I have found that Gaussian/Bader analysis appears to give a pathologically incorrect result for the transition meatals. The DFT/B3PW91 is used in my system and the basis for metal atoms is Lanl2dz.
The results are listed here
Pt5Ru2 cluster
ACF.valence.dat
::::::::::::::
# X Y Z CHARGE MIN DIST ATOMIC VOL
--------------------------------------------------------------------------------
1Pt 3.9507 2.4481 -0.3570 13.8570 2.0257 4070.2870
2Pt 3.9517 -2.4477 -0.3569 13.7653 2.0258 4160.2340
3Pt -3.9507 2.4479 -0.3570 13.7856 2.0221 4101.9390
4Pt -3.9517 -2.4476 -0.3569 13.6827 2.0089 4071.7984
5Ru -0.0000 2.1709 2.3503 13.7845 1.8381 2218.5353
6Ru -0.0000 -2.1720 2.3489 13.6088 1.8471 2242.0260
7Ru 0.0001 -0.0002 -2.1682 13.5164 1.8366 1112.3983
--------------------------------------------------------------------------------
VACUUM CHARGE: 0.0000
VACUUM VOLUME: 0.0000
NUMBER OF ELECTRONS: 96.0003
I can't understand the result of the Bader analysis, . Why are the Pt and Ru valence charges around 13.7 instead of around 10 and 8 ?
Your kind response is highly appreciated.pcntsfad
Bader analysis of transition metal for Gaussian cube file
Moderator: moderators
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gwlsw890118
- Posts: 2
- Joined: Sun Dec 29, 2013 11:02 am
Re: Bader analysis of transition metal for Gaussian cube fil
I'm guessing that your Pt pseudopotential has 12 (10xd+2xs) explicit electrons and Ru has 16 (8xd+2xs+6xp). This would give the correct total number of electrons, 96. Then, the analysis is saying that Pt has taken charge from Ru, and the Pt is charged by -1.7 and the Ru by +2.3.
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gwlsw890118
- Posts: 2
- Joined: Sun Dec 29, 2013 11:02 am
Re: Bader analysis of transition metal for Gaussian cube fil
Thank you Pro Henkelman. I used the same method and basis in my caculation, but the results of bader analysis are so different.
Pt6Ru
ACF.valence.dat
::::::::::::::
# X Y Z CHARGE MIN DIST ATOMIC VOL
--------------------------------------------------------------------------------
1 Pt 3.8726 1.9626 -0.9133 17.2923 1.8839 4414.2153
2 Pt 4.0000 -2.7893 0.4049 16.9641 1.9566 4621.2002
3 Pt 0.0018 3.3759 1.7269 16.1574 1.9028 2445.1753
4 Pt -3.8713 1.9650 -0.9114 17.2798 1.9306 4306.2658
5 Pt -4.0021 -2.7878 0.4033 16.9722 1.9221 4711.5082
6 Pt -0.0005 -0.9434 -2.2018 15.9425 1.9423 1597.9607
7 Pt -0.0009 -1.3880 2.6437 15.3906 1.7891 1705.7702
--------------------------------------------------------------------------------
VACUUM CHARGE: 0.0000
VACUUM VOLUME: 0.0000
NUMBER OF ELECTRONS: 115.9990
Pt5Ru2
ACF.valence.dat
::::::::::::::
# X Y Z CHARGE MIN DIST ATOMIC VOL
--------------------------------------------------------------------------------
1Pt -4.0432 -2.4452 -0.1408 16.1086 2.0500 4148.8034
2Pt -4.0429 2.4470 -0.1408 16.0819 2.0472 4207.1053
3Pt 4.0408 -2.4474 -0.1416 16.1085 2.0727 4225.3026
4Pt 4.0462 2.4449 -0.1421 16.0865 2.0742 4144.6516
5Pt -0.0023 -0.0012 -2.1288 14.4200 2.0059 1595.5747
6Ru -0.0002 -2.2032 2.3904 13.5942 1.8263 2225.9868
7Ru 0.0026 2.2066 2.3855 13.6002 1.8270 2231.6845
--------------------------------------------------------------------------------
VACUUM CHARGE: 0.0000
VACUUM VOLUME: 0.0000
NUMBER OF ELECTRONS: 105.9999
However, when I used these clusters to adsorb a CO molecule, the result following.
