MATLAB Examples

# condense_atom.m

• This function tries to minimize the box size and remove gaps between molecules along x,y,z
• Tested 15/04/2017
• Please report bugs to michael.holmboe@umu.se

## Examples

• atom = wrap_atom_func(atom,Box_dim);
```function atom = condense_atom(atom,Box_dim,s) x_shift=num2cell([[atom.x]-min([atom.x])]'); [atom(:).x]=deal(x_shift{:}); y_shift=num2cell([[atom.y]-min([atom.y])]'); [atom(:).y]=deal(y_shift{:}); z_shift=num2cell([[atom.z]-min([atom.z])]'); [atom(:).z]=deal(z_shift{:}); Box_dim(1)=max([atom.x]);Box_dim(2)=max([atom.y]);Box_dim(3)=max([atom.z]); for repeat=1:10; %s=0.5; x_shift=0;y_shift=0;z_shift=0; for i=1:s:Box_dim(1) j=i-s; ind_hi=find([atom.x]>=(j)); ind_lo=find([atom.x]<=(i)); ind=intersect(ind_lo,ind_hi); if length(ind)==0 && length(ind_hi) > 0; shift=num2cell([[atom(ind_hi).x]-s]'); [atom(ind_hi).x]=deal(shift{:}); x_shift=x_shift+s; end end Box_dim(1)=Box_dim(1)-x_shift for i=1:s:Box_dim(2) j=i-s; ind_hi=find([atom.y]>=(j)); ind_lo=find([atom.y]<=(i)); ind=intersect(ind_lo,ind_hi); if length(ind)==0 && length(ind_hi) > 0; shift=num2cell([[atom(ind_hi).y]-s]'); [atom(ind_hi).y]=deal(shift{:}); y_shift=y_shift+s; end end Box_dim(2)=Box_dim(2)-y_shift for i=1:s:Box_dim(3) j=i-s; ind_hi=find([atom.z]>=(j)); ind_lo=find([atom.z]<=(i)); ind=intersect(ind_lo,ind_hi); if length(ind)==0 && length(ind_hi) > 0; shift=num2cell([[atom(ind_hi).z]-s]'); [atom(ind_hi).z]=deal(shift{:}); z_shift=z_shift+s; end end Box_dim(3)=Box_dim(3)-z_shift end assignin('caller','Box_dim',Box_dim) ```