function NanoVis(filename,flag_bond)
%NanoVis(filename,flag_bond) (beta version) displays an atomistic structure whose atom coordinates are
%reported in file called "filename".
%The formats supported are "gen" and "xyz".
%flag_bond is related to display mode and can be:
%1 ->normal mode (default)
%0 ->spacefill mode (more fast)
%Giuseppe Romano, Rome, Please report bugs to giuseppe.romano@uniroma2.it
%Default control
if nargin==2
fbond=min(flag_bond,1);
else
fbond=1;
end
%Graphics quality
n=10; %10 is raccomanded"
%Bonds color
colorbond=[1 1 0];
%%%Read the structure
fid = fopen(filename,'r');
if fid==-1
disp(strcat('File "',filename,'" does not exist'));
return
end
%Default properties
set(gcf,'DefaultSurfaceLineStyle','none')
set(gcf,'DefaultSurfaceFaceColor',colorbond)
if strcmpi(filename(end-2:end),'gen')
%Read a "gen" file
natom = fscanf(fid,'%i');
%%read the atom species%%%%%%%%%%%%%%%%%%%%%%
a=fscanf(fid,'%s\n',1);
kk=0;
a=[];
while (numel(a) == 0)
kk=kk+1;
sp(kk) = {fscanf(fid,'%s',1)};
a=str2num(char(sp(kk)));
end
species=sp(1:end-1)';
ltype=numel(species);
%fill the properties matix reading from "DataBase.dat"
properties=zeros(ltype,6); %properties matrix
for k1=1:ltype
properties(k1,1:6)=(pick_properties(species(k1)));
end
%Read atom coordinates
pos=zeros(3,1);
for k1=1:natom
if ~(k1==1)
fscanf(fid,'%i',1);
end
%Read coordinates
data(k1,1)=fscanf(fid,'%i',1);
data(k1,2)=fscanf(fid,'%f',1);
data(k1,3)=fscanf(fid,'%f',1);
data(k1,4)=fscanf(fid,'%f\n',1);
%read valence
valence(k1)=round(properties(data(k1,1),3));
end
else
%Read a "xyz" file
natom = fscanf(fid,'%i\n');
fscanf(fid,'%i\n');
data=zeros(natom,4);
properties=[];
species=[];
for k1=1:natom
sp = fscanf(fid,'%c',2);
I=strmatch(sp,species,'exact');
if (numel(I)==0)
newproperties=pick_properties(sp);
properties=[properties;newproperties];
species=[species;sp];
data(k1,1)=size(properties,1);
else
data(k1,1)=I;
end
%Read coordinates
data(k1,2)=fscanf(fid,'%f',1);
data(k1,3)=fscanf(fid,'%f',1);
data(k1,4)=fscanf(fid,'%f\n',1);
%read valence
valence(k1)=round(properties(data(k1,1),3));
end
end
fclose(fid);
%The matrix properties size is number_of_species X 6
%where the columns meaning is
%1 Ray
%2 Bonding lenght
%3 valence
%4 r-color
%5 g-color
%6 b-color
%%%draw the structure%%%%%%
if fbond==1
a=1;
else
a=2;
end
if fbond==1
%%%Draw atoms%%%%%
[Sx Sy Sz]=sphere(n);
for k1=1:natom
color=properties(data(k1,1),4:6);
Ray=a*properties(data(k1,1),1);
surface(Ray*Sx + data(k1,2),Ray*Sy + data(k1,3),Ray*Sz + data(k1,4),'FaceColor',color)
end
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%
%draw bond as cylinders
[xcyl,ycyl,zcyl]=cylinder(1,n); %z-oriented
dirc=[1e-10 1e-10 10000']; %Create a vector with a z-direction
nv=0;
bn=zeros(1,natom);
for k1=1:natom-1
%valence check
if bn(k1)<valence(k1)
for k2=k1+1:natom
%valence check
if bn(k2)<valence(k2)
%Calculate the k1-k2 atoms distance
r=((data(k1,2)-data(k2,2))^2+(data(k1,3)-data(k2,3))^2+(data(k1,4)-data(k2,4))^2)^(1/2);
%The atoms k1-k2 are bonded if the sum of their bonding
%lenght are less that r
if (r <= properties(data(k1,1),2)+properties(data(k2,1),2))
%The valences maust be increased
bn(k1)=bn(k1)+1;
bn(k2)=bn(k2)+1;
%Set the bond ray
Ray=min(properties(data(k1,1),1),properties(data(k2,1),1))/3;
if fbond==0
line([data(k1,2),data(k2,2)],[data(k1,3),data(k2,3)],[data(k1,4),data(k2,4)],'Color',colorbond,'LineWidth',2*Ray);
else
%XData
a=xcyl*Ray;
%YData
b=ycyl*Ray;
%ZData
c=zcyl;
%first atom position
pc(1,1:3)=data(k1,2:4);
%second atom position
pc(2,1:3)=data(k2,2:4);
%Bond creation
[m,I]=sort(pc(:,3));
a1=I(1);
b1=I(2);
h=surface(a+pc(a1,1),b+pc(a1,2),r*c+pc(a1,3),'FaceColor',colorbond);
a=pc(b1,:)-pc(a1,:);
b=dirc;
cr(1) = b(3)*a(2) - b(2)*a(3);
cr(2) = b(1)*a(3) - b(3)*a(1);
cr(3) = b(2)*a(1) - b(1)*a(2);
dir=pc(a1,:)+cr;
alfa=(180/pi)*(atan2(pc(b1,3)-pc(a1,3),((pc(b1,1)-pc(a1,1))^2+(pc(b1,2)-pc(a1,2))^2)^(1/2))-pi/2);
rotate(h,dir,alfa,pc(a1,:)+1e-6)
end
end
end
end
end
end
%Axis and figure properties
lighting gouraud
camlight
rotate3D on
set(gca,'DataAspectRatio',[ 1 1 1 ])
set(gca,'PlotBoxAspectRatio',[ 1 1 1 ])
set(gca,'CameraViewAngleMode','manual')
set(gcf,'Color',[0.3 0.6 0.7])
set(gcf,'Name','Atomistic Visualizer: NanoVis')
camproj('perspective')
set(gca,'XTick',[])
set(gca,'YTick',[])
set(gca,'ZTick',[])
axis off
hold off
function[data]=pick_properties(Str)
%This function gives the data properties of a given species (Str) by
%reading from file "DataBase.dat"
fid2=fopen('DataBase.dat');
fgets(fid2);
a=1;
while (a==1)
fscanf(fid2,'%i',1);
Sp=fscanf(fid2,'%s',1);
if strcmpi(strtok(Sp),strtok(Str))
for k1=1:6
data(k1)=fscanf(fid2,'%f',1);
end
a=0;
end
fscanf(fid2,'%*[^\n]',1);
end
fclose(fid2);
