Strain energy is reduced by incorporating smaller atoms into the atomic positions under compression and larger atoms in atomic positions under tension leading to an ordered structure.
PQR files contain the atomic positions of all of the atoms in the system in addition to their charge and radii.
In this way, we showed that the atomic positions of all carbon atoms in AGNRs can be calculated by the formula, and so we can perform the analysis without the need to its structural relaxations.
This compromises the quality of polar interaction networks for all models (regardless of protocol) since buried waters usually participate in direct or bridging hydrogen-bonding interactions and can thus affect the atomic positions of their partner atoms.
For nanostructures, containing less than 500 atoms in the unit cell, all the atomic positions are calculated using the first principles methods based on the density functional theory, with full relaxation and re-bonding allowed.
As the ab initio computations are highly time consuming, the DOS for structures containing more than 500 atoms, has been calculated without relaxation of the atomic positions.
The atomic positions were optimized by minimization of the forces (below 2 mRy/au) acting on the atoms simultaneously with the self-consistent-field cycle as implemented by Marks.
The angles between rows indicate rotational symmetries of the atomic positions.
The atomic positions were stable when refined.
The atomic positions of all structures are relaxed with residual forces smaller than 0.01 eV/Å.
Instead an often used approach is to obtain the atomic positions directly from the experimental images.
