plot_atom

This function draws the atom struct in 3D. Its very basic.
It can display bonds over the pbc if supplied with a Bond_index from bond_angle_atom(). It can also indicate the axis directions.
For fancier plots, use the vmd(atom,Box_dim) function if you have VMD installed and the PATH2VMD() function set up accordingly

Version
Contact
Examples

Version

2.11

Contact

Please report problems/bugs to michael.holmboe@umu.se

Examples

plot_atom(atom,Box_dim)
plot_atom(atom,Box_dim,2) % 2 is a scale factor
plot_atom(atom,Box_dim,1,Bond_index) % Bond_index from bond_angle_atom()
plot_atom(atom,Box_dim,1,[],'axis') % Will indicate the axis ind=find(ismember(Bond_index(:,1),6)|ismember(Bond_index(:,2),6)),:)
plot_atom(atom,Box_dim,Bond_index(ind)) To see all bonds to index=6

function plot_atom(atom,varargin)

Atom_label=unique([atom.type]);
plotted_Atom_label=[];

if nargin>1

    Box_dim=varargin{1};

    if numel(Box_dim)==1
        Box_dim(1)=Box_dim(1);
        Box_dim(2)=Box_dim(1);
        Box_dim(3)=Box_dim(1);
    end
    % Sets plot limits for the data
    xlo = floor(min([-5 -5+min([atom.x])])); xhi = 2 + ceil(max([max([atom.x]) Box_dim(1)])/10)*10;
    ylo = floor(min([-5 -5+min([atom.y])])); yhi = 2 + ceil(max([max([atom.y]) Box_dim(2)])/10)*10;
    zlo = floor(min([0 0+min([atom.z])])); zhi = 2 + ceil(max([max([atom.z]) Box_dim(3)])/10)*10;
else
    xlo = floor(min([-5 -5+min([atom.x])])); xhi = 2 + ceil(max(max([atom.x]))/10)*10;
    ylo = floor(min([-5 -5+min([atom.y])])); yhi = 2 + ceil(max(max([atom.y]))/10)*10;
    zlo = floor(min([0 0+min([atom.z])])); zhi = 2 + ceil(max(max([atom.z]))/10)*10;
end


if xhi < 10
    xhi=15;
end

if yhi < 10
    yhi=15;
end

if zhi < 10
    zhi=15;
end

% figure('units','normalized','position',[0 .2 .6 .8])
hold on
rotate3d on;
camlight(220,210,'infinite');
set(gca,'Color',[1 1 1],'PlotBoxAspectRatio',[(xhi-xlo)/(zhi-zlo) (yhi-ylo)/(zhi-zlo) (zhi-zlo)/(zhi-zlo)],'FontSize',24);
set(gcf,'Color',[1,1,1]);

if nargin > 2
    scalefactor=200*varargin{2};
else
    scalefactor=200;
end

maxY=max([atom.y])+1;

for i = 1:length(Atom_label)
    %     disp('%%%%')
    %     Atom_label(i)
    ind=[];
    radii = scalefactor*2*abs(radius_vdw(Atom_label(i)));
    if strncmpi(Atom_label(i),'H',1)
        radii=radii/4;
    end
    color =  element_color(Atom_label(i));
    %     disp('%%%%')
    ind=strncmpi([atom.type],Atom_label(i),3);
    if numel(ind)==0
        ind=strncmpi([atom.type],Atom_label(i),2);
    end
    if numel(ind)==0
        ind=strncmpi([atom.type],Atom_label(i),1);
    end
    if strncmpi([atom(ind).type],'Ow',2) | strncmpi([atom(ind).type],'Hw',2)
        scatter3([atom(ind).x],[atom(ind).y],[atom(ind).z],...
            radii(1),...
            'MarkerEdgeColor','none',...
            'MarkerFaceColor',color,...
            'MarkerFaceAlpha',0.25...
            );
        alpha(.2)
        plotted_Atom_label=[plotted_Atom_label Atom_label(i)];
    end
end

for i = 1:length(Atom_label)
    %     disp('%%%%')
    %     Atom_label(i)
    ind=[];
    radii = scalefactor*2*abs(radius_vdw(Atom_label(i)));
    if strncmpi(Atom_label(i),'H',1)
        radii=radii/4;
    end
    color =  element_color(Atom_label(i));
    %     disp('%%%%')
    ind=strncmpi([atom.type],Atom_label(i),3);
    if numel(ind)==0
        ind=strncmpi([atom.type],Atom_label(i),2);
    end
    if numel(ind)==0
        ind=strncmpi([atom.type],Atom_label(i),1);
    end

    %         plot3([atom(ind).x],[atom(ind).y],[atom(ind).z],...
    %             'o',...
    %             'LineWidth',0.5,...
    %             'MarkerEdgeColor',[0 0 0],...
    %             'MarkerFaceColor',color,...
    %             'MarkerSize',.1*radii);
    % %                 'MarkerFaceColor',[1 0 0];

    if strncmpi([atom(ind).type],'Ow',2) | strncmpi([atom(ind).type],'Hw',2)
        %         plotted_Atom_label=[plotted_Atom_label Atom_label(i)];
        %         scatter3([atom(ind).x],[atom(ind).y],[atom(ind).z],...
        %             radii,...
        %             'MarkerEdgeColor','none',...
        %             'MarkerFaceColor',color,...
        %             'MarkerFaceAlpha',0.75...
        %             );
        %         alpha(.1)
    else
        scatter3([atom(ind).x],[atom(ind).y],[atom(ind).z],...
            radii,...
            'MarkerEdgeColor','none',...
            'MarkerFaceColor',color,...
            'MarkerFaceAlpha',0.25...
            );
        plotted_Atom_label=[plotted_Atom_label Atom_label(i)];
    end
end

% Draw bonds
if nargin > 3
    if numel(varargin{3})>0
        Bond_index=varargin{3};
        for i=1:size(Bond_index,1)
            Bond_index(i,1);
            Bond_index(i,2);
            plot3([atom(Bond_index(i,1)).x atom(Bond_index(i,2)).x],...
                [atom(Bond_index(i,1)).y atom(Bond_index(i,2)).y],...
                [atom(Bond_index(i,1)).z atom(Bond_index(i,2)).z],...
                'Color',[.5 .5 .5],...
                'LineWidth',3);
        end
    end
end

% Draw the axis in the lower left corner
if nargin > 4
    plot3([xlo+1 xlo+5],[ylo+1 ylo+1],[zlo+1 zlo+1],...
        'r-',...
        'LineWidth',2);
    plot3([xlo+1 xlo+1],[ylo+1 ylo+5],[zlo+1 zlo+1],...
        'g-',...
        'LineWidth',2);
    plot3([xlo+1 xlo+1],[ylo+1 ylo+1],[zlo+1 zlo+5],...
        'b-',...
        'LineWidth',2);
end

% Also draw the actual simulation box...
if nargin>1
    Simbox = draw_box_atom(Box_dim,[0 0 0],1);
end

fig = gcf;
% set(gca,'Color',[1 1 1]);
xlabel('X [Å]'); ylabel('Y [Å]'); zlabel('Z [Å]');
axis([xlo xhi ylo yhi zlo zhi],'equal');
legend(plotted_Atom_label);
%     if numel(Atom_label{i})>2
%         legend(Atom_label{i}(1:2))
%     else
%         legend(Atom_label{i}(1))
%     end

view([0,0]);

end

plot_atom

Contents

Version

Contact

Examples