Corrected errors in main.ml

Matlab_code/ODE.m

@@ -1,103 +1,50 @@
 function dydt= ODE(t, y, parameters)
-dmI = parameters(1);
-Kq = parameters(2);
-wt = parameters(3);
-dA = parameters(4);
-vm = parameters(5);
-wm = parameters(6);
-w0 = parameters(7);
-nr = parameters(8);
-s = parameters(9);
-hA = parameters(10);
-hI = parameters(11);
-thetax = parameters(12);
-wA = parameters(13);
-kI = parameters(14);
-nx = parameters(15);
-wq = parameters(16);
-kA = parameters(17);
-we = parameters(18);
-hq = parameters(19);
-wr = parameters(20);
-dm = parameters(21);
-dI = parameters(22);
-ns = parameters(23);
-kb = parameters(24);
-M = parameters(25);
-Kt = parameters(26);
-wI = parameters(27);
-dmA = parameters(28);
-thetar = parameters(29);
-gammamax = parameters(30);
-ku = parameters(31);
-Kgamma = parameters(32);
-Km = parameters(33);
-vt = parameters(34);
+m1 = parameters(1);
+m2 = parameters(2);
+fa0 = parameters(3);
+fb0 = parameters(4);
+sinkZf = parameters(5);
+sinkCf = parameters(6);
+ii = parameters(7);
+sourceS0f = parameters(8);
+k = parameters(9);
+sourceXf = parameters(10);
+hh = parameters(11);
+sinkYf = parameters(12);
+gg = parameters(13);
+f1 = parameters(14);
 
 
-si = y(1);
-a = y(2);
-mr = y(3);
-mt = y(4);
-mm = y(5);
-mq = y(6);
-mA = y(7);
-mI = y(8);
-r = y(9);
-cr = y(10);
-ct = y(11);
-cm = y(12);
-cq = y(13);
-cA = y(14);
-cI = y(15);
-et = y(16);
-em = y(17);
-q = y(18);
-A = y(19);
-I = y(20);
+A = y(1);
+B = y(2);
+S0 = y(3);
+S1 = y(4);
+C = y(5);
+X = y(6);
+Y = y(7);
+Z = y(8);
+E = y(9);
+F = y(10);
+G = y(11);
+M1 = y(12);
+M2 = y(13);
 
 
-Rt = cr+ct+cm+cq; 
-alpha = (A/kA)^hA; 
-beta = (I/kI)^hI; 
-gamma = gammamax*a/(Kgamma+a); 
-omegam = wm*a/(thetax+a); 
-omegaq = wq*a/(thetax+a)/(1+(q/Kq)^hq); 
-omegar = wr*a/(thetar+a); 
-omegat = we*a/(thetax+a); 
-vcat = em*vm*si/(Km+si); 
-vimp = et*vt*s/(Kt+s); 
-R = alpha/(1+alpha+beta+alpha*beta); 
-lam = gamma*Rt/M; 
-nuA = cA*gamma/nx; 
-nuI = cI*gamma/nx; 
-num = cm*gamma/nx; 
-nuq = cq*gamma/nx; 
-nur = cr*gamma/nr; 
-nut = ct*gamma/nx; 
-omegaA = wA*R*a/(thetax+a); 
-omegaI = wI*R*a/(thetax+a); 
+ff = 2*hh; 
 