Pt6Ru-CO
ACF.valence.dat
::::::::::::::
# X Y Z CHARGE MIN DIST ATOMIC VOL
--------------------------------------------------------------------------------
1Pt -3.6968 1.6439 0.8311 16.0135 1.9019 3979.3700
2Pt -3.6854 -2.7853 -1.3629 18.1987 1.9546 3817.0860
3Pt 0.0016 4.5271 -0.6332 16.1948 1.9119 3271.7812
4Pt 3.6976 1.6415 0.8326 16.0061 1.9112 3960.1858
5Pt 3.6845 -2.7873 -1.3620 18.2018 1.9636 3823.0070
6Pt -0.0010 -1.6548 2.0439 15.8963 1.6030 462.9785
7Ru 0.0010 0.0407 -2.6819 15.4212 1.7957 1165.9252
8c -0.0040 -2.9166 5.3287 2.3140 0.1838 390.5523
9o -0.0061 -3.7418 7.3463 7.7676 1.2401 3276.8496
--------------------------------------------------------------------------------
VACUUM CHARGE: 0.0000
VACUUM VOLUME: 0.0000
NUMBER OF ELECTRONS: 126.0140
Pt5Ru2-CO
ACF.valence.dat
::::::::::::::
# X Y Z CHARGE MIN DIST ATOMIC VOL
--------------------------------------------------------------------------------
1Pt -3.3796 -3.2620 -0.3409 16.3467 1.9870 3271.3943
2Pt -4.4279 1.5003 -0.0408 13.9229 1.4995 2132.9506
3Pt 4.4459 -1.9858 0.0235 16.0851 2.0256 4419.8402
4Pt 3.9901 2.8217 -0.3908 16.2409 2.0538 3594.4661
5Pt 0.2479 -0.2461 -2.0386 16.0103 1.9087 1301.1465
6Ru 0.3200 -2.1806 2.6695 13.5858 1.9156 2457.1179
7Ru -0.0293 2.3438 2.3276 13.6380 1.8893 1963.6748
8C -5.4331 4.8248 -0.1211 2.4921 0.0244 915.0607
9O -6.0685 6.9103 -0.2143 7.8233 1.4102 4168.8796
--------------------------------------------------------------------------------
VACUUM CHARGE: 0.0000
VACUUM VOLUME: 0.0000
NUMBER OF ELECTRONS: 116.1452
Pt4Ru3-CO
ACF.valence.dat
::::::::::::::
# X Y Z CHARGE MIN DIST ATOMIC VOL
--------------------------------------------------------------------------------
1Pt 4.5479 1.2910 -0.0952 9.9196 1.3849 2313.5254
2Pt 3.1027 -3.3305 -0.5223 15.4590 2.0273 3371.8616
3Pt -3.9057 2.8753 -0.5068 14.9943 2.0267 5974.9724
4Pt -4.5202 -1.8768 -0.0717 14.5480 2.0194 3260.3721
5Ru 0.1415 2.3103 2.0644 13.6494 1.8131 1860.1510
6Ru -0.4793 -2.1577 2.5312 13.6432 1.7871 2469.3235
7Ru -0.2564 -0.1279 -2.4513 13.5702 1.8200 1330.2173
8C 5.7544 4.5527 -0.0608 2.3665 0.1520 749.1803
9O 6.5113 6.5995 -0.0872 8.1916 1.5204 3006.7696
--------------------------------------------------------------------------------
VACUUM CHARGE: 0.0000
VACUUM VOLUME: 0.0000
NUMBER OF ELECTRONS: 106.3418
I can't understand how to define explicit electrons and why the results are different in the same method and basis?
Pt6Ru
ACF.valence.dat
::::::::::::::
# X Y Z CHARGE MIN DIST ATOMIC VOL
--------------------------------------------------------------------------------
1 Pt 3.8726 1.9626 -0.9133 17.2923 1.8839 4414.2153
2 Pt 4.0000 -2.7893 0.4049 16.9641 1.9566 4621.2002
3 Pt 0.0018 3.3759 1.7269 16.1574 1.9028 2445.1753
4 Pt -3.8713 1.9650 -0.9114 17.2798 1.9306 4306.2658
5 Pt -4.0021 -2.7878 0.4033 16.9722 1.9221 4711.5082
6 Pt -0.0005 -0.9434 -2.2018 15.9425 1.9423 1597.9607
7 Pt -0.0009 -1.3880 2.6437 15.3906 1.7891 1705.7702
--------------------------------------------------------------------------------
VACUUM CHARGE: 0.0000
VACUUM VOLUME: 0.0000
NUMBER OF ELECTRONS: 115.9990
Pt5Ru2
ACF.valence.dat
::::::::::::::
# X Y Z CHARGE MIN DIST ATOMIC VOL
--------------------------------------------------------------------------------
1Pt -4.0432 -2.4452 -0.1408 16.1086 2.0500 4148.8034
2Pt -4.0429 2.4470 -0.1408 16.0819 2.0472 4207.1053
3Pt 4.0408 -2.4474 -0.1416 16.1085 2.0727 4225.3026
4Pt 4.0462 2.4449 -0.1421 16.0865 2.0742 4144.6516
5Pt -0.0023 -0.0012 -2.1288 14.4200 2.0059 1595.5747
6Ru -0.0002 -2.2032 2.3904 13.5942 1.8263 2225.9868
7Ru 0.0026 2.2066 2.3855 13.6002 1.8270 2231.6845
--------------------------------------------------------------------------------
VACUUM CHARGE: 0.0000
VACUUM VOLUME: 0.0000
NUMBER OF ELECTRONS: 105.9999
However, when I used these clusters to adsorb a CO molecule, the result following.
