MATLAB Examples

# orto_atom.m

• This function transforms a triclinic atom struct to an orthogonal one
• Tested 15/04/2017
• Please report bugs to michael.holmboe@umu.se

## Examples

• atom = orto_atom(atom,Box_dim)
• atom = orto_atom(atom,Box_dim,[alfa beta gamma],'angle')
• atom = orto_atom(atom,Box_dim,[xy xz yz],'tilt')
```function atom = orto_atom(atom,Box_dim,varargin) if nargin > 2 angleparam=cell2mat(varargin(1)); angletype=varargin(2); if strncmpi(angletype,'angle',5) a=Box_dim(1); b=Box_dim(2); c=Box_dim(3); % Angle values alfa=angleparam(1); beta=angleparam(2); gamma=angleparam(3); lx = a; xy = b * cos(deg2rad(gamma)); ly = (b^2-xy^2)^.5; xz = c*cos(deg2rad(beta)); yz = (b*c*cos(deg2rad(alfa))-xy*xz)/ly; lz = (c^2 - xz^2 - yz^2)^0.5; else % Tilt values a=Box_dim(1); b=Box_dim(2); c=Box_dim(3); xy=angleparam(1); xz=angleparam(2); yz=angleparam(3); lx = a; ly = (b^2-xy^2)^.5; lz = (c^2 - xz^2 - yz^2)^0.5; alfa=rad2deg(acos((ly*yz+xy*xz)/(b*c))) beta=rad2deg(acos(xz/c)); gamma=rad2deg(acos(xy/b)); end elseif size(Box_dim,2) == 9 lx=Box_dim(1); ly=Box_dim(2); lz=Box_dim(3); xy=Box_dim(6); xz=Box_dim(8); yz=Box_dim(9); a=lx; b=(ly^2+xy^2)^.5; c=(lz^2+xz^2+yz^2)^.5; alfa=rad2deg(acos((ly*yz+xy*xz)/(b*c))); beta=rad2deg(acos(xz/c)); gamma=rad2deg(acos(xy/b)); else disp('Something is wrong with Box_dim, what are you trying to do?') end Box_dim(Box_dim<0.00001&Box_dim>-0.00001)=0; if sum(Box_dim(4:end))== 0 Box_dim=Box_dim(1:3); end % Straight from wikipedia % From fractional coordinates volume=a*b*c*(1 - cos(deg2rad(alfa))^2 - cos(deg2rad(beta))^2 - cos(deg2rad(gamma))^2 + 2*cos(deg2rad(alfa))*cos(deg2rad(beta))*cos(deg2rad(gamma)))^.5; v=(1 - cos(deg2rad(alfa))^2 - cos(deg2rad(beta))^2 - cos(deg2rad(gamma))^2 + 2*cos(deg2rad(alfa))*cos(deg2rad(beta))*cos(deg2rad(gamma)))^.5; FromFrac=[a b*cos(deg2rad(gamma)) c*cos(deg2rad(beta));... 0 b*sin(deg2rad(gamma)) c*(cos(deg2rad(alfa))-cos(deg2rad(beta))*cos(deg2rad(gamma)))/sin(deg2rad(gamma));... 0 0 c*v/sin(deg2rad(gamma))]; % To fractional coordinates ToFrac=[1/a -cos(deg2rad(gamma))/(a*sin(deg2rad(gamma))) (cos(deg2rad(alfa))*cos(deg2rad(gamma))-cos(deg2rad(beta)))/(a*v*sin(deg2rad(gamma)));... 0 1/(b*sin(deg2rad(gamma))) (cos(deg2rad(beta))*cos(deg2rad(gamma))-cos(deg2rad(alfa)))/(b*v*sin(deg2rad(gamma)));... 0 0 sin(deg2rad(gamma))/(c*v)]; % FromFrac*ToFrac XYZ_labels=[atom.type]'; XYZ_data=[[atom.x]' [atom.y]' [atom.z]']; XYZ_data_frac=XYZ_data;XYZ_data_orto=XYZ_data; for i=1:size(atom,2) XYZ_data_frac(i,:)=ToFrac*[XYZ_data(i,1) XYZ_data(i,2) XYZ_data(i,3)]'; XYZ_data_orto(i,:)=[lx ly lz].*XYZ_data_frac(i,:); atom(i).x=XYZ_data_orto(i,1); atom(i).y=XYZ_data_orto(i,2); atom(i).z=XYZ_data_orto(i,3); atom(i).xfrac=XYZ_data_frac(i,1); atom(i).yfrac=XYZ_data_frac(i,2); atom(i).zfrac=XYZ_data_frac(i,3); end Box_dim=[lx ly lz]; lx ly lz a b c volume assignin('caller','orto_Box_dim',Box_dim); assignin('caller','Box_volume',a*b*c*v); ```