Usage: normalc [-h/--help] File.molf i1 [i2] [i3] [i4] [--version] ------------------------------------------------------------------ The file to be used as input (File.molf) must be in MOLDEN format; name is irrelevant, as long as it contains the data for vibrational frequencies. Options: -h Help function (this message) (or --help) --version Show version number The first integer (i1) needs to be there always, the others (i2, i3, i4) are optional. Depending on how many integers are present, different contributions to the normal modes will be recovered. In all cases, the contributions are ordered with the largest contributions reported first (max. 10 are shown). If only one integer is present, the contributions of that atom to the different normal modes are obtained. Otherwise, the Cartesian displacement vector for a specific coordinate is projected onto each normal mode. i1: contributions of atom i1 to the normal modes are obtained i1 i2: contributions of bond i1-i2 to the normal modes are obtained i1 i2 i3: contributions of angle i1-i2-i3 to the normal modes are obtained i1 i2 i3 i4: contributions of dihedral i1-i2-i3-i4 to the normal modes are obtained The atom contributions are normalized: when summed over all normal modes they add up to 1.0. Additionally, information about the total contribution of that atom to the normal modes is given: Sum of atomic contributions for atom 1: 0.188786 The contributions shown below are normalized. Frequency Contr. -------------------------- 56 892.25 0.229858 25 339.89 0.127711 21 304.36 0.088301 ... Note that this example is for an iron atom, which does not move too much in this transition-metal complex. It moves most in the 892.25 cm^-1 mode, which corresponds to 23% of all the iron's contributions to normal modes. Other atoms may contribute much more, especially if they are lighter, and a total contribution > 1 may be observed. It is most easily understood for a four-atom complex like [FAl(O₂)]⁰, which has six vibrational frequencies. Sum of atomic contributions for atom 1: 1.258293 Sum of atomic contributions for atom 2: 1.943591 Sum of atomic contributions for atom 3: 1.399148 Sum of atomic contributions for atom 4: 1.399148 ------------------------------------------------------ Sum 6.000180 I.e., the total sum of atomic contributions adds up to the total number of vibrations, after normalization. For a bond, similar information is shown: The contributions shown below for bond 1-7 are not normalized. Frequency Contr. -------------------------- 63 1009.23 0.320167 35 632.81 0.172136 19 273.81 0.161648 ... Note that the contributions of the bonds, angles, dihedrals are not normalized.