/*******************************************************************
 *                                                                  *
 * This P-Lingua file is free software: you can redistribute        *
 * it and/or modify it under the terms of the GNU General           *
 * Public License as published by the Free Software Foundation,     *
 * either version 3 of the License, or (at your option) any         *
 * later version.                                                   *
 *                                                                  *
 * This P-Lingua file is distributed in the hope that it will       *
 * be useful, but WITHOUT ANY WARRANTY; without even the implied    *
 * warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. *
 * See the GNU General Public License for more details.             *
 *                                                                  *
 * For more information about the license,                          * 
 * see <http://www.gnu.org/licenses/>.                              *
 *                                                                  *
 * For more information about P-Lingua,                             *
 * see <http://www.p-lingua.org/>                                   *
 *                                                                  *
 * Copyright (c) Research Group on Natural Computing                *
 *               http://www.gcn.us.es                               *
 *                                                                  *
 ********************************************************************
 *                                                                  *
 * This P-Lingua file specifies the model                           *
 * of the Bearded Vulture ecosystem described in the paper:         *
 *                                                                  *
 * 	http://www.gcn.us.es/10BWMC/10BWMCvolII/papers/dcba.pdf         *
 *                                                                  *
 * At the end of this P-Lingua file, there are some necessary       *
 * parameters for the model (defined as P-Lingua global variables). *
 * The parameters values included in this file have been obtained   *
 * from the referenced paper. These values are enough to run        *
 * simulations of the model by using the pLinguaCore library.       *
 *                                                                  *
 ********************************************************************/

@model<probabilistic>

def main()
{
	call init_membrane_structure();
	call init_multisets();
	call init_rules();
}

def init_membrane_structure()
{
   @mu= [[[ [  ]'2 ]'1]'101,101]'global;
}

def init_multisets()
{
	let alpha = 0;
	let alpha = alpha + q{1,j} : 1<= j <= 21;
	let alpha = @ceil (alpha * 1.1 * 682);
	@ms(1) += X{i,j}*q{i,j} : 0<=j<=k{i,4},1<=i<=7;
	@ms(2) = C, B*alpha;
}

def init_rules()
{
	/************************************/
	/* Reproduction rules for ungulates */
	/************************************/	
	/* Adult males */
	/* r0.i.j */ [X{i,j}]'1 --> [Y{i,j}]'1 :: 1-k{i,13} : k{i,2}<=j<=k{i,4},2<=i<=7;

	/* Adult females that reproduce */	
	/* r1.i.j */ [X{i,j}]'1 --> [Y{i,j},Y{i,0}]'1 :: k{i,5}*k{i,13} :  k{i,2}<=j<k{i,3},2<=i<=7,i<>3;
	
	/* Red Deer females produce 50% of female and 50% of male springs */
	/* r2.j */ [X{3,j}]'1 --> [Y{3,j},Y{3,0}]'1 :: k{3,5}*k{3,13}*0.5 :  k{3,2}<=j<k{3,3};
	/* r3.j */ [X{3,j}]'1 --> [Y{3,j},Y{4,0}]'1 :: k{3,5}*k{3,13}*0.5 :  k{3,2}<=j<k{3,3};
	
	/* Fertile adult females that do not reproduce */	
	/* r4.i.j */ [X{i,j}]'1 --> [Y{i,j}]'1 :: (1-k{i,5})*k{i,13} : k{i,2}<=j<k{i,3},2<=i<=7;

	/* Not fertile adult females */
	/* r5.i.j */ [X{i,j}]'1 --> [Y{i,j}]'1 :: k{i,13} : k{i,3}<=j<=k{i,4},2<=i<=7;

	/* Young ungulates that do not reproduce */
	/* r6.i.j */ [X{i,j}]'1 --> [Y{i,j}]'1 :: 1 : 0<=j<k{i,2},2<=i<=7;

	/****************************************/
	/* Growth rules for the bearded vulture */
	/****************************************/
	/* r7.j */ [X{1,j}]'1 --> [Y{1,k{1,2}-1},Y{1,j}]'1 :: k{1,6}+k{1,10} : k{1,2}<=j<k{1,4};
	/* r8.j */ [X{1,j}]'1 --> [Y{1,j}]'1 :: 1-k{1,6}-k{1,10} : k{1,2}<=j<k{1,4};
	/* r9   */ [X{1,k{1,4}}]'1 --> [Y{1,k{1,2}-1},Y{1,k{1,4}}] :: k{1,6};
	/* r10  */ [X{1,k{1,4}}]'1 --> [Y{1,k{1,4}}]'1 :: 1-k{1,6};

	/*********************************/
	/* Mortality rules for ungulates */
	/*********************************/
	/* Young ungulates which survive */	
	/* r11.i.j */ Y{i,j}[ ]'2 --> [Z{i,j}]'2 :: 1-k{i,7}-k{i,8} : 0<=j<k{i,1},2<=i<=7;
	
	/* Young ungulates which die */
	/* r12.i.j */ Y{i,j}[ ]'2 --> [B*k{i,11}]'2 :: k{i,8} : 0<=j<k{i,1},2<=i<=7;
	
	/* Young ungulates which are retired from the ecosystem */
	/* r13.i.j */ Y{i,j}[]'2 --> [ ]'2 :: k{i,7} : 0<=j<k{i,1},2<=i<=7;

