For the purpose of exploring microscopic structure structures and
functions of molecules, crystals and soft condensed matters in
the atomicsize （1 Angstrom), we adopt quantum mechanical
simulation method that relies on the density functional theory.
It describes electrons within atoms and molecules by their density
via the Kohn-Sham equation. This method is thus called ab-initio
or first principle molecular dynamics (FPMD) simulations.
We are refining this first principle code to treat atomic movement
and also material deformation through chemical reactions. This type
of the simulation codes is required to study microscopic behavior of
materials at the interface of high temperature fusion plasmas without
making a priori assumptions, unlike the case of macroscopic transport
codes. The left figure shows the FPMD run of hydrogen atoms
adsorbed to the graphite surface. These hydrogen atoms cut the bonds
between carbons at the surface, make a hydrocarbon atom,
which runs away from the graphite surface.
Figure: A sequence of the final states of graphite surface
due to addition of one hydrogen atom at a time. Gray and
white spheres represent carbon and hydrogen atoms,
respectively (calculated using the Siesta code, developed
by ICMAB group of Spain).
Because of increasing complexity, the Schroedinger
equation, which exactly describes every electrons can be
solved only up to five electrons. However, real material
consists of a huge number of electrons (and nuclei),
and such a system is virtually insolvable even with the
fastest supercomputer. On the other hand, if one treats electrons
collectively through their density instead of wave functions of
each electron, the equation becomes much simpler and solvable
(density functional theory). This method is widely adopted for
studies of physical properties and chemical reactions on the
atomic level.
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