tile_atom.m

This function tiles the atom struct similar to replicate atom, but with a translation along some direction. Triclinic version untestd but might work..

Function arguments
Version
Contact
Examples

Function arguments

atom is the normal atom struct
Box_dim is the normal Box_dim variable
replicate is a [1x3] row vector indicating the replicating factors in x/y/z or a/b/c directions, resp.
translate is a [1x3] row vector indicating the translation factors in x/y/z or a/b/c directions, resp.

Version

2.11

Contact

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

Examples

atom = tile_atom(atom,Box_dim,[6 4 1],[0 2.7 0]) % Basic input arguments
atom = tile_atom(atom,Box_dim,[6 4 1],[0 2.7 0],'xyz') % tiles in the order of the dimensions x-y-z * atom = tile_atom(atom,Box_dim,[6 4 1],[0 2.7 0],'xyz','addmolid') % Adds an increasingly new MolID to each new tile entry

function atom = tile_atom(atom,Box_dim,replicate,translate,varargin)

if numel(replicate)==1
    replicate(1)=replicate(1);
    replicate(2)=replicate(1);
    replicate(3)=replicate(1);
end
replicate(replicate==0)=1;

if numel(translate)==1
    translate(1)=translate(1);
    translate(2)=translate(1);
    translate(3)=translate(1);
end

if numel(Box_dim)==1
    Box_dim(1)=Box_dim(1);
    Box_dim(2)=Box_dim(1);
    Box_dim(3)=Box_dim(1);
end

if length(Box_dim)==9
    Box_dim_tric=Box_dim;
    atom = orto_atom(atom,Box_dim_tric);
end

if nargin>4
    dim_order=char(varargin{1});
else
    dim_order='xyz';
end

if nargin>5
    addmolid=1;
else
    addmolid=0;
end

if size(atom,2)>0

    combinedatom_dim=atom;
    molid=[atom(1).molid];
    for j=1:3

        if j == strfind(dim_order,'x')
            if j == 1
                combinedatomx=atom;
                for i=1:replicate(1)
                    if i > 1
                        newatom=atom;
                        if addmolid==1
                            molid=molid+1;
                            [newatom.molid]=deal(molid);
                        end
                        x_shift=num2cell([atom.x]+(i-1)*Box_dim(1)+translate(1)); [newatom.x]=deal(x_shift{:});
                        y_shift=num2cell(([atom.y]+translate(2)*(i-1))); [newatom.y]=deal(y_shift{:});
                        z_shift=num2cell(([atom.z]+translate(3)*(i-1))); [newatom.z]=deal(z_shift{:});
                        combinedatomx=[combinedatomx newatom];
                    end
                end
            else
                combinedatomx=combinedatom_dim;
                for i=1:replicate(1)
                    if i > 1
                        newatom=combinedatom_dim;
                        x_shift=num2cell([combinedatom_dim.x]+(i-1)*Box_dim(1)+translate(1)); [newatom.x]=deal(x_shift{:});
                        combinedatomx=[combinedatomx newatom];
                    end
                end
            end
            combinedatom_dim=combinedatomx;
            disp('x - dim')
            length(combinedatom_dim)

        elseif j == strfind(dim_order,'y')
            if j == 1
                combinedatomy=atom;
                for i=1:replicate(2)
                    if i > 1
                        newatom=atom;
                        if addmolid==1
                            molid=molid+1;
                            [newatom.molid]=deal(molid);
                        end
                        y_shift=num2cell([atom.y]+(i-1)*Box_dim(2)); [newatom.y]=deal(y_shift{:});
                        x_shift=num2cell(([atom.x]+translate(1)*(i-1))); [newatom.x]=deal(x_shift{:});
                        z_shift=num2cell(([atom.z]+translate(3)*(i-1))); [newatom.z]=deal(z_shift{:});
                        combinedatomy=[combinedatomy newatom];
                    end
                end
            else
                combinedatomy=combinedatom_dim;
                for i=1:replicate(2)
                    if i > 1
                        newatom=combinedatom_dim;
                        y_shift=num2cell([combinedatom_dim.y]+(i-1)*Box_dim(2)); [newatom.y]=deal(y_shift{:});
                        combinedatomy=[combinedatomy newatom];
                    end
                end
            end
            combinedatom_dim=combinedatomy;
            disp('y - dim')
            length(combinedatom_dim)

        elseif j == strfind(dim_order,'z')
            if j == 1
                combinedatomz=atom;
                for i=1:replicate(3)
                    if i > 1
                        newatom=atom;
                        if addmolid==1
                            molid=molid+1;
                            [newatom.molid]=deal(molid);
                        end
                        z_shift=num2cell([atom.z]+(i-1)*Box_dim(3)); [newatom.z]=deal(z_shift{:});
                        x_shift=num2cell(([atom.x]+translate(1)*(i-1))); [newatom.x]=deal(x_shift{:});
                        y_shift=num2cell(([atom.y]+translate(2)*(i-1))); [newatom.y]=deal(y_shift{:});
                        combinedatomz=[combinedatomz newatom];
                    end
                end
            else
                combinedatomz=combinedatom_dim;
                for i=1:replicate(3)
                    if i > 1
                        newatom=combinedatom_dim;
                        z_shift=num2cell([combinedatom_dim.z]+(i-1)*Box_dim(3)); [newatom.z]=deal(z_shift{:});
                        combinedatomz=[combinedatomz newatom];
                    end
                end
            end
            combinedatom_dim=combinedatomz;
            disp('z - dim')
            length(combinedatom_dim)
        end
    end

    atom=combinedatom_dim;

end

Box_dim=[Box_dim(1)*replicate(1) Box_dim(2)*replicate(2) Box_dim(3)*replicate(3)];

if exist('Box_dim_tric','var')
    atom = triclinic_atom(atom,Box_dim,[replicate(1)*Box_dim_tric(6) replicate(3)*Box_dim_tric(8) replicate(2)*Box_dim_tric(9)],'tiltfactors');
    Box_dim=triclinic_Box_dim;
end

if size(atom,2)>0

    atom=update_atom(atom);

    XYZ_data=[[atom.x]' [atom.y]' [atom.z]']; XYZ_labels=[atom.type]';

    assignin('caller','XYZ_labels',XYZ_labels);
    assignin('caller','XYZ_data',XYZ_data);

end

assignin('caller','Box_dim',Box_dim);

tile_atom.m

Contents

Function arguments

Version

Contact

Examples