I would like to understand how to read the molecular orbitals output?
I need to know how to interpret what they correspond to. May someone please help?
/nethome/cmckinnery3/Thio_Ag/3plus_pvd/dec3_test/MoreDist9/ b3lyp_opt_Thio_Ag.out
Here is part of my output.
Molecular orbitals for symmetry species 1

Orbital 65 66 67 68 69 70 71
1 C :1s 0.0233 0.0005 0.0220 0.0001 0.0001 0.0001 0.0000
2 C :1s 0.0421 0.0010 0.0523 0.0002 0.0002 0.0001 0.0000
3 C :1s 0.1169 0.0022 0.0873 0.0006 0.0006 0.0003 0.0000
4 C :1s 0.0154 0.0031 0.0169 0.0030 0.0028 0.0015 0.0000
5 C :2px 0.0259 0.0586 0.0739 0.0718 0.0466 0.0259 0.0000
6 C :2py 0.0028 0.2165 0.0196 0.2776 0.1816 0.1009 0.0000
7 C :2pz 0.2178 0.0042 0.1564 0.0004 0.0003 0.0001 0.0000
8 C :2px 0.0091 0.0283 0.0129 0.0477 0.0283 0.0157 0.0000
9 C :2py 0.0003 0.1069 0.0036 0.1845 0.1101 0.0612 0.0000
10 C :2pz 0.0431 0.0008 0.0661 0.0004 0.0001 0.0000 0.0000
12 C :2py 0.0005 0.0090 0.0019 0.0339 0.0198 0.0110 0.0000
13 C :2pz 0.0140 0.0003 0.0058 0.0004 0.0007 0.0004 0.0000
14 C :3d2 0.0002 0.0059 0.0014 0.0091 0.0105 0.0059 0.0000
15 C :3d1 0.0050 0.0114 0.0016 0.0023 0.0121 0.0067 0.0000
17 C :3d1+ 0.0187 0.0033 0.0059 0.0007 0.0031 0.0017 0.00
Molecular Orbitals Output
 jmelo
 Posts: 64
 Joined: 27 Aug 2013, 16:59
 First name(s): Juan
 Middle name(s): Ignacio
 Last name(s): Melo
 Affiliation: Dpto. Fisica Fac. Ciencias Exactas y Naturales, Univ. Bs As. And IFIBA CONICET
 Country: Argentina
 Location: Facultad de Ciencas Exactas y Naturales, Universidad de Buenos Aires, Argentina
 Contact:
Re: Molecular Orbitals Output
Dear Carla,
Your M.O’s are a linear combination of the given atomic basis set.
In the case you show, the columns corresponds to each M.O order by its energy,
and the rows are which atomic orbital is involved.
The coefficient at each position is the corresponding coefficient that your ground state solver has given. i.e HartreeFock if so.
I hope this helps you.
Best regards.
jmelo
Your M.O’s are a linear combination of the given atomic basis set.
In the case you show, the columns corresponds to each M.O order by its energy,
and the rows are which atomic orbital is involved.
The coefficient at each position is the corresponding coefficient that your ground state solver has given. i.e HartreeFock if so.
I hope this helps you.
Best regards.
jmelo

 Posts: 14
 Joined: 12 Dec 2013, 12:43
 First name(s): Erik
 Middle name(s): Donovan
 Last name(s): Hedegård
 Affiliation: University of Southern Denmark
 Country: Denmark
 Contact:
Re: Molecular Orbitals Output
Dear Carla
To add to jmelos (completely correct) answer, you can also visualize the MOs, using the molden program.
Dalton outputs a molden input file "the molden.inp" (it is stored in the .tar.gz file), which can be read by the program "molden".
you unpack your .tar.gz file by the command tar xzf yourfile.tar.gz
Molden can be found here: http://www.cmbi.ru.nl/molden/howtoget.html (and it is freely available)
Best regards
Erik
To add to jmelos (completely correct) answer, you can also visualize the MOs, using the molden program.
Dalton outputs a molden input file "the molden.inp" (it is stored in the .tar.gz file), which can be read by the program "molden".
you unpack your .tar.gz file by the command tar xzf yourfile.tar.gz
Molden can be found here: http://www.cmbi.ru.nl/molden/howtoget.html (and it is freely available)
Best regards
Erik