 
 dydt(size(y,1),1)= 0;
-dydt(1)= +vimp  -vcat  -lam*si ;
-dydt(2)=  + ns * vcat  -nr * nur  -nx * nut  -nx * num  -nx * nuq  -nx * nuA  -nx * nuI  -lam*a ;
-dydt(3)= +omegar  -kb*r*mr  +ku*cr  +nur  -dm*mr  -lam*mr ;
-dydt(4)= +omegat  -kb*r*mt  +ku*ct  +nut  -dm*mt  -lam*mt ;
-dydt(5)= +omegam  -kb*r*mm  +ku*cm  +num  -dm*mm  -lam*mm ;
-dydt(6)= +omegaq  -kb*r*mq  +ku*cq  +nuq  -dm*mq  -lam*mq ;
-dydt(7)= +w0  +omegaA  -kb*r*mA  +ku*cA  +nuA  -dmA*mA  -lam*mA ;
-dydt(8)= +w0  +omegaI  -kb*r*mI  +ku*cI  +nuI  -dmI*mI  -lam*mI ;
-dydt(9)= -kb*r*mr  +ku*cr  -kb*r*mt  +ku*ct  -kb*r*mm  +ku*cm  -kb*r*mq  +ku*cq  -kb*r*mA  +ku*cA  -kb*r*mI  +ku*cI   + 2. * nur  +nut  +num  +nuq  +nuA  +nuI  -lam*r ;
-dydt(10)= +kb*r*mr  -ku*cr  -nur  -lam*cr ;
-dydt(11)= +kb*r*mt  -ku*ct  -nut  -lam*ct ;
-dydt(12)= +kb*r*mm  -ku*cm  -num  -lam*cm ;
-dydt(13)= +kb*r*mq  -ku*cq  -nuq  -lam*cq ;
-dydt(14)= +kb*r*mA  -ku*cA  -nuA  -lam*cA ;
-dydt(15)= +kb*r*mI  -ku*cI  -nuI  -lam*cI ;
-dydt(16)= +nut  -lam*et ;
-dydt(17)= +num  -lam*em ;
-dydt(18)= +nuq  -lam*q ;
-dydt(19)= +nuA  -dA*A  -lam*A ;
-dydt(20)= +nuI  -dI*I  -lam*I ;
+dydt(1)= -k*A  +fa0*S0  +fa0*S0  -f1*A*B ;
+dydt(2)= +k*A  +fb0*S1  -f1*A*B ;
+dydt(3)= +sourceS0f  -fa0*S0  -fa0*S0 ;
+dydt(4)= -fb0*S1 ;
+dydt(5)= +f1*A*B  -sinkCf*C ;
+dydt(6)= +sourceXf ;
+dydt(7)= -sinkYf*Y ;
+dydt(8)= -5. * sinkZf*Z^5 ;
+dydt(9)= -ff*E  -gg*E ;
+dydt(10)=  + 0.4 * ff*E  -hh*F  +ii*G ;
+dydt(11)= +gg*E  +hh*F  -ii*G ;
+dydt(12)= -m1*M1  +m2*M2 ;
+dydt(13)= +m1*M1  -m2*M2 ;
 end

Matlab_code/initial.m

@@ -1,24 +1,17 @@
 function init = initial () 
  %define initial conditions
- si = 0;
- a = 10000.0;
- mr = 0;
- mt = 0;
- mm = 0;
- mq = 0;
- mA = 0;
- mI = 0;
- r = 10.0;
- cr = 0;
- ct = 0;
- cm = 0;
- cq = 0;
- cA = 0;
- cI = 0;
- et = 0;
- em = 0;
- q = 0;
- A = 10.0;
- I = 0;
- init = [ si a mr mt mm mq mA mI r cr ct cm cq cA cI et em q A I ];
+ A = 0;
+ B = 0;
+ S0 = 0;
+ S1 = 0;
+ C = 0;
+ X = 0;
+ Y = 0;
+ Z = 0;
+ E = 0;
+ F = 0;
+ G = 0;
+ M1 = 0;
+ M2 = 0;
+ init = [ A B S0 S1 C X Y Z E F G M1 M2 ];
 end

Matlab_code/main.m

@@ -7,23 +7,16 @@
  tf = 1e5; 
  [t,y] = ode15s(@(t,y) ODE(t, y, parameters), [t0,tf], init);
 %assign species names
- si = y(:, 1);
- a = y(:, 2);
- mr = y(:, 3);
- mt = y(:, 4);
- mm = y(:, 5);
- mq = y(:, 6);
- mA = y(:, 7);
- mI = y(:, 8);
- r = y(:, 9);
- cr = y(:, 10);
- ct = y(:, 11);
- cm = y(:, 12);
- cq = y(:, 13);
- cA = y(:, 14);
- cI = y(:, 15);
- et = y(:, 16);
- em = y(:, 17);
- q = y(:, 18);
- A = y(:, 19);
- I = y(:, 20);
+ A = y(:, 1);
+ B = y(:, 2);
+ S0 = y(:, 3);
+ S1 = y(:, 4);
+ C = y(:, 5);
+ X = y(:, 6);
+ Y = y(:, 7);
+ Z = y(:, 8);
+ E = y(:, 9);
+ F = y(:, 10);
+ G = y(:, 11);
+ M1 = y(:, 12);
+ M2 = y(:, 13);

