About atomic coordinates in siesta or in general: follow this link Atomic Coordinates.
Basics of DFT:
In DFT, Kohn-Sham equations are solved iteratively and in a self consistent manner to get the ground state energy. SCF cycle: SCF is used. Once the ground state energy ( and ground state charge density) of the system is known, we can calculate the properties derivable from these quantities .......
About Pseudopotentials:
1. Norm conserving pseudopotentials.
2. Ultra soft pseudopotentials: follow this link USPP.
3. Projector augmented wave method: lies midway between pseudopotential PW method and LAPW method.
Lattice dynamics: means dynamics in periodic arrays of vibrating atoms in solids. Lattice dynamics deals vibrational frequencies of collective excitations produced by periodic array of vibrating atoms in solids.
Dynamical matrix formulation for phonons with harmonic approximation:
Anharmonic interactions and displacive phase transition (with soft modes):
QHA (Quasi Harmonic Approximation) and thermodynamical properties:
Thermal conductivity:
WILL BE ADDED ....
Molecular dynamics: means dynamics of atoms in molecules/clusters etc.
Heart of Statistical physics : Ergodicity hypothesis.
Difference between MD (Molecular Dynamics) and MC (Monte Carlo) method:
Different Ensembles:
(NVE), (NVT), (mu,VT), (NPT) ...
Which one to choose?
Algorithms in MD:
TO BE ADDED....