	/* Adult ungulates that don't arrive at an average life expectancy */
	/* Those which survive */
	/* r14.i.j */ Y{i,j}[ ]'2 --> [Z{i,j}]'2 ::1-k{i,10} : k{i,1}<=j<k{i,4},2<=i<=7;
	
	/* Those which die */
	/* r15.i.j */ Y{i,j}[ ]'2 --> [B*k{i,12}]'2::k{i,10} : k{i,1}<=j<k{i,4},2<=i<=7;

	/* Ungulates that arrive at an average life expectancy*/
	/* Those which die in the ecosystem */
	/* r16.i */ Y{i,k{i,4}}[ ]'2 --> [B*k{i,12}]'2 :: k{i,9}+(1-k{i,9})*k{i,10} : 2<=i<=7;
	
	/* Those which die and are retired from the ecosystem */
	/* r17.i */ Y{i,k{i,4}}[]'2 --> [ ]'2 :: (1-k{i,9})*(1-k{i,10}) : 2<=i<=7;

	/*******************************************/
	/* Mortality rules for the bearded vulture */
	/*******************************************/
	/* r18.j */ Y{1,j}[ ]'2 --> [Z{1,j}]'2 :: 1-k{1,10} : k{1,2}<=j<k{1,4};
	/* r19.j */ Y{1,j}[ ]'2 --> []'2 :: k{1,10} : k{1,2}<=j<k{1,4};	
 	/* r20   */ Y{1,k{1,4}}[ ]'2 --> [Z{1,k{1,2}-1}]'2 :: 1 ;
	/* r21   */ Y{1,k{1,2}-1}[ ]'2 --> [Z{1,k{1,2}-1}]'2 :: 1 ;

	/*****************/	
	/* Feeding rules */
	/*****************/
	/* r22.i.j */ [Z{i,j},B*k{i,14}]'2 --> X{i,j+1} +[ ]'2 :: 1 : 0<=j<=k{i,4},1<=i<=7;

	/*****************/
	/* Balance rules */
	/*****************/
	/* Elimination of remaining bones */
	/* r23 */ +[B]'2 --> [ ]'2 :: 1;
	
	/* Adult animals that die because they have not enough food */
	/* r24.i.j */ +[Z{i,j}]'2 --> [B*k{i,12}]'2 :: 1 : k{i,1}<=j<=k{i,4},1<=i<=7;
	
	/* Young animals that die because they have not enough food */
	/* r25.i.j */ +[Z{i,j}]'2 --> [B*k{i,11}]'2 :: 1 : 0<=j<k{i,1},1<=i<=7;

	/* Change the polarization */
	/* r26 */ +[C]'2 --> [C]'2 :: 1;
	
}

/************************/
/* Parameter values     */
/************************/

/*******************/
/* Bearded Vulture */
/*******************/
k{1,1} = 1;
k{1,2} = 8;
k{1,3} = 20;
k{1,4} = 21;
k{1,5} = 0.38;
k{1,6} = 0.05; 
k{1,7} = 0;
k{1,8} = 0.06;
k{1,9} = 1;
k{1,10} = 0.12; 
k{1,11} = 0;
k{1,12} = 0;
k{1,13} = 0.5;
k{1,14} = 460;


/********************/
/* Pyrenean Chamois */
/********************/
k{2,1} = 1;
k{2,2} = 2;
k{2,3} = 18;
k{2,4} = 18;
k{2,5} = 0.75;
k{2,6} = 0; 
k{2,7} = 0;
k{2,8} = 0.6;
k{2,9} = 1;
k{2,10} = 0.06;
k{2,11} = 6;
k{2,12} = 12;
k{2,13} = 0.55;
k{2,14} = 0; 


/*******************/
/* Red Deer Female */
/*******************/
k{3,1} = 1;
k{3,2} = 2;
k{3,3} = 17;
k{3,4} = 17;
k{3,5} = 0.75;
k{3,6} = 0; 
k{3,7} = 0;
k{3,8} = 0.39;
k{3,9} = 1;
k{3,10} = 0.06;
k{3,11} = 15;
k{3,12} = 30;
k{3,13} = 1;
k{3,14} = 0; 


/*****************/
/* Red Deer Male */
/*****************/
k{4,1} = 1;
k{4,2} = 2;
k{4,3} = 0; 
k{4,4} = 20;
k{4,5} = 0; 
k{4,6} = 0; 
k{4,7} = 0;
k{4,8} = 0.39; 
k{4,9} = 1;
k{4,10} = 0.36;
k{4,11} = 24;
k{4,12} = 48;
k{4,13} = 0;
k{4,14} = 0; 


/***************/
/* Fallow Deer */
/***************/
k{5,1} = 1;
k{5,2} = 2;
k{5,3} = 12;
k{5,4} = 12;
k{5,5} = 0.55;
k{5,6} = 0; 
k{5,7} = 0;
k{5,8} = 0.5;
k{5,9} = 1;
k{5,10} = 0.06;
k{5,11} = 2;
k{5,12} = 4;
k{5,13} = 0.75;
k{5,14} = 0; 


/************/
/* Roe Deer */
/************/
k{6,1} = 1;
k{6,2} = 1;
k{6,3} = 10;
k{6,4} = 10;
k{6,5} = 1;
k{6,6} = 0; 
k{