Drawing 3d crystal lattice with molecular layer in tikz

Question

I would like to achieve the following diagram (may be colored) wit Tikz. enter image description here
Here is what I have done till now:
i)Drawing a 3d cube with Tikz
ii)Get the Molecular layer from here
Here is my code:

\documentclass{article}
\usepackage{tikz}
\usetikzlibrary{calc,fadings,decorations.pathreplacing}
\begin{document}
\begin{tikzpicture}
\pgfmathsetmacro{\cubex}{4}
\pgfmathsetmacro{\cubey}{4}
\pgfmathsetmacro{\cubez}{4}
\draw (0,0,0) -- ++(-\cubex,0,0) -- ++(0,-\cubey,0) -- ++(\cubex,0,0) -- cycle;
\draw (0,0,0) -- ++(0,0,-\cubez) -- ++(0,-\cubey,0) -- ++(0,0,\cubez) -- cycle;
\draw (0,0,0) -- ++(-\cubex,0,0) -- ++(0,0,-\cubez) -- ++(\cubex,0,0) -- cycle;
\end{tikzpicture}
\\[1cm]
\begin{tikzpicture}
  \def\nuPi{3.1459265}
  \foreach \i in {11,10,...,0}{% This one doesn't matter
    \foreach \j in {5,4,...,0}{% This will crate a membrane
                               % with the front lipids visible
      % top layer
      \pgfmathsetmacro{\dx}{rand*0.1}% A random variance in the x coordinate
      \pgfmathsetmacro{\dy}{rand*0.1}% A random variance in the y coordinate,
                                     % gives a hight fill to the lipid
      \pgfmathsetmacro{\rot}{rand*0.1}% A random variance in the
                                      % molecule orientation
      \shade[ball color=red] ({\i+\dx+\rot},{0.5*\j+\dy+0.4*sin(\i*\nuPi*10)}) circle(0.45);
      \shade[ball color=gray] (\i+\dx,{0.5*\j+\dy+0.4*sin(\i*\nuPi*10)-0.9}) circle(0.45);
      \shade[ball color=gray] (\i+\dx-\rot,{0.5*\j+\dy+0.4*sin(\i*\nuPi*10)-1.8}) circle(0.45);
      % bottom layer
      \pgfmathsetmacro{\dx}{rand*0.1}
      \pgfmathsetmacro{\dy}{rand*0.1}
      \pgfmathsetmacro{\rot}{rand*0.1}
      \shade[ball color=gray] (\i+\dx+\rot,{0.5*\j+\dy+0.4*sin(\i*\nuPi*10)-2.8}) circle(0.45);
      \shade[ball color=gray] (\i+\dx,{0.5*\j+\dy+0.4*sin(\i*\nuPi*10)-3.7}) circle(0.45);
      \shade[ball color=red] (\i+\dx-\rot,{0.5*\j+\dy+0.4*sin(\i*\nuPi*10)-4.6}) circle(0.45);
    }
  }
\end{tikzpicture}
\end{document}

enter image description here

How do I fix the layer onto the cube is my ultimate question and drawing the inner cube as in the diagram (preferably with axes)

Given the example at the top of your post and the two pictures at the bottom, it is not clear to me what you try to achieve. — cjorssen, May 12 '14 at 07:25
@cjorssen, I want to draw the diagram as in the first figure . But I am able to draw the cube and the layer separately. How do I merge these two? — subham soni, May 12 '14 at 07:26
@subhamsoni: you can try using the overlay option for the cube. — Claudio Fiandrino, May 12 '14 at 07:27

score 8 · Answer 1 · edited Jun 10 '20 at 12:32

You can simply move the drawing of the cube into the same tikzpicture as the molecules. Also, I would not recommend using a random number generator to place the molecules since you want to draw over them. Instead place them on a grid to get the crystal structure.

Below is something that should allow you to achieve what you want by tweaking the parameters:

enter image description here

Notes:

I used join=round to get a better edge on the cube corners. See In TikZ when is "line join=miter" the preferrable over "line join=round"?.

