MATLAB Examples

# hist_atom.m

• This function is used to calculate density profiles in the Z-direction
• Tested when? Does it work?
• Please report bugs to michael.holmboe@umu.se

## Examples

• Hist = hist_atom(atom,0.02)
```function Hist = hist_atom(atom,s) ind_H=find(strncmp([atom.fftype],'H',1)); ind_O=find(strncmp([atom.fftype],'O',1)); ind_rm = [ind_H ind_O]; atom(ind_H)=[]; % ind_S=find(strncmp([atom.fftype],'S',1)); % atom=[atom atom(ind_S) atom(ind_S) atom(ind_S) atom(ind_S) atom(ind_S)]; ind_C=find(strncmp([atom.fftype],'C',1)); atom=[atom atom(ind_C) atom(ind_C)]; Coord = [atom.x; atom.y; atom.z]'; % xmin=min(Coord(:,1)); % ymin=min(Coord(:,2)); % zmin=min(Coord(:,3)); Coord = [Coord(:,1)-mean(Coord(:,1))+50 Coord(:,2)-mean(Coord(:,2))+50 Coord(:,3)-mean(Coord(:,3))+50]; Bins = (0:s:s*1000)'; Hist=hist(Coord,Bins); sigma = 4; window = 100; x = linspace(-window / 2, window / 2, window); gaussFilter = exp(-x .^ 2 / (2 * sigma ^ 2)); gaussFilter = gaussFilter / sum(gaussFilter); % normalize %Hist(:,1)=filter(gaussFilter,1, Hist(:,1)); for i=1:3 Hist(:,i)=conv(Hist(:,i), gaussFilter, 'same'); Hist(:,i)=Hist(:,i)/sum(Hist(:,i)); end % assignin('caller','Bins',Bins); % assignin('caller','Coord',Coord); % assignin('caller','xmin',xmin); % assignin('caller','ymin',ymin); % assignin('caller','zmin',zmin); ```