UT theoretical chemistry code forum

I am playing with Bader code on gaussian output of a water molecule. The BCF.dat looks weird to me:
# X Y Z CHARGE ATOM DISTANCE
-------------------------------------------------------------------------
1 0.0000 -1.4415 -0.8307 0.5068 3 0.0643
2 -0.4474 0.0000 0.3126 3.6713 2 0.4583
3 0.4473 0.0000 0.3126 3.2309 2 0.4582
4 0.0000 1.4415 -0.8307 0.5068 1 0.0644
5 0.0000 0.0000 0.2131 0.0839 2 0.0001
-------------------------------------------------------------------------
There are five maxima and no. 2 and 3 are located pretty far from atom 2.

I did bader on the example cube file on your website just for comparison. And here is what the ACF.dat looks like:
# X Y Z CHARGE ATOM DISTANCE
-------------------------------------------------------------------------
1 0.0000 -1.4362 0.9827 0.3766 3 0.0060
2 0.0000 0.0000 -0.1512 9.2510 2 0.0282
3 0.0000 1.4362 0.9827 0.3766 1 0.0059
-------------------------------------------------------------------------

Also, in the ACF.dat, the # of electrons shows as ~8, which is supposed to be ~10.

This is how I did it. First I ran opt and sp in Gaussian with input as below:
%chk=h2o.chk
#mp2/6-31G density=MP2 opt

h2o

0 1
H 0.0000 -1.4362 0.9827
O 0.0000 0.0000 -0.1512
H 0.0000 1.4362 0.9827

--Link1--

%chk=h2o.chk
#mp2/6-31G density=MP2 guess=read geom=allcheckpoint

Then generate the cube file with the following command:
cubegen 0 density=MP2 h2o.fchk h2o.cube 201 h
(I use 201 here just to be consistent with the example charge file, however I got different much smaller grid size, 0.049 vs 0.075)
I have used coarser grip points for cubegen, also used DFT for g09 calculation. Didn't change much.
I wonder if I did anything wrong or I am missing any steps.

I found that only the order of atomic positions are different in BCF.dat.

The BCF file will show basins for all charge density maxima. When you do not have core charges, the maximum at atomic centers can fragment into two or more Bader volumes. Hence the output of our code, which reports both the Bader volumes (BCF) and the atomic volumes (ACF) in which the Bader volumes are assigned to the nearest atomic centers.

In your case, it looks like the hydrogen atoms have well-defined maxima and charges of 0.5068. The remaining 6.9864 electrons are at the oxygen atom, but in three fragments. The fact that you see 8 total electrons instead of 10 indicates that you have not included the 1s electrons in your calculation for O. This also explains the fragmentation of that atomic volume. Never-the-less, since you probably do not care about the region near the center of the O atom, the charges in your ACF file (0.5068 for the H atoms and 6.9864 for O, leading to a net charge of -0.9864 on O) are reasonable.