Tip
All input files can be downloaded: Files
.
nddo
This option controls how to perform an NDDO (like AM1, PM3, etc.) calculation.
Options
- charge
Value
An integer
Default
0
Define the total charge of the system.
- spin2p1
Value
An integer
Default
1
for even number of electrons2
for odd number of electronsDefine the spin multiplicity of the system, i.e., \(2S+1\), where \(S\) is the spin of the system. For example, to consider the singlet and triplet state, one should set
spin2p1
to1
and3
, respectively.
- max_it
Value
A non-negative integer
Default
150
Define the maximum number of SCF iteration.
- print_MO
Print molecular orbital coefficients. Without this, only molecular orbital energies and occupancies are printed.
- use_hcore
Use the core Hamiltonian matrix as the initial guess. Without this, the superposition of atomic NDDO densities is used as the initial guess.
- print_level
Value
PrintNone
for restricted SCF (alpha and beta orbitals are restricted to be identical)PrintEssentials
for unrestricted SCF (alpha and beta orbitals are not necessarily identical)PrintDetails
for unrestricted SCF (alpha and beta orbitals are not necessarily identical)Default
PrintEssentials
The information printing level.
- density_cov
Value
A real number
Default
1.E-9
The density matrix convergence threshold for SCF calculations.
Theoretical Background
The NDDO (Neglect of Diatomic Differential Overlap) method is a semi-empirical quantum chemistry method that simplifies the calculation of electronic structures in molecules. It is based on the Hartree-Fock theory but introduces several approximations to reduce computational cost while maintaining reasonable accuracy for many systems. The following NDDO-based methods are implemented in Qbics:
mndo
am1
am1d
rm1
pm3
pm3d
pm6
pmo
pmow
Input Examples
Note that, in all examples below, you can change energy
to opt
to do geometry optimization, or md
to do molecular dynamics.
Example: NDDO Geometry Optimization of Congo Red Anion
We perform an NDDO geometry optimization of the Congo Red anion, which is of charge -2. The input file is as follows:
1mol
2 N -1.54332513 -2.09816265 1.04511234
3 C -1.24833878 -0.93106019 0.36508274
4 C -2.25957296 -0.07865002 -0.14856083
5 N -3.66148390 -0.29307361 -0.15493448
6 N -4.18863626 -1.27534731 0.37531946
7 C -5.60908641 -1.45451288 0.28158560
8 C -6.44457282 -0.83932131 -0.67188202
9 C -7.79728533 -1.15798249 -0.73630174
10 C -8.36065510 -2.08786360 0.14739783
11 C -9.77016879 -2.45880897 0.04894333
12 C -10.37218322 -2.63400200 -1.20423937
13 C -11.70230579 -3.02737161 -1.30728487
14 C -12.47656958 -3.25031163 -0.15160638
15 N -13.86557539 -3.62919999 -0.14487415
16 N -14.32966893 -4.17706047 -1.14625475
17 C -15.69877226 -4.57627884 -1.20899537
18 C -16.68973206 -4.15262107 -0.27475128
19 C -18.01024266 -4.49443901 -0.39532055
20 S -19.17268148 -3.86811281 0.81316397
21 O -19.75454266 -5.01617220 1.39840350
22 O -18.38630356 -3.10248890 1.70179250
23 O -20.10356966 -3.11120162 0.06462974
24 C -18.41112808 -5.32846881 -1.47222133
25 C -19.77910594 -5.71132399 -1.62198661
26 C -20.17834220 -6.53295026 -2.64390564
27 C -19.22910471 -7.02196171 -3.56998588
28 C -17.90832650 -6.66645352 -3.45632203
29 C -17.46190253 -5.80234089 -2.41478734
30 C -16.07656666 -5.41039373 -2.29229722
31 N -15.13888043 -5.91803387 -3.19440229
32 C -11.87474269 -3.05051931 1.11034028
33 C -10.54202081 -2.66675984 1.20101906
34 C -7.53790038 -2.67731355 1.11825020
35 C -6.18479683 -2.37215059 1.18838640
36 C -1.87591174 1.15335474 -0.77615212
37 C -0.57261374 1.52889060 -0.93591287
38 S -0.22263048 3.07410672 -1.76404123
39 C 0.45596204 0.67936168 -0.44539542
40 C 1.82678779 1.04190252 -0.60713363
41 C 2.83356234 0.24415341 -0.12687164
42 C 2.52009139 -0.95668533 0.54667961
43 C 1.20940505 -1.33293101 0.71264279
44 C 0.14025272 -0.53616115 0.21319920
45 H -2.46523916 -2.46286272 0.99215794
46 H -0.83173045 -2.78829762 1.08002006
47 H -6.03185765 -0.10143589 -1.37897310
48 H -8.43461236 -0.66688250 -1.48777738
49 H -9.78049223 -2.47062911 -2.11801307
50 H -12.14290958 -3.16255408 -2.30720734
51 H -16.38964262 -3.50879982 0.57744179
52 H -20.50886405 -5.32738427 -0.88397665
53 H -21.23309870 -6.82252491 -2.75059996
54 H -19.55988556 -7.69221994 -4.37548943
55 H -17.19714755 -7.08561026 -4.18243768
56 H -15.48438601 -6.05340540 -4.11792530
57 H -14.24364693 -5.48258085 -3.17857290
58 H -12.46209252 -3.20084844 2.03078572
59 H -10.08787943 -2.51709145 2.19260752
60 H -7.96893149 -3.40122514 1.82663096
61 H -5.56169201 -2.85401081 1.95772702
62 H -2.67308708 1.82553392 -1.15690810
63 H 2.05510061 1.99022309 -1.12996590
64 H 3.88606179 0.53247497 -0.25657336
65 H 3.33326449 -1.58194610 0.94036557
66 H 1.01518864 -2.26662032 1.25943530
67 O -1.49324251 3.61129258 -2.06889525
68 O 0.51932929 3.83612909 -0.83254053
69 O 0.53967816 2.71626705 -2.90040345
70end
71
72nddo
73 charge -2
74 spin2p1 1
75end
76
77task
78 opt am1
79end
You can also change am1
to pm3
, pm6
, etc. to use other NDDO methods listed in the table above. The final geometry is shown below:
