\contentsline {section}{\numberline {1}Overview}{2}
\contentsline {section}{\numberline {2}How to Use: An Example}{3}
\contentsline {subsection}{\numberline {2.1}To Build}{3}
\contentsline {subsection}{\numberline {2.2}To Use}{3}
\contentsline {subsection}{\numberline {2.3}A Closer Look at the Script File}{4}
\contentsline {section}{\numberline {3}Code Structure}{6}
\contentsline {section}{\numberline {4}Control Variables and Functions}{8}
\contentsline {subsection}{\numberline {4.1}List of Control Variables and Functions}{8}
\contentsline {subsection}{\numberline {4.2}Log File and Control}{9}
\contentsline {subsection}{\numberline {4.3}Make Perfect Lattice}{9}
\contentsline {subsection}{\numberline {4.4}File I/O}{9}
\contentsline {subsection}{\numberline {4.5}X-window Display}{10}
\contentsline {subsection}{\numberline {4.6}Structure Manipulation}{10}
\contentsline {subsection}{\numberline {4.7}Conjugate Gradient Relaxation}{10}
\contentsline {subsection}{\numberline {4.8}External Fortran Calls}{10}
\contentsline {subsection}{\numberline {4.9}Molecular Dynamics Simulation}{10}
\contentsline {subsection}{\numberline {4.10}Parallel Execution}{10}
\contentsline {section}{\numberline {5}More Examples}{10}
