Density functional theory simulations of molecules
The aim of the task was to investigate the Diazene (N2H2) and P(OH)5 molecules and to analyse the changes occurring to their structures when the number of electrons surrounding them also changes. Density Functional Theory (DFT) simulations were used in a bid to study the behavior of the molecules; DFT allows understanding the quantum mechanical effects experienced by materials due to the presence of electrons. Figure 1 shows the cis- form of the diazene molecule and the P(OH)5 molecule.
Steps to reproduce
The code essentially utilises the Klenmar-Bylander pseudopotentials in the section denoted as &ATOMS to decrease the computational time required for the simulation to occur as it scales linearly with the basis set. The geometry optimizations carried out are repeated single point calculations in which the atomic positions are updated according to which forces act on them. The input file is divided into sections starting with &NAME and ending with &END, text which is outside of these sections is not taken into account, care must be taken in writing the sections in capital letters or else they will be ignored, all input files are required to have &CPMD, &SYSTEM and &ATOMS sections. The output file contains a list of xyz coordinates which pinpoint the position of the two nitrogen and hydrogen atoms in the molecule over step number, from this coordinate file it will be possible to use VMD to measure the change in bond length and angle. The CPMD code differs from the Optimised Potentials for Liquid Systems (OPLS) force field code in that the OPLS code makes all the interaction sites centre on the atoms, and does not take into account lone pairs of electrons. OPLS code is best suited to study liquid properties including density and heat of vaporization. The CPMD code is capable of modelling electrons, a feature which is not available when using OPLS code.