Pseudo atoms

A 'P' line should look like:

P Pseudo_atom_index Pseudo_atom_type Numb_real_atoms Real_atom_indices

These parameters encode the pseudo atom information as given in Section 5.3.2. Pseudo_atom_index is the atom index, which should be a number between NATM+1 and NATM+NPSEUDO, where NATM is the number of real atoms in the model, and NPSEUDO the number of pseudo atoms. Pseudo_atom_type is the numerical pseudo atom type, as given in Table B.3. The pseudo atom is defined as an average of Numb_real_atoms, of indices Real_atom_indices. For example,

P    144   1   3    120 121 122
creates a pseudo atom at index 144, which is a gravity center of the 3 atoms 120, 121 and 122.

Table B.3: Numerical pseudo atom types
Numeric pseudo atom type Pseudo atom type
1 pseudo_atom.GravityCenter
2 virtual_atom.CH1
3 virtual_atom.CH1A
4 pseudo_atom.CH2
5 virtual_atom.CH2
6 pseudo_atom.CH31
7 pseudo_atom.CH32