MATLAB Script: Importing, Sorting, and Analyzing CONTCAR Data

This MATLAB assignment involves creating a script to analyze data from a CONTCAR file, a standard format in materials science for representing crystal structures. The script begins by importing data from a specified text file, initializing variables, and handling the file reading process. The data is then sorted, and calculations are performed, including multiplying atom vectors based on lattice vectors. The script presents the data through 3D plots of atomic positions for different atom types (Na, Mn, O, and Li). The code includes functions for vector multiplication and plotting, demonstrating modular programming principles. The code also includes clearing and closing all MATLAB windows.

Clearing and closing all MATLAB windows.........................................................................................1
Import data from text file..................................................................................................................1
Sorting data.......................................................................................................................................2
Calculations.......................................................................................................................................2
Presenting data..................................................................................................................................2
Functions...........................................................................................................................................4
Clearing and closing all MATLAB windows
clear;
clc;
close all;
Import data from text file.
Script for importing data from the following text file: To extend the code to different selected data or
a different text file, generate a function instead of a script. Initialize variables.
filename = 'C:\Users\User\Desktop\NERDY\1076792\22061663_CONTCAR_2.txt';% Change the folder name to
the one you have stored your text file.
delimiter = ' ';
% Read columns of data as text:
% For more information, see the TEXTSCAN documentation.
formatSpec = '%s%s%s%s%[^\n\r]';
% Open the text file.
fileID = fopen(filename,'r');
% Read columns of data according to the format.
% This call is based on the structure of the file used to generate this
% code. If an error occurs for a different file, try regenerating the code
% from the Import Tool.
dataArray = textscan(fileID, formatSpec, 'Delimiter', delimiter, 'MultipleDelimsAsOne', true, 'TextType', 'string',
'ReturnOnError', false);
% Close the text file.
fclose(fileID);
% Convert the contents of columns containing numeric text to numbers.
% Replace non-numeric text with NaN.
raw = repmat({''},length(dataArray{1}),length(dataArray)-1);
for col=1:length(dataArray)-1
raw(1:length(dataArray{col}),col) = mat2cell(dataArray{col}, ones(length(dataArray{col}), 1));
end
numericData = NaN(size(dataArray{1},1),size(dataArray,2));
for col=[1,2,3,4]
% Converts text in the input cell array to numbers. Replaced non-numeric
% text with NaN.
rawData = dataArray{col};
for row=1:size(rawData, 1)
% Create a regular expression to detect and remove non-numeric prefixes and
% suffixes.

regexstr = '(?<prefix>.*?)(?<numbers>([-]*(\d+[\,]*)+[\.]{0,1}\d*[eEdD]{0,1}[-+]*\d*[i]{0,1})|([-]*(\d+
[\,]*)*[\.]{1,1}\d+[eEdD]{0,1}[-+]*\d*[i]{0,1}))(?<suffix>.*)';
try
result = regexp(rawData(row), regexstr, 'names');
numbers = result.numbers;
% Detected commas in non-thousand locations.
invalidThousandsSeparator = false;
if numbers.contains(',')
thousandsRegExp = '^[-/+]*\d+?(\,\d{3})*\.{0,1}\d*$';
if isempty(regexp(numbers, thousandsRegExp, 'once'))
numbers = NaN;
invalidThousandsSeparator = true;
end
end
% Convert numeric text to numbers.
if ~invalidThousandsSeparator
numbers = textscan(char(strrep(numbers, ',', '')), '%f');
numericData(row, col) = numbers{1};
raw{row, col} = numbers{1};
end
catch
raw{row, col} = rawData{row};
end
end
end
% Replace non-numeric cells with NaN
R = cellfun(@(x) ~isnumeric(x) && ~islogical(x),raw); % Find non-numeric cells
raw(R) = {NaN}; % Replace non-numeric cells
% Create output variable
CONTCAR2 = cell2mat(raw);
% Clear temporary variables
clearvars filename delimiter formatSpec fileID dataArray ans raw col numericData rawData row regexstr result
numbers invalidThousandsSeparator thousandsRegExp R;
Sorting data
a=CONTCAR2(3,1:3); % Change the variables names according to your data in your text file
b=CONTCAR2(4,1:3); % Matrix containing the vectors a,b,c
c=CONTCAR2(5,1:3);
Na=CONTCAR2(9:15,1:3); % Matrix containing vectors of the various atoms e.g. Na
Mn=CONTCAR2(16:21,1:3);
O=CONTCAR2(22:37,1:3);
Li=CONTCAR2(38:39,1:3);
Calculations
Multiplying vectors a, b and c with atom vectors

Mn=multi(Mn,a,b,c);
Na=multi(Na,a,b,c);
O=multi(O,a,b,c);
Li=multi(Li,a,b,c);
% Calculating dimensions
Presenting data
plott(Na)
plott(Mn)
plott(Li)
plott(O)

Functions
Function to multiply the vectors
function aa=multi(bb,a,b,c)
[x y]=size(bb);% Obtaining the number of rows and columns
for i=1:x% Multiplying the atoms vector according to vectors a, b and c
if i>x
break;
else
bb(i,1:3)=a.*bb(i,1:3);
end
if i+1>x
break;
else
bb(i+1,1:3)=b.*bb(i+1,1:3);
end
if i+2>x
break;
else
bb(i+2,1:3)=c.*bb(i+2,1:3);
end
i=i+2;
end
aa=bb;
end

% Function to plot the data
function bb=plott(cc)
figure;
plot3(cc(:,1),cc(:,2),cc(:,3),'o')
grid on;
end
Published with MATLAB® R2018b