gistfile1.tex

\documentclass{standalone}

\usepackage{tikz}

\begin{document}
    \begin{tikzpicture}
        \newcommand*{\shear}{0.2}
        \newcommand*{\height}{1.0}
        \newcommand*{\radius}{0.1}
        \newcommand*{\xspacing}{1}
        \newcommand*{\yspacing}{0.5}
    
        % two-dimensional lattice, with three dimensional basis
        % decreasing counter, otherwise there will be lines through the circles
        \foreach \x in {4,...,0}{
            \foreach \y/\dx in {3,...,0}{
                % primitive vectors
                \draw (\x+\y*\shear-\xspacing/2 , \y*\yspacing            )
                    -- (\x+\y*\shear+\xspacing/2, \y*\yspacing            );
                \draw (\x+\y*\shear-\shear/2    , \y*\yspacing-\yspacing/2)
                    -- (\x+\y*\shear+\shear/2   , \y*\yspacing+\yspacing/2);
                \draw (\x+\y*\shear             , \y*\yspacing            )
                    -- (\x+\y*\shear            , \y*\yspacing+\height    );
    
                % base
                \fill[white] (\x+\y*\shear, \y*\yspacing        ) circle(\radius);
                \draw        (\x+\y*\shear, \y*\yspacing        ) circle(\radius);
    
                \fill[gray]  (\x+\y*\shear, \y*\yspacing+\height) circle(\radius);
                \draw        (\x+\y*\shear, \y*\yspacing+\height) circle(\radius);
            }
        }
    \end{tikzpicture}
\end{document}