MATLAB Examples

# create_atom.m

• This function creates atoms within a certain region defined by limits
• Can also add ions on a plane by setting Lx|Ly|Lz to 0 or something small
• Tested 15/07/2017
• Please report bugs to michael.holmboe@umu.se

## Examples

• atom = create_atom('Na','Na',[10 20 30],10)
• atom = create_atom('Na','Na',[10 20 30],10,1.5)
• atom = create_atom('Na','Na',[10 20 30],10,1.5,in_atom)
function atom = create_atom(type,resname,limits,nmax,varargin)

if iscell(type)==0;type={type}; end
if iscell(resname)==0;resname={resname};end

if nargin > 4
scale=varargin{1};
else
scale=2;
end
atom = add2atom(type,[0 0 0],resname,[]);

if numel(limits)==1;
Lx=limits(1);
Ly=limits(1);
Lz=limits(1);
limits(4)=limits(1);
limits(5)=limits(1);
limits(6)=limits(1);
limits(1:3)=0;
elseif numel(limits)==3;
Lx=limits(1);
Ly=limits(2);
Lz=limits(3);
limits(4)=limits(1);
limits(5)=limits(2);
limits(6)=limits(3);
limits(1:3)=0;
elseif numel(limits)==6;
Lx=limits(4)-limits(1);
Ly=limits(5)-limits(2);
Lz=limits(6)-limits(3);
end

nx=ceil(Lx/Box_dim_temp(1));
ny=ceil(Ly/Box_dim_temp(2));
nz=ceil(Lz/Box_dim_temp(3));

atom=replicate_atom(atom,Box_dim_temp,[nx ny nz]); % nx/ny/nz==0 is set to 1 in replicate_atom

molid=num2cell([1:size(atom,2)]);
[atom.molid]=deal(molid{:});

% Move things around a little bit
for i=1:size(atom,2);
end

if (limits(1)+limits(2)+limits(3)) ~= 0;
disp('Translating the water box');
atom=translate_atom(atom,[limits(1) limits(2) limits(3)],'all');
end

disp('nAtom before merge')
size(atom,2)

if nargin==6 && size(varargin{2},2) > 0;
in_atom=varargin{2};
if size(atom,2) > 10000 || size(in_atom,2) > 10000
natom_block=size(atom,2)/(nx*ny*nz);
atom_count=1;atom_merged=[];count=1;
while atom_count< size(atom,2)
atom_block= atom(atom_count:atom_count+natom_block-1);
atom_merged = [atom_merged atom_block];
atom_count=atom_count+natom_block;
disp('water box number...')
count=count+1
end
atom=atom_merged;
else
end
else
atom = slice_atom(atom,limits,0);
end
% assignin('base','atom3',atom);
atom=update_atom(atom);

% Randomize order of the particles
nAtoms=size(atom,2);
ind_rand=randperm(nAtoms);
ind_sel=ismember(ind_rand,1:nAtoms);
atom_ind=ind_rand(ind_sel);
atom=atom(atom_ind);

% Delete particles if not using the <maxion> option
if iscellstr({nmax}) == 0;
if nmax > size(atom,2)
disp('Ooops, you asked for too many particles...')
disp('Max number of particles allowed without changing scale is:')
size(atom,2)
atom=atom(1:nmax);
else
atom=atom(1:nmax);
end
end

disp('nIon after merge')
size(atom,2)

atom=update_atom(atom);

assignin('caller','limits',limits);