Code:

\documentclass{article}
\usepackage{tikz}
\usetikzlibrary{calc,fadings,decorations.pathreplacing}
\tikzset{My Line Style/.style={ultra thick, blue, fill=yellow!10, fill opacity=0.5, join=round}}
\begin{document}
\begin{tikzpicture}
    \newcommand{\Radius}{0.45}%
    \newcommand{\ZFactor}{1.5\Radius}%
    \newcommand{\YFactor}{2.0\Radius}%
    \newcommand{\XFactor}{2.0*\Radius}%
\foreach \z in {0,...,4} {
  \pgfmathsetmacro{\ZCoord}{\ZFactor*\z}
  \foreach \x in {0,...,10} {
      \pgfmathsetmacro{\XCoord}{\YFactor*\x}
      \foreach \y in {0,...,6} {
          \pgfmathsetmacro{\YCoord}{\XFactor*\y}
          \shade[ball color=gray!20] (\XCoord,\YCoord,\ZCoord) circle(\Radius);
      }
  }

}
%% Select the ones to highlight
    \foreach \z in {2,...,4} {
      \pgfmathsetmacro{\ZCoord}{\ZFactor\z}
      \foreach \x in {4,...,6} {
          \pgfmathsetmacro{\XCoord}{\YFactor\x}
          \foreach \y in {3,...,5} {
              \pgfmathsetmacro{\YCoord}{\XFactor*\y}
              \shade[ball color=red!40] (\XCoord,\YCoord,\ZCoord) circle(\Radius);
          }
      }
  }
%% Draw the cube
  \begin{scope}[shift={(3.5\XFactor,2.5\YFactor,-4\ZFactor)}]%xshift=4\Radius cm, yshift=4\Radius]
        \pgfmathsetmacro{\cubex}{2\XFactor}
        \pgfmathsetmacro{\cubey}{2\YFactor}
        \pgfmathsetmacro{\cubez}{3\ZFactor}
        \draw [My Line Style] (0,0,0) -- ++(-\cubex,0,0) -- ++(0,-\cubey,0) -- ++(\cubex,0,0) -- cycle;
        \draw [My Line Style] (0,0,0) -- ++(0,0,-\cubez) -- ++(0,-\cubey,0) -- ++(0,0,\cubez) -- cycle;
        \draw [My Line Style] (0,0,0) -- ++(-\cubex,0,0) -- ++(0,0,-\cubez) -- ++(\cubex,0,0) -- cycle;
    \end{scope}
\end{tikzpicture}
\end{document}

Huh? It is a cube. If you mean to say that it does not align with the molecules, then you just need to adjust your coordinates. — Peter Grill, May 12 '14 at 07:41
No @Peter Grill. See the picture. The molecules form a perfect cube. — subham soni, May 12 '14 at 07:43
@subhamsoni: actually Peter is telling you that he provided you an example: if you adjust the coordinates of the cube you will be able to align with the molecules. Otherwise you have to change way to draw molecules.. — Claudio Fiandrino, May 12 '14 at 07:53

score 6 · Answer 2 · answered May 12 '14 at 09:02

Another answer, which IMHO reflects more accurately the crystal structure.

\documentclass{standalone}
\usepackage{tikz}
\usetikzlibrary{calc,fadings,decorations.pathreplacing}
\begin{document}

% You can tweak these
\colorlet{odd plane}{black!20}
\colorlet{even plane}{black!20}
\def\ballradius{0.45}


\def\DrawRow#1#2{
    \foreach \x in {0,...,#2}
       \shade[ball color=ball] ($(#1) +(\x, 0,0)$) circle(\ballradius);
}
\def\DrawOddPlane#1{ 
  \pgfmathsetmacro{\aux}{#1-1}
  \colorlet{ball}{odd plane}
  \foreach \z in {0,...,#1} {
      \DrawRow{0,0,\z}{#1}
      \if\z#1\relax\else
      \DrawRow{0.5,0,\z+0.5}{\aux}
      \fi
  }
}
\def\DrawEvenPlane#1{ 
  \pgfmathsetmacro{\aux}{#1-1}
  \colorlet{ball}{even plane}
  \foreach \z in {0,...,#1} {
      \DrawRow{0.5,0,\z}{\aux}
      \if\z#1\relax\else
      \DrawRow{0,0,\z+0.5}{#1}
      \fi
  }
}

