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Development of the AOMix suite of programs (see the AOMix manual for a complete description) is a continuous project from 1997. 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 specific project) is possible on a contract basis. Please contact the author if you are interested.
November 2020: instructional video on how to setup AOMix-FO calculations for energy decomposition analysis is posted and can be downloaded from the AOMix download page.
AOMix, Revision 6.94: Reading of Gaussian 16 output files is enabled.
AOMix, Revision 6.92b: Reading of Q-Chem output files (versions 4.3 and 5.0) is enabled. Reading of orbital symmetry data from ORCA output files is enabled. Reading of Turbomole output files for spin-unrestricted calculations is improved. Reading of Gaussian 09 output files for relativistic DKH2 (Douglas-Kroll-Hess) Hamiltonian calculations is improved. The AOMix output section for overlap and charge transfer integrals is modified to have six decimal figures for FO overlap integrals. The AOMix output section for symmetry contributions to Mayer bond orders is modified to include the total:
Alpha-spin orbitals: ================= Symmetry Contributions to Mayer Bond Orders ================= Resolved contributions to 2(PA*S)(PA*S) that are greater than 0.02 FR1 FR2 A1 B2 B1 A2 TOTAL 1C 13Ru 0.07 0.07 0.02 0.05 0.21 2C 13Ru 0.07 0.07 0.02 0.05 0.21 3C 13Ru 0.15 0.00 0.12 0.00 0.27 5C 13Ru 0.15 0.00 0.12 0.00 0.27 7C 13Ru 0.07 0.07 0.02 0.05 0.21 9C 13Ru 0.07 0.07 0.02 0.05 0.21 13Ru 14N 0.08 0.13 0.11 0.01 0.33 13Ru 15N 0.08 0.13 0.11 0.01 0.33 ...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 7.319For 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, 908–914 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, 1787–1799).
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:
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 123Here 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)= 0.0173C 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.
Regular AOMix calculations with non-default fragments (such as a user-defined list of atoms/orbitals) are executed by the following command:
such asAOMix.exe output-file-to-be-processed fragment-list-file
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 0.0000AOMix: 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:
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-1AOMix: 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:
These data can be helpful in the analysis of molecular orbital calculations.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= -0.094AOMix-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:
- The wave function verification procedure is extended.
- AOMix writes two UCSF Chimera attribute files. The first file (with atomic attributes) allows easy visualization of atom-based properties:
- atomic MPA-, NPA- and LPA-derived charges of atoms/fragments,
- MPA-, NPA- 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 generates a UCSF Chimera attribute file. This file allows easy visualization of atomic contributions to the frontier orbitals (10 HOMOs and 10 LUMOs).
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.