How to resolve the error

Unable to perform assignment because the size of the left

side is 39978-by-1 and the size of the right side is

39987-by-1.

Error in Stress_analysis (line 46)

coordinate_all(:,i,j) = C{1,j};

Code is here.

%% Read dump file
 
 clc, clear, close all
 disp('A script to deal with the dump file of lammps.');
 tic;
 
 %% Set up some parameters related to the dump file
 
 % Inpute / Output file name
 in_file = 'D:\NewWorkPost18May2023\DSC\PPT_Data\DumpFiles\Thin_Film\SiO2-Cr-Au\BeforeAnnealing\atom_300K.dump';                                                                         % Dump file name
 save_file_name_1 = 'coordinate_all.mat';                                            % Output  file for coordinate data
 
 % Read the information of the simulation box in the dump file
 fileID = fopen(in_file, 'r');
 atoms = textscan(fileID, '%n', 1, 'HeaderLines', 3, 'Delimiter', '\t');      % Number of particles   (You should read the textscan command carefully)
 box = textscan(fileID, '%n %n', 3, 'HeaderLines', 2, 'Delimiter', '\t');    % Extract box information
 fclose(fileID);
 
 Total_atoms = 39978;                                                                     % Number of atoms 
 len_header = 9;                                                                                   % Skip comments          (may have to  change acording to your system )
 N = Total_atoms + len_header;                                                           % Length of block
 
 %%  Parameters from MD simulation
 
 Output_interval = 100000;                                                                  % Dump output interval (step)
 Total_running_steps = 1000000;                                                         % The total number of running steps of lammps during the production period
 Ns = Total_running_steps / Output_interval;                                       % Total number of dump point  (number of frames)
 
 % If you have more output (columns) in your dump file, you must modify this value
 
 dump_columns = 14;                                                                            % The number of columns in the dump file (Modify according to your own output)
 
 %% Deal with data
 
 coordinate_all = zeros(Total_atoms, dump_columns, Ns);
 fileID = fopen(in_file);
 form = '%f ';
 formatSpec = repmat(form, 1, dump_columns);                                 % Equivalent to the number of dump_columns = x
 
 for i = 1:Ns
     
      C = textscan(fileID, formatSpec, N, 'HeaderLines', len_header, 'Delimiter', '\t');
     
      for  j = 1 : dump_columns
          
            coordinate_all(:,i,j) = C{1,j};                                                       % Extract all the coordinate information (Including all frames)
                                                                                                              % Of course, it can also contain only the information you want (need to modify)
      end
end
fclose(fileID);
save(save_file_name_1, 'coordinate_all') 
frame_traversala = coordinate_all(:, :, 5);
frame_traversalb = coordinate_all(:, :, 6);
frame_traversalc = coordinate_all(:, :, 7);
frame_traversald = coordinate_all(:, :, 8);
frame_traversale = coordinate_all(:, :, 9);
frame_traversalf =  coordinate_all(:, :, 10);                                                 % For test 
%%%%% data processing %%%%%%
frame_traversala(:,1:4)= [];
frame_traversala(:,2:7)= [];
frame_traversala(:,3:4)= [];
Ba = sortrows(frame_traversala,1);
Ba(:,2) = 0.0001*Ba(:,2);   % pzz in GPa
pressurea = Ba(:,2);
deptha = Ba(:,1);
frame_traversalb(:,1:4)= [];
frame_traversalb(:,2:7)= [];
frame_traversalb(:,3:4)= [];
Bb = sortrows(frame_traversalb,1);
Bb(:,2) = 0.0001*Bb(:,2);   % pzz in GPa
pressureb = Bb(:,2);
depthb = Bb(:,1);
frame_traversalc(:,1:4)= [];
frame_traversalc(:,2:7)= [];
frame_traversalc(:,3:4)= [];
Bc = sortrows(frame_traversalc,1);
Bc(:,2) = 0.0001*Bc(:,2);   % pzz in GPa
pressurec = Bc(:,2);
depthc = Bc(:,1);
frame_traversald(:,1:4)= [];
frame_traversald(:,2:7)= [];
frame_traversald(:,3:4)= [];
Bd = sortrows(frame_traversald,1);
Bd(:,2) = 0.0001*Bd(:,2);   % pzz in GPa
pressured = Bd(:,2);
depthd = Bd(:,1);
frame_traversale(:,1:4)= [];
frame_traversale(:,2:7)= [];
frame_traversale(:,3:4)= [];
Be = sortrows(frame_traversale,1);
Be(:,2) = 0.0001*Be(:,2);   % pzz in GPa
pressuree = Be(:,2);
depthe = Be(:,1);
frame_traversalf(:,1:4)= [];
frame_traversalf(:,2:7)= [];
frame_traversalf(:,3:4)= [];
Bf = sortrows(frame_traversalf,1);
Bf(:,2) = 0.0001*Bf(:,2);   % pzz in GPa
pressuref = Bf(:,2);
depthf = Bf(:,1);
depth = [deptha depthb depthc depthd depthe depthf];
pressure = [pressurea pressureb pressurec pressured pressuree pressuref];
depth = mean(depth,2);
pressure = mean(pressure,2);
plot(depth,pressure);
%%%%%% binning%%%%%%%%%%%%%%%
edges = (-9.8:0.5:128);
[~,~,loc]=histcounts(depth,edges);
meany = accumarray(loc(:),pressure(:))./accumarray(loc(:),1);
xmid = 0.5*(edges(1:end-1)+edges(2:end));
figure
hold on; 
plot(xmid,meany,'r')
%%

Answer 1

[Cris LaPierre]

You have indexed a set of rows that is different in size from the number of elements you are trying to assign to it. They must be the same size.

A = [1;2];
A(:,1) = (1:3)'

Unable to perform assignment because the size of the left side is 2-by-1 and the size of the right side is 3-by-1.

[Tejasva Vashistha]

Can you specifically check line 46 in the code and suggest changes?

[Cris LaPierre]

The issue is exactly the same as the example code I shared above. For some reason, your variable C is not the size you are expecting it to be. Your options are to adjust the row assignment in coordinate_all to match the size of C, or adjust the rows of C you are assignment to match the size of coordinate_all.

For the example above, you could do this.

A = [1;2];
B = (1:3)';
A(:,1) = B(1:size(A,1),1)

A = 2×1

1 2

% or
A(1:size(B,1),1) = B(:,1)

A = 3×1

1 2 3

You need to decide which approach is best for you application.