\begin{tikzpicture}
   \foreach \y in {0,...,3} {
      \begin{scope}[yshift=\y cm]
          \DrawOddPlane{3}
      \end{scope}
      \if\y3\relax\else
      \begin{scope}[yshift=\y cm + 0.5cm]
          \DrawEvenPlane{3}
      \end{scope}
      \fi
  }
    \pgfmathsetmacro{\cubex}{1}
    \pgfmathsetmacro{\cubey}{1}
    \pgfmathsetmacro{\cubez}{1}
    \draw (3,3,3) -- ++(-\cubex,0,0) -- ++(0,-\cubey,0) -- ++(\cubex,0,0) -- cycle;
    \draw (3,3,3) -- ++(0,0,-\cubez) -- ++(0,-\cubey,0) -- ++(0,0,\cubez) -- cycle;
    \draw (3,3,3) -- ++(-\cubex,0,0) -- ++(0,0,-\cubez) -- ++(\cubex,0,0) -- cycle;
\end{tikzpicture}
\end{document}

Produces:

Result

You can tweak the color of the balls for even and odd planes, and the ball radius, for example:

% You can tweak these
\colorlet{odd plane}{black!20}
\colorlet{even plane}{green!20}
\def\ballradius{0.3}

Result:

Result2

score 2 · Accepted Answer · answered May 12 '14 at 08:50

I tried to exclude complex bits of code and maths. This is the brute force attack.

\documentclass{article}
\usepackage{tikz}
%\usetikzlibrary{calc,fadings,decorations.pathreplacing}

\tikzset{My Line Style/.style={ultra thick, blue, fill=yellow!10, fill opacity=0.5,join=round}}

\begin{document}
\begin{tikzpicture}[rotate around x=5] 
    \foreach \x in {0,1,2,3,4,5,6}{% 
      \foreach \z in {0,1,2,3,4,5,6}{%      
      \shade[ball color=gray] (\x,0,\z) circle(0.5);
      }
    }
    \foreach \x in {0.5,1.5,2.5,3.5,4.5,5.5}{%
      \foreach \z in {0,1,2,3,4,5,6}{%
      \shade[ball color=gray] (\x,{sqrt(0.74)},\z) circle(0.5);
      }
    }
    \foreach \x in {0,1,2,3,4,5,6}{%
      \foreach \z in {0,1,2,3,4,5,6}{%
      \shade[ball color=gray] (\x,{2*sqrt(0.74)},\z) circle(0.5);
      }
    }
    \foreach \x in {0.5,1.5,2.5,3.5,4.5,5.5}{%
      \foreach \z in {0,1,2,3,4,5,6}{%
      \shade[ball color=gray] (\x,{3*sqrt(0.74)},\z) circle(0.5);
      }
    }
    \foreach \x in {0,1,2,3,4,5,6}{%
      \foreach \z in {0,1,2,3,4,5,6}{%
      \shade[ball color=gray] (\x,{4*sqrt(0.74)},\z) circle(0.5);
      }
    }
    \foreach \x in {0.5,1.5,2.5,3.5,4.5,5.5}{%
      \foreach \z in {0,1,2,3,4,5,6}{%
      \shade[ball color=gray] (\x,{5*sqrt(0.74)},\z) circle(0.5);
      }
    }
    \foreach \x in {0,1,2,3,4,5,6}{%
      \foreach \z in {0,1,2,3,4,5,6}{%
      \shade[ball color=gray] (\x,{6*sqrt(0.74)},\z) circle(0.5);
      }
    }

    \draw [My Line Style] (6,{4*sqrt(0.74)},6) -- (4,{4*sqrt(0.74)},6) -- (4,{6*sqrt(0.74)},6) -- 
                          (6,{6*sqrt(0.74)},6) -- cycle;
    \draw [My Line Style] (4,{6*sqrt(0.74)},6) -- (4,{6*sqrt(0.74)},4) -- (6,{6*sqrt(0.74)},4) --
                          (6,{6*sqrt(0.74)},6) -- cycle;
    \draw [My Line Style] (6,{4*sqrt(0.74)},6) -- (6,{4*sqrt(0.74)},4) -- (6,{6*sqrt(0.74)},4) --
                          (6,{6*sqrt(0.74)},6) -- cycle;
\end{tikzpicture}
\end{document}

enter image description here

Drawing 3d crystal lattice with molecular layer in tikz

3 Answers3

Notes:

Code:

Linked