.. tip:: All input files can be downloaded: :download:`Files `. nddo ===== .. contents:: :local: This option controls how to perform an NDDO (like AM1, PM3, etc.) calculation. Options ------------ .. option:: charge .. list-table:: :stub-columns: 1 :widths: 5 20 * - Value - An integer * - Default - ``0`` Define the total charge of the system. .. option:: spin2p1 .. list-table:: :stub-columns: 1 :widths: 5 20 * - Value - An integer * - Default - ``1`` for even number of electrons * - - ``2`` for odd number of electrons Define the spin multiplicity of the system, i.e., :math:`2S+1`, where :math:`S` is the spin of the system. For example, to consider the singlet and triplet state, one should set :option:`spin2p1` to ``1`` and ``3``, respectively. .. option:: max_it .. list-table:: :stub-columns: 1 :widths: 5 20 * - Value - A non-negative integer * - Default - ``150`` Define the maximum number of SCF iteration. .. option:: print_MO Print molecular orbital coefficients. Without this, only molecular orbital energies and occupancies are printed. .. option:: 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. .. option:: print_level .. list-table:: :stub-columns: 1 :widths: 5 20 * - 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. .. option:: density_cov .. list-table:: :stub-columns: 1 :widths: 5 20 * - 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: .. list-table:: * - ``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: .. code-block:: :caption: nddo-1.inp :linenos: mol N -1.54332513 -2.09816265 1.04511234 C -1.24833878 -0.93106019 0.36508274 C -2.25957296 -0.07865002 -0.14856083 N -3.66148390 -0.29307361 -0.15493448 N -4.18863626 -1.27534731 0.37531946 C -5.60908641 -1.45451288 0.28158560 C -6.44457282 -0.83932131 -0.67188202 C -7.79728533 -1.15798249 -0.73630174 C -8.36065510 -2.08786360 0.14739783 C -9.77016879 -2.45880897 0.04894333 C -10.37218322 -2.63400200 -1.20423937 C -11.70230579 -3.02737161 -1.30728487 C -12.47656958 -3.25031163 -0.15160638 N -13.86557539 -3.62919999 -0.14487415 N -14.32966893 -4.17706047 -1.14625475 C -15.69877226 -4.57627884 -1.20899537 C -16.68973206 -4.15262107 -0.27475128 C -18.01024266 -4.49443901 -0.39532055 S -19.17268148 -3.86811281 0.81316397 O -19.75454266 -5.01617220 1.39840350 O -18.38630356 -3.10248890 1.70179250 O -20.10356966 -3.11120162 0.06462974 C -18.41112808 -5.32846881 -1.47222133 C -19.77910594 -5.71132399 -1.62198661 C -20.17834220 -6.53295026 -2.64390564 C -19.22910471 -7.02196171 -3.56998588 C -17.90832650 -6.66645352 -3.45632203 C -17.46190253 -5.80234089 -2.41478734 C -16.07656666 -5.41039373 -2.29229722 N -15.13888043 -5.91803387 -3.19440229 C -11.87474269 -3.05051931 1.11034028 C -10.54202081 -2.66675984 1.20101906 C -7.53790038 -2.67731355 1.11825020 C -6.18479683 -2.37215059 1.18838640 C -1.87591174 1.15335474 -0.77615212 C -0.57261374 1.52889060 -0.93591287 S -0.22263048 3.07410672 -1.76404123 C 0.45596204 0.67936168 -0.44539542 C 1.82678779 1.04190252 -0.60713363 C 2.83356234 0.24415341 -0.12687164 C 2.52009139 -0.95668533 0.54667961 C 1.20940505 -1.33293101 0.71264279 C 0.14025272 -0.53616115 0.21319920 H -2.46523916 -2.46286272 0.99215794 H -0.83173045 -2.78829762 1.08002006 H -6.03185765 -0.10143589 -1.37897310 H -8.43461236 -0.66688250 -1.48777738 H -9.78049223 -2.47062911 -2.11801307 H -12.14290958 -3.16255408 -2.30720734 H -16.38964262 -3.50879982 0.57744179 H -20.50886405 -5.32738427 -0.88397665 H -21.23309870 -6.82252491 -2.75059996 H -19.55988556 -7.69221994 -4.37548943 H -17.19714755 -7.08561026 -4.18243768 H -15.48438601 -6.05340540 -4.11792530 H -14.24364693 -5.48258085 -3.17857290 H -12.46209252 -3.20084844 2.03078572 H -10.08787943 -2.51709145 2.19260752 H -7.96893149 -3.40122514 1.82663096 H -5.56169201 -2.85401081 1.95772702 H -2.67308708 1.82553392 -1.15690810 H 2.05510061 1.99022309 -1.12996590 H 3.88606179 0.53247497 -0.25657336 H 3.33326449 -1.58194610 0.94036557 H 1.01518864 -2.26662032 1.25943530 O -1.49324251 3.61129258 -2.06889525 O 0.51932929 3.83612909 -0.83254053 O 0.53967816 2.71626705 -2.90040345 end nddo charge -2 spin2p1 1 end task opt am1 end 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: .. figure:: figs/nddo-1.jpg