write_atom_xyz.m

Contents

Version

2.11

Contact

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

Examples

function write_atom_xyz(atom,varargin)

if nargin==2
    filename_out=varargin{1};
else
    Box_dim=varargin{1};
    filename_out=varargin{2};
end


if regexp(filename_out,'.xyz') ~= false
    filename_out = filename_out;
else
    filename_out = strcat(filename_out,'.xyz');
end

nAtoms=size([atom.x],2)
fid = fopen(filename_out, 'wt');
fprintf(fid, '%-5i\r\n',nAtoms);

if exist('Box_dim','var')
    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)==3
        fprintf(fid, '# %10.5f%10.5f%10.5f\r\n',Box_dim);
    elseif length(Box_dim)==6
        fprintf(fid, '# %10.5f%10.5f%10.5f%10.5f%10.5f%10.5f\r\n',Box_dim);
    elseif length(Box_dim)==9
        fprintf(fid, '# %10.5f%10.5f%10.5f%10.5f%10.5f%10.5f%10.5f%10.5f%10.5f\r\n',Box_dim);
    end
else
    fprintf(fid, '# No Box_dim\r\n');
end

for i = 1:nAtoms
    Atom_section(1:4) = [atom(i).type, atom(i).x, atom(i).y, atom(i).z];
    fprintf(fid, '%-5s%10.5f%10.5f%10.5f\r\n', Atom_section{1:4});
end

fprintf(fid, '\r\n');

fclose(fid);
disp('.xyz structure file written')

Published with MATLAB® R2022a