Pt6Ru-CO
ACF.valence.dat
::::::::::::::
# X Y Z CHARGE MIN DIST ATOMIC VOL
--------------------------------------------------------------------------------
1Pt -3.6968 1.6439 0.8311 16.0135 1.9019 3979.3700
2Pt -3.6854 -2.7853 -1.3629 18.1987 1.9546 3817.0860
3Pt 0.0016 4.5271 -0.6332 16.1948 1.9119 3271.7812
4Pt 3.6976 1.6415 0.8326 16.0061 1.9112 3960.1858
5Pt 3.6845 -2.7873 -1.3620 18.2018 1.9636 3823.0070
6Pt -0.0010 -1.6548 2.0439 15.8963 1.6030 462.9785
7Ru 0.0010 0.0407 -2.6819 15.4212 1.7957 1165.9252
8c -0.0040 -2.9166 5.3287 2.3140 0.1838 390.5523
9o -0.0061 -3.7418 7.3463 7.7676 1.2401 3276.8496
--------------------------------------------------------------------------------
VACUUM CHARGE: 0.0000
VACUUM VOLUME: 0.0000
NUMBER OF ELECTRONS: 126.0140
Pt5Ru2-CO
ACF.valence.dat
::::::::::::::
# X Y Z CHARGE MIN DIST ATOMIC VOL
--------------------------------------------------------------------------------
1Pt -3.3796 -3.2620 -0.3409 16.3467 1.9870 3271.3943
2Pt -4.4279 1.5003 -0.0408 13.9229 1.4995 2132.9506
3Pt 4.4459 -1.9858 0.0235 16.0851 2.0256 4419.8402
4Pt 3.9901 2.8217 -0.3908 16.2409 2.0538 3594.4661
5Pt 0.2479 -0.2461 -2.0386 16.0103 1.9087 1301.1465
6Ru 0.3200 -2.1806 2.6695 13.5858 1.9156 2457.1179
7Ru -0.0293 2.3438 2.3276 13.6380 1.8893 1963.6748
8C -5.4331 4.8248 -0.1211 2.4921 0.0244 915.0607
9O -6.0685 6.9103 -0.2143 7.8233 1.4102 4168.8796
--------------------------------------------------------------------------------
VACUUM CHARGE: 0.0000
VACUUM VOLUME: 0.0000
NUMBER OF ELECTRONS: 116.1452
Pt4Ru3-CO
ACF.valence.dat
::::::::::::::
# X Y Z CHARGE MIN DIST ATOMIC VOL
--------------------------------------------------------------------------------
1Pt 4.5479 1.2910 -0.0952 9.9196 1.3849 2313.5254
2Pt 3.1027 -3.3305 -0.5223 15.4590 2.0273 3371.8616
3Pt -3.9057 2.8753 -0.5068 14.9943 2.0267 5974.9724
4Pt -4.5202 -1.8768 -0.0717 14.5480 2.0194 3260.3721
5Ru 0.1415 2.3103 2.0644 13.6494 1.8131 1860.1510
6Ru -0.4793 -2.1577 2.5312 13.6432 1.7871 2469.3235
7Ru -0.2564 -0.1279 -2.4513 13.5702 1.8200 1330.2173
8C 5.7544 4.5527 -0.0608 2.3665 0.1520 749.1803
9O 6.5113 6.5995 -0.0872 8.1916 1.5204 3006.7696
--------------------------------------------------------------------------------
VACUUM CHARGE: 0.0000
VACUUM VOLUME: 0.0000
NUMBER OF ELECTRONS: 106.3418
I can't understand how to define explicit electrons and why the results are different in the same method and basis?
Re: Bader analysis of transition metal for Gaussian cube fil
I really don't understand what the problem is. You posted a Bader analysis of a Pt-Ru complex which seems reasonable to me. Now you have 3 more calculations -- can you be more explicit about your concerns? I am looking at the Pt56RuCO complex and (trying to guess at the valence charges of Pt=16, Ru=16, C=6, O=8) this gives partial charges of Pt from 0 to -2, Ru of +0.6, C of +3.7 and O of 0.2.
But honestly, I just don't understand the confusion here. The Bader analysis adds up the total number of electrons around each atom. If you want to know the partial charge, you just need to subtract the valence -- the explicit number of electrons being modeled in your electronic structure calculation -- in order to obtain the partial charge.
But honestly, I just don't understand the confusion here. The Bader analysis adds up the total number of electrons around each atom. If you want to know the partial charge, you just need to subtract the valence -- the explicit number of electrons being modeled in your electronic structure calculation -- in order to obtain the partial charge.