thRed.m

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%                                                                         
%                     Author: Andrea Somma;                                
%                     Politecnico of Milan                                 
%                                                                         
% thRed reduces a Chemkin thermodynamics sheet into a shorter version of it, 
% containing only the requested ones and converts the file into a matlab matrix
% 
% - trRed(filePath, species): where "filePath" is the path to the chemkin
%       thermo sheet and "specie" is a string vector of the wanted
%       species.

function thRed(thermo_data_name,species)
El = ["D";
"H";
"He";
"Li";
"Be";
"B";
"C";
"N";
"O";
"F";
"Ne";
"Na";
"Mg";
"Al";
"Si";
"P";
"S";
"Cl";
"AR";
"K";
"Ca";
"Sc";
"Ti";
"V";
"Cr";
"Mn";
"Fe";
"Co";
"Ni";
"Cu";
"Zn";
"Ga";
"Ge";
"As";
"Se";
"Br";
"Kr";
"Rb";
"Sr";
"Y";
"Zr";
"Nb";
"Mo";
"Ru";
"Rh";
"Pd";
"Ag";
"Cd";
"In";
"Sn";
"Sb";
"Te";
"I";
"Xe";
"Cs";
"Ba";
"La";
"Ce";
"Pr";
"Nd";
"Sm";
"Eu";
"Gd";
"Tb";
"Dy";
"Ho";
"Er";
"Tm";
"Yb";
"Lu";
"Hf";
"Ta";
"W";
"Re";
"Os";
"Ir";
"Pt";
"Au";
"Hg";
"Tl";
"Pb";
"Bi";
"Th";
"U"];

MM = [2.01410100000000;
1.00800000000000;
4.00260200000000;
6.94000000000000;
9.01218200000000;
10.8100000000000;
12.0110000000000;
14.0070000000000;
15.9990000000000;
18.9984032000000;
20.1797000000000;
22.9897692800000;
24.3050000000000;
26.9815386000000;
28.0850000000000;
30.9737620000000;
32.0600000000000;
35.4500000000000;
39.9480000000000;
39.0983000000000;
40.0780000000000;
44.9559120000000;
47.8670000000000;
50.9415000000000;
51.9961000000000;
54.9380450000000;
55.8450000000000;
58.9331950000000;
58.6934000000000;
63.5460000000000;
65.3800000000000;
69.7230000000000;
72.6300000000000;
74.9216000000000;
78.9600000000000;
79.9040000000000;
83.7980000000000;
85.4678000000000;
87.6200000000000;
88.9058500000000;
91.2240000000000;
92.9063800000000;
95.9600000000000;
101.070000000000;
102.905500000000;
106.420000000000;
107.868200000000;
112.411000000000;
114.818000000000;
118.710000000000;
121.760000000000;
127.600000000000;
126.904470000000;
131.293000000000;
132.905451900000;
137.327000000000;
138.905470000000;
140.116000000000;
140.907650000000;
144.242000000000;
150.360000000000;
151.964000000000;
157.250000000000;
158.925350000000;
162.500000000000;
164.930320000000;
167.259000000000;
168.934210000000;
173.054000000000;
174.966800000000;
178.490000000000;
180.947880000000;
183.840000000000;
186.207000000000;
190.230000000000;
192.217000000000;
195.084000000000;
196.966569000000;
200.590000000000;
204.380000000000;
207.200000000000;
208.980400000000;
232.038060000000;
238.028910000000];

    % preparing cells
    dataTh = cell(numel(species)*4,5);
    % readmode thermodinamics file
    ReadFileID = fopen(strcat(thermo_data_name), 'rt');
    % creating directory if not ex
    if ~exist("thermo_models/")
       mkdir("thermo_models/")
    end
    % read first line
    textLine = fgetl(ReadFileID);
    % start counters
    lineCounter = 1;
    specieCounter = 1;
    element = string;

    % looping on lines
    while ischar(textLine)
        if isempty(regexp(textLine, '\S', 'once')) == 0
            if textLine(1) ~= '!'
                specie_name = split(textLine);
                if any(strcmp(species,specie_name(1)))
                    % calculating mass weight
                    PM = 0;
                    mass = strtrim(textLine(25:44));
                    mass_splitted = split(mass);
                    index_to_cut = find(isnan(str2double(mass_splitted)), 1, 'last' ) + 1;
                    mass_raw = strjoin(mass_splitted(1:index_to_cut),"");
                    idx_char = isstrprop(mass_raw,'alpha');
                    start_idx = 1;
                    counter_mm = 1;
                    element = string;

                    for i = 2:length(mass_raw)
                        if idx_char(i) ~= idx_char(i-1)
                            element(counter_mm) = mass_raw(start_idx:(i-1));
                            start_idx = i;
                            counter_mm = counter_mm +1;
                        end
                    end
                    element(counter_mm) = mass_raw(start_idx:end);
    
                    counter_mm2 = 1;
                    for i = 1:length(element)/2
                        indx_El = find(El==element(counter_mm2));
                        PM = MM(indx_El) * str2double(element(counter_mm2+1)) + PM;
                        counter_mm2 = counter_mm2 + 2;
                    end

                    % start saving
                    dataTh(specieCounter*4-3,1) = specie_name(1);
                    dataTh(specieCounter*4-3,5) = num2cell(PM);
                    dataTh(specieCounter*4-3,2) = join(cellstr(element),',');
                    for j = 1:3
                        textLine = fgetl(ReadFileID);
                        for i = 1:5
                            dataTh(j+specieCounter*4-3,i) = cellstr(strtrim(textLine(i*15-14:i*15)));
                        end
                    end
                specieCounter = specieCounter + 1;
                end
            end
        end


        % Read the next line.
        textLine = fgetl(ReadFileID);
        lineCounter = lineCounter + 1;
    end
    fclose(ReadFileID);
    save("./thermo_models/red.mat","dataTh")
end