Matlab_code/parameters.m

@@ -1,38 +1,18 @@
 function params = parameters ()  
  %define parameters
- dmI = 0.12;
- Kq = 152219;
- wt = 4.14;
- dA = 0.29;
- vm = 5800;
- wm = 4.14;
- w0 = 0.01;
- nr = 7459;
- s = 1e4;
- hA = 2;
- hI = 4;
- thetax = 4.38;
- wA = 640;
- kI = 160;
- nx = 300;
- wq = 948.93;
- kA = 160;
- we = 4.14;
- hq = 4;
- wr = 930;
- dm = 0.1;
- dI = 0.06;
- ns = 0.5;
- kb = 1;
- M = 1e8;
- Kt = 1000;
- wI = 320;
- dmA = 0.88;
- thetar = 426.87;
- gammamax = 1260;
- ku = 1;
- Kgamma = 7;
- Km = 1000;
- vt = 726;
- params = [ dmI Kq wt dA vm wm w0 nr s hA hI thetax wA kI nx wq kA we hq wr dm dI ns kb M Kt wI dmA thetar gammamax ku Kgamma Km vt ];
+ m1 = 3;
+ m2 = 5.4;
+ fa0 = 10;
+ fb0 = 8;
+ sinkZf = 1;
+ sinkCf = 10;
+ ii = 5;
+ sourceS0f = 1;
+ k = 3;
+ sourceXf = 1;
+ hh = 10;
+ sinkYf = 9;
+ gg = 0;
+ f1 = 5;
+ params = [ m1 m2 fa0 fb0 sinkZf sinkCf ii sourceS0f k sourceXf hh sinkYf gg f1 ];
 end

_build/_digests

@@ -1,26 +1,20 @@
-"Rule: ocaml dependencies ml (%=lexer )": "~g\226\141Fp\023\194\185>\224\181\245\244\176%"
-"Rule: ocaml: menhir dependencies (%=parser )": "\001\158H\0294\173\242ubb\222\147\208K7\028"
-"Resource: /Users/andreeabeica/Desktop/ODEgen/parser.mly": "\020\230\243\141\228|\236\018\242\152\018\161\158\142\255\002"
-"Rule: ocaml: ml & cmi -> cmx & o (%=lexer )": "\190\151K\235)8\246\184V\141r/\233\156\146'"
-"Rule: ocaml: ml & cmi -> cmx & o (%=parser )": "q\159\228\176 \227\\\224=\241\1297\188\251{>"
-"Resource: /Users/andreeabeica/Desktop/ODEgen/main.ml": "\195\196\251\253\206\144Y\\\237\176[\247\167\232K\242"
-"Resource: /home/andreea/Bureau/ODEgen/parser.mly": "\170\005\025~(^\182d\217\235\226\147\180>S>"
-"Resource: /home/andreea/Bureau/ODEgen/lexer.mll": "\227\023\172\190\216g\199ZT\216\2327k\027K\r"
-"Rule: ocamllex (%=lexer )": "|\209\151C\2214~\230\127\186\200L\169\202\b/"
-"Rule: ocaml dependencies ml (%=parser )": "\178\154m fT]\199i\137\235r\166\255\210\002"
-"Rule: ocaml: ml & cmi -> cmo (%=parser )": "C\175\2558\136\231\246\141`2a\219\178\029\220%"
-"Resource: /home/andreea/Bureau/ODEgen/ast.mli": "k-\002\160+\149\012Q\174@%NT\006\231O"
-"Rule: ocaml: ml -> cmo & cmi (%=lexer )": "^R\157x\016\165\130\218\166VD\158ZI\198\169"
+"Rule: ocaml dependencies ml (%=lexer )": "\150u\255\219i\237]\"\190\168\180T|VP9"
+"Rule: ocaml: menhir dependencies (%=parser )": "i\001dl~/\136\185\200\232p\006\231\219\227\233"
+"Resource: /Users/andreeabeica/Desktop/ODEgen/parser.mly": "Q23\149\185\212\012-\206\176\000\152\218\184\166\235"
+"Rule: ocaml: ml & cmi -> cmx & o (%=lexer )": "\2025B\133\214\181E\tZ\153\204\238\005\142\191\145"
+"Rule: ocaml: ml & cmi -> cmx & o (%=parser )": "\215\016\168\130\132\199tl\184|\222]\175O#p"
+"Resource: /Users/andreeabeica/Desktop/ODEgen/main.ml": "].e\238\147\182\164\0111\247\199\165\131\185\166Z"
+"Rule: ocamllex (%=lexer )": "ea0\022\028W-\197\1435\164XE\194\248d"
+"Rule: ocaml dependencies ml (%=parser )": "r\144J\020\179\193\187\254\200\135\192\011\139\209\154U"
+"Rule: ocaml: ml -> cmo & cmi (%=lexer )": "\194\188\144\174r\146\224\250\237\021\005\164\238\146\253\235"
 "Rule: ocaml dependencies mli (%=ast )": "\001\1978\172\006\018Xn\b\194\158\214~\252Z\190"
-"Resource: /Users/andreeabeica/Desktop/ODEgen/lexer.mll": "\227\023\172\190\216g\199ZT\216\2327k\027K\r"
-"Rule: ocaml: ml & cmi -> cmx & o (%=main )": "U\180\141\189w})\213\228\164\221N\011\023\003\198"
-"Rule: ocaml: cmo* -> byte (%=main )": "\152\186\184y*\142\133/\1782ax\012\189\012F"
-"Rule: ocaml: ml -> cmo & cmi (%=main )": "\012Q\245\168\205\016|\247\162d\b\236fYyW"
+"Resource: /Users/andreeabeica/Desktop/ODEgen/lexer.mll": "(\173\171\181\146'p\147\239\145\159\151\t\197\144\031"
+"Rule: ocaml: ml & cmi -> cmx & o (%=main )": "\230\161\211\223\198\164\158\160\172\232P\198\027>\165\142"
+"Rule: ocaml: ml -> cmo & cmi (%=main )": "\158V\n\194\222GE~\217\143G\129\029[nD"
 "Rule: ocaml: mli -> cmi (%=ast )": "\142\235\172&\156A\232\147\153\029\179\127\181J\215]"
-"Resource: /home/andreea/Bureau/ODEgen/main.ml": "_\195lwh_\028\254\203\207\234\229\159\027\215\163"
-"Rule: ocaml dependencies mli (%=parser )": "\b\213\203\207\164N\146\156;\228\234\145\1585^\234"
-"Rule: ocaml dependencies ml (%=main )": "\017\238\160\209I4a\1418\tD\017w:\181\137"
-"Rule: ocaml: menhir (%=parser )": "\221$\r\204\176\206s\000!\180\172U\017/Z\017"
-"Rule: ocaml: mli -> cmi (%=parser )": "LZ\247\133\007\1969\129T\r^\012\251\218\209\185"
+"Rule: ocaml dependencies mli (%=parser )": "\220\218Vv\225\204,\150\1608\224\244\185\134\143\165"
+"Rule: ocaml dependencies ml (%=main )": "\165\141>\166\004\017\182xc\245\231dw\174\218\146"
+"Rule: ocaml: menhir (%=parser )": "i\1842V\183\232\172\250\195vuvG|\n."
+"Rule: ocaml: mli -> cmi (%=parser )": "\175\020\242.\157\216\180\154A\216\142\230IHw\177"
 "Resource: /Users/andreeabeica/Desktop/ODEgen/ast.mli": "k-\002\160+\149\012Q\174@%NT\006\231O"
-"Rule: ocaml: cmx* & o* -> native (%=main )": "\135Yc\211\155\158\170\207 \212H\151*x\189\194"
+"Rule: ocaml: cmx* & o* -> native (%=main )": "-\182\0062uU@\154\131\231\158\231W{\026c"

