read_coord

read_coord

Internal coordinates used for the parametrization of the coupling in dQ-EVB, DG-EVB or TREQ coupling terms is read in from the file coord_def.inp.

If this keyword is not present (only possible for evbopt), the set of internal coordinates will be calculated automatically based on the structures along the reaction path. The 5 coordinates with the largest fluctuation along the reaction path (or the given set of reference structures) will be chosen for the set. If the number of chosen coordinates shall be raised, add the keyword num_coord.

If the keyword is present, the file coord_def.inp will be read. It has the following format: One coordinate per line, defined as:

• [ind1] [ind2]: Bond length between atoms ind1 and ind2
• [ind1] [ind2] [ind3]: Bond angle between atoms ind1, ind2 and ind3
• 0 [ind1] [ind2] [ind3] [ind4]: Torsional angle between atoms ind1, ind2, ind3 and ind4
• 1 [ind1] [ind2] [ind3] [ind4]: Out of plane coordinate defined by ind1, ind2, ind3 and ind4

Example:

1 3
2 3
1 2 3
0 1 2 4 5

Here, the bonds between atoms 1 and 2, 2 and 3, the angle between atoms 1, 2 and 3 and the torsion between atoms 1, 2, 4 and 5 are taken into the coordinate set.

Note: For dQ and DG-EVB is is usually advantageous to chose a subset of coordinates that are most relevant to the reaction of interest, e.g., the forming and breaking bond of an atom exchange reaction. For TREQ, on the other hand, a full (redundant or nunredundant) set of internals must be chosen due to the direct interpolation region! If the coordinate set is incomplete, atom mergings might happen.