copy_atom.m

Contents

Version

2.11

Contact

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

Examples

  1. new_atom=copy_atom(atom,'Al','Mgo','ION') % Basic input arguments
  2. new_atom=copy_atom(atom,'Al','Mgo','ION',[0 0 10]) % Translates the copied sites
  3. new_atom=copy_atom(atom,'Al','Mgo','ION',[0 0 10],10) % Translates and copies only 10 sites
function new_atom=copy_atom(atom,atomtype,new_atomtype,new_resname,varargin)

% Find all original atomtypes to replace
ind_atomtype=find(strcmp([atom.type],atomtype));

if nargin>4
    trans_vec=varargin{1};
else
    trans_vec=[0 0 0];
end

if length(ind_atomtype) > 2
    ind_atomtype=ind_atomtype(randperm(length(ind_atomtype)));
end

% Duplicate the atomtype entries into a new In_atom struct
if nargin == 6
    % Uses the num last entries...
    num=cell2mat(varargin(2));
    new_atom=atom(ind_atomtype(end-num+1:end));
else
    % Uses all entries...
    new_atom=atom(ind_atomtype);
end

% Rename all
index=num2cell(1:size(new_atom,2));
molid=num2cell(([1:size(new_atom,2)]+[atom(end).molid]));
[new_atom.molid]=deal(molid{:});
[new_atom.index]=deal(index{:});
[new_atom.resname]=deal({new_resname});
[new_atom.type]=deal({new_atomtype});
[new_atom.fftype]=deal({new_atomtype});

if max(abs(trans_vec))>0
    new_atom = translate_atom(new_atom,trans_vec,'all')
end

end


Published with MATLAB® R2022a