_build/_log

@@ -22,7 +22,7 @@ ocamlc.opt -c -o lexer.cmo lexer.ml # cached
 # Target: main.cmo, tags: { byte, compile, extension:cmo, extension:ml, file:main.cmo, file:main.ml, implem, ocaml, quiet }
 ocamlc.opt -c -o main.cmo main.ml
 + ocamlc.opt -c -o main.cmo main.ml
-File "main.ml", line 645, characters 6-603:
+File "main.ml", line 680, characters 6-603:
 Warning 10: this expression should have type unit.
 # Target: parser.ml.depends, tags: { extension:ml, file:parser.ml, ocaml, ocamldep, quiet }
 ocamldep.opt -modules parser.ml > parser.ml.depends # cached
@@ -33,7 +33,7 @@ ocamlopt.opt -c -o lexer.cmx lexer.ml # cached
 # Target: main.cmx, tags: { compile, extension:cmx, extension:ml, file:main.cmx, file:main.ml, implem, native, ocaml, quiet }
 ocamlopt.opt -c -o main.cmx main.ml
 + ocamlopt.opt -c -o main.cmx main.ml
-File "main.ml", line 645, characters 6-603:
+File "main.ml", line 680, characters 6-603:
 Warning 10: this expression should have type unit.
 # Target: main.native, tags: { dont_link_with, extension:native, file:main.native, link, native, ocaml, program, quiet }
 ocamlopt.opt str.cmxa parser.cmx lexer.cmx main.cmx -o main.native