MATLAB Examples

# unwrap_atom.m

• This function unwraps the atom struct along the dimension dim
• Tested 21/07/2016, there has been bugs.. does it work?
• Please report bugs to michael.holmboe@umu.se

## Examples

• atom = unwrap_atom(atom,Box_dim,'x')
• atom = unwrap_atom(atom,Box_dim,'xyz')
```function atom = unwrap_atom(atom,Box_dim,dim) atom_Tot=atom; for m=unique([atom_Tot.molid]); atom = atom_Tot([atom_Tot.molid]==m); %Broken_molid=[]; if sum(ismember(dim,'x'))>0; Broken_molid=[]; disp('Unwrap in x') % for i=1:max([atom(:).molid]) % ind=find([atom.molid]==i); % for j=ind(2:end) % if abs(atom(j).x-atom(j-1).x)>Box_dim(1)/2; % Broken_molid=[Broken_molid i]; % end % end % end % % Broken_ind=find(ismember([atom.molid],Broken_molid)); % % atom = median_atom(atom); % % ind_med_hi=find([atom.med_x]>=Box_dim(1)/2); % ind_med_hi=intersect(ind_med_hi,Broken_ind); % ind_lo=find([atom.x]<Box_dim(1)/2&[atom.x]<([atom.med_x]-1.1*Box_dim(1)/2)); % ind_wrap=intersect(ind_med_hi,ind_lo); % shift=num2cell([atom(ind_wrap).x]+Box_dim(1)); % [atom((ind_wrap)).x]=deal(shift{:}); % % ind_med_lo=find([atom.med_x]<=Box_dim(1)/2); % ind_med_lo=intersect(ind_med_lo,Broken_ind); % ind_hi=find([atom.x]>Box_dim(1)/2); % ind_hi=find([atom.x]>Box_dim(1)/2&[atom.x]>([atom.med_x]+1.1*Box_dim(1)/2)); % ind_wrap=intersect(ind_med_lo,ind_hi); % shift=num2cell([atom(ind_wrap).x]-Box_dim(1)); % [atom((ind_wrap)).x]=deal(shift{:}); % % ind_2hi=find([atom.x]>Box_dim(1)/2+.7*Box_dim(1)); % shift=num2cell([atom(ind_2hi).x]-Box_dim(1)); % [atom((ind_2hi)).x]=deal(shift{:}); % % ind_2lo=find([atom.x]<Box_dim(1)/2-.7*Box_dim(1)); % shift=num2cell([atom(ind_2lo).x]+Box_dim(1)); % [atom((ind_2lo)).x]=deal(shift{:}); for k=2:size(atom,2) if (atom(k).x-mean([atom(1:k-1).x]))<-Box_dim(1)/2; atom(k).x=atom(k).x+Box_dim(1); elseif (atom(k).x-mean([atom(1:k-1).x]))>Box_dim(1)/2; atom(k).x=atom(k).x-Box_dim(1); end end end if sum(ismember(dim,'y'))>0; Broken_molid=[]; disp('Unwrap in y') % for i=1:max([atom(:).molid]) % ind=find([atom.molid]==i); % for j=ind(2:end) % if abs(atom(j).y-atom(j-1).y)>Box_dim(2)/2; % Broken_molid=[Broken_molid i]; % end % end % end % % Broken_ind=find(ismember([atom.molid],Broken_molid)); % % ind_med_hi=find([atom.med_y]>=Box_dim(2)/2); % ind_med_hi=intersect(ind_med_hi,Broken_ind); % ind_lo=find([atom.y]<Box_dim(2)/2&[atom.y]<([atom.med_y]-1.1*Box_dim(2)/2)); % ind_wrap=intersect(ind_med_hi,ind_lo); % shift=num2cell([atom(ind_wrap).y]+Box_dim(2)); % [atom((ind_wrap)).y]=deal(shift{:}); % % ind_med_lo=find([atom.med_y]<=Box_dim(2)/2); % ind_med_lo=intersect(ind_med_lo,Broken_ind); % ind_hi=find([atom.y]>Box_dim(2)/2&[atom.y]>([atom.med_y]+1.1*Box_dim(2)/2)); % ind_wrap=intersect(ind_med_lo,ind_hi); % shift=num2cell([atom(ind_wrap).y]-Box_dim(2)); % [atom((ind_wrap)).y]=deal(shift{:}); % % ind_2hi=find([atom.y]>Box_dim(2)/2+.7*Box_dim(2)) % shift=num2cell([atom(ind_2hi).y]-Box_dim(2)); % [atom((ind_2hi)).y]=deal(shift{:}); % % ind_2lo=find([atom.y]<Box_dim(2)/2-.7*Box_dim(2)) % shift=num2cell([atom(ind_2lo).y]+Box_dim(2)); % [atom((ind_2lo)).y]=deal(shift{:}); for k=2:size(atom,2) if (atom(k).y-mean([atom(1:k-1).y]))<-Box_dim(2)/2; atom(k).y=atom(k).y+Box_dim(2); elseif (atom(k).y-mean([atom(1:k-1).y]))>Box_dim(2)/2; atom(k).y=atom(k).y-Box_dim(2); end end end if sum(ismember(dim,'z'))>0; Broken_molid=[]; disp('Unwrap in z') % for i=1:max([atom(:).molid]) % ind=find([atom.molid]==i); % for j=ind(2:end) % if abs(atom(j).z-atom(j-1).z)>Box_dim(3)/2; % Broken_molid=[Broken_molid i]; % end % end % end % % Broken_ind=find(ismember([atom.molid],Broken_molid)); % % ind_med_hi=find([atom.med_z]>=Box_dim(3)/2); % ind_med_hi=intersect(ind_med_hi,Broken_ind); % ind_lo=find([atom.z]<Box_dim(3)/2&[atom.z]<([atom.med_z]-1.1*Box_dim(3)/2)); % ind_wrap=intersect(ind_med_hi,ind_lo); % shift=num2cell([atom(ind_wrap).z]+Box_dim(3)); % [atom((ind_wrap)).z]=deal(shift{:}); % % ind_med_lo=find([atom.med_z]<=Box_dim(3)/2); % ind_med_lo=intersect(ind_med_lo,Broken_ind); % ind_hi=find([atom.z]>Box_dim(3)/2&[atom.z]>([atom.med_z]+1.1*Box_dim(3)/2)); % ind_wrap=intersect(ind_med_lo,ind_hi); % shift=num2cell([atom(ind_wrap).z]-Box_dim(3)); % [atom((ind_wrap)).z]=deal(shift{:}); % % ind_2hi=find([atom.z]>Box_dim(3)/2+.7*Box_dim(3)); % shift=num2cell([atom(ind_2hi).z]-Box_dim(3)); % [atom((ind_2hi)).z]=deal(shift{:}); % % ind_2lo=find([atom.z]<Box_dim(3)/2-.7*Box_dim(3)); % shift=num2cell([atom(ind_2lo).z]+Box_dim(3)); % [atom((ind_2lo)).z]=deal(shift{:}); for k=2:size(atom,2) if (atom(k).z-mean([atom(1:k-1).z]))<-Box_dim(3)/2; atom(k).z=atom(k).z+Box_dim(3); elseif (atom(k).z-mean([atom(1:k-1).z]))>Box_dim(3)/2; atom(k).z=atom(k).z-Box_dim(3); end end atom = median_atom(atom); xshift=0;yshift=0;zshift=0; if [atom(1).med_x]>Box_dim(1); xshift=-Box_dim(1); elseif [atom(1).med_x]<0; xshift=Box_dim(1); end if [atom(1).med_y]>Box_dim(2); yshift=-Box_dim(2); elseif [atom(1).med_y]<0; yshift=Box_dim(2); end if [atom(1).med_z]>Box_dim(3); zshift=-Box_dim(3); elseif [atom(1).med_z]<0; zshift=Box_dim(3); end atom=translate_atom(atom,[xshift yshift zshift],'all'); end [atom_Tot([atom_Tot.molid]==m).x]=atom.x; [atom_Tot([atom_Tot.molid]==m).y]=atom.y; [atom_Tot([atom_Tot.molid]==m).z]=atom.z; end % atom_Tot = rmfield(atom_Tot,'med_x'); % atom_Tot = rmfield(atom_Tot,'med_y'); % atom_Tot = rmfield(atom_Tot,'med_z'); atom = atom_Tot; ```