tube_atom.m

This quirky function can be used to create a nano-tube or nano-roll of the coordinates from an atom struct. It works best if the the input atom struct consists of one centered unit cell (to keep the number of atoms down). You can always the replicate_atom() function later to build the entire roll/tube.
See needed variables/parameters below on line 22-27 and 37 to play around with. For non-centrosymmetric layers, chosing +R or -R on line 45 allow you to choose the type of inner-surface atoms. The spiral_vector and Rshift on 37 can be used to skew the spiral in the x and/or the y direction/s.

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Examples

Version

2.11

Contact

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

Examples

atom = tube_atom(atom,Box_dim,Radii)

function atom = tube_atom(atom,Box_dim,Dim,nUC,AngularRange,UCaccuracy,deltaaccuracy,Rshift)

% Dim=2; % 1 for X-direction, 2 for the Y-direction
% nUC=36; % Ideal number of unit cells per revolution
% AngularRange=2*360; % Ideal number of revolutions, ie n*360deg. The final angular range might be different..
% UCaccuracy=0.05; % Connected to UC placement accuracy, lower is better, but harder.. will affect the actual angular range
% deltaaccuracy=0.4; % Connected to UC placement speed, higher is faster, but worse.. will affect the actual angular range
% Rshift=0.3; % Lateral shift in Å between each UC, resulting in a roll rather than a tube (Rshift=0)

if Dim==1
    L=Box_dim(1);
elseif Dim==2
    L=Box_dim(2);
elseif Dim==3
    L=Box_dim(3);
end

spiral_vector = [0   0   Rshift*(Rshift/(Rshift+i/AngularRange/2))] % [0 0 0] makes a tube, anything else creates a spiral roll perpendicular to [x y z]
R = L*nUC/(2*pi) % Target inner radii
Cf = 2*pi*R % Target inner circumference, not used

atom=translate_atom(atom,-[min([atom.x]) min([atom.y]) max([atom.z])]);
atom=replicate_atom(atom,Box_dim,[1 1 1]);

atom=translate_atom(atom,-Box_dim./2);
atom=translate_atom(atom,[0 0 R]); % Try also -R, do you see any difference

System=atom;
nUCreal=nUC*AngularRange/360;
prev_temp=atom;AngleList(1)=0;DeltaList(1)=0;

for i=1:nUCreal
    A=0;delta=0;angle=0;MajorAtomicOverlap=0;
    while abs(A-L)>(UCaccuracy*L)

        if A-L > UCaccuracy*L
            angle=(i-1)*AngularRange/nUCreal-delta;
        elseif A-L < UCaccuracy*L
            angle=(i-1)*AngularRange/nUCreal+delta;
        end

        if angle<AngleList(end)
            angle=AngleList(end);
        end

        %         if angle>AngularRange
        %             disp('angle larger than the AngularRange')
        %             [angle AngularRange]
        %
        %         end

        if Dim==1
            trans_temp = spiral_atom(atom,Box_dim,[angle 0 0],i*spiral_vector);
        elseif Dim==2
            trans_temp = spiral_atom(atom,Box_dim,[0 angle 0],i*spiral_vector);
        elseif Dim==3
            disp('Not supported in Z')
            pause
            %             trans_temp = spiral_atom(atom,Box_dim,[0 0 angle],i*[0 0 Rshift]);
        end

        D=dist_matrix_noPBC_atom(trans_temp,prev_temp);
        A=mean(diag(D));
        delta=delta+deltaaccuracy;

    end

    angle

    DeltaList(i)=delta;
    AngleList(i)=angle;
    System=update_atom({System trans_temp});
    prev_temp=trans_temp;

    %     if mod(i,10)==1
    %         if i > 1
    %             i-1
    %         end
    %     end

end

if Rshift==0
    D=dist_matrix_noPBC_atom(atom,trans_temp);
    A=mean(diag(D));
    disp('last-to-first distance         ideal distance')
    [A L]
    if A-L > UCaccuracy*L
        disp('Play around with AngularRange and UCaccuracy to optimize the sealing of the tube')
    elseif A-L < UCaccuracy*L
        disp('Play around with AngularRange and UCaccuracy to optimize the sealing of the tube')
    end
end

atom=System;

assignin('caller','DeltaList',DeltaList);
assignin('caller','AngleList',AngleList);
disp('.')
disp('.')
disp('.')
disp('Note that this function offers no error-checking in terms of overlapping atoms')
disp('..no clever math can be found here..')

tube_atom.m

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Examples