 Posts: 595
 Joined: 15 Oct 2013, 05:37
 First name(s): Peter
 Middle name(s): Robert
 Last name(s): Taylor
 Affiliation: Tianjin University
 Country: China
Re: Molecular Orbitals Output
Some additional points about the MO coefficients. If the calculation
(either at user request or by automatic detection) employs symmetry, then
the "basis functions" that are used are symmetryadapted orbitals. Since
these are always linear combinations of the same AOs on the different
centres (e.g., in H_2 they would be 1s_A + 1s_B, or 2pz_A  2pz_B, where
the atoms are labelled A and B) we just print the type of the AO, so 1s,
2pz, etc. The expansion of the symmetry orbitals in the actual individual
atomic basis functions can be printed by the program during the initial
reading of input.
In your example case let us look at MO 65, which is the leftmost column of
coefficients. We can see that the primary contribution to this MO comes
from a 2pz orbital on a carbon, at least of the 17 rows that are printed
(it's basis function 7 in the numbering) and the next most important is
the third s function on that carbon (row 3).
Note that basis functions will be labelled 1s, 2p, 3d, etc. This is
because it is usual in Gaussian basis function programs to use the lowest
"principal" quantum number possible for each angular type. One typically
does not use 2s, 3s, 4s Gaussiantype orbitals (and actually 2s, 4s, 6s...
would anyway create problems in the integral calculation). So, as I say,
1s, 2p, 3d, 4f is what you will see printed out. Finally, the default in
Dalton is to use basis functions whose angular parts are real spherical
harmonics. s functions of course have an "angular part" that is unity. p
functions have an angular part that is px, py, or pz. But when you get to
d functions and higher the notation would get much messier: you'd have to
print out things like "3dx2y2" and this is a nuisance as well as creating
some very long basis function labels some of which would be almost
incomprehensible (is it useful to see a label like 5g6x2z26y2z2x4+y4 ?!).
We therefore adopted the convention that the angular momentum projection
quantum number is used to label the components of shells of d and higher
functions. Other than the d shell it is not clear how useful it is to
give a mapping here of the Dalton labels to explicit angular types, but
contact me if you want to know about f's, g's, etc. (the g function at
the end of the previous paragraph is labelled 5g2+ in Dalton).
d functions
2+ x2  y2
1+ xz
0 2z2  x2  y2
1 yz
2 xy
Note that while most programs construct and label basis functions in a
similar way, it should never be assumed that the conventions used are
identical between different programs. For example, the phase of some
combinations in Turbomole is different from the phase in Dalton for some f
and g functions.
If you need to know more about all this contact me directly. And please
sign up for the Dalton forum! I am sure the old mailing list will be shut
down at some point.
Best regards
Pete
(either at user request or by automatic detection) employs symmetry, then
the "basis functions" that are used are symmetryadapted orbitals. Since
these are always linear combinations of the same AOs on the different
centres (e.g., in H_2 they would be 1s_A + 1s_B, or 2pz_A  2pz_B, where
the atoms are labelled A and B) we just print the type of the AO, so 1s,
2pz, etc. The expansion of the symmetry orbitals in the actual individual
atomic basis functions can be printed by the program during the initial
reading of input.
In your example case let us look at MO 65, which is the leftmost column of
coefficients. We can see that the primary contribution to this MO comes
from a 2pz orbital on a carbon, at least of the 17 rows that are printed
(it's basis function 7 in the numbering) and the next most important is
the third s function on that carbon (row 3).
Note that basis functions will be labelled 1s, 2p, 3d, etc. This is
because it is usual in Gaussian basis function programs to use the lowest
"principal" quantum number possible for each angular type. One typically
does not use 2s, 3s, 4s Gaussiantype orbitals (and actually 2s, 4s, 6s...
would anyway create problems in the integral calculation). So, as I say,
1s, 2p, 3d, 4f is what you will see printed out. Finally, the default in
Dalton is to use basis functions whose angular parts are real spherical
harmonics. s functions of course have an "angular part" that is unity. p
functions have an angular part that is px, py, or pz. But when you get to
d functions and higher the notation would get much messier: you'd have to
print out things like "3dx2y2" and this is a nuisance as well as creating
some very long basis function labels some of which would be almost
incomprehensible (is it useful to see a label like 5g6x2z26y2z2x4+y4 ?!).
We therefore adopted the convention that the angular momentum projection
quantum number is used to label the components of shells of d and higher
functions. Other than the d shell it is not clear how useful it is to
give a mapping here of the Dalton labels to explicit angular types, but
contact me if you want to know about f's, g's, etc. (the g function at
the end of the previous paragraph is labelled 5g2+ in Dalton).
d functions
2+ x2  y2
1+ xz
0 2z2  x2  y2
1 yz
2 xy
Note that while most programs construct and label basis functions in a
similar way, it should never be assumed that the conventions used are
identical between different programs. For example, the phase of some
combinations in Turbomole is different from the phase in Dalton for some f
and g functions.
If you need to know more about all this contact me directly. And please
sign up for the Dalton forum! I am sure the old mailing list will be shut
down at some point.
Best regards
Pete

 Posts: 6
 Joined: 19 Feb 2014, 00:20
 First name(s): Carla
 Last name(s): Mckinney
 Affiliation: Norfolk State University
 Country: United States
Re: Molecular Orbitals Output
Thank you I will look into this information!!!
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