FO option: 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: the ENERGYRANGE keyword is added. This keyword instructs the AOMix 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: AOMix 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-FO: the program output is extended to include (if needed) the full LCFO-MO matrix.

AOMix-FO: 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
Theoret. Chem. Acc., 2008, 119, 57-65 [PDF]

AOMix: the CUBE keyword is added. This keyword instructs the AOMix 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: 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:

AOMix: the additional information is recorded in AOMix 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: an extra option has been added for presenting density-of-states plot data: line DOS plots.

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

AOMix: 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: 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.

AOMix: the AOMix output has been extented to include the calculation of symmetry components of Mayer bond orders.

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

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

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

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Last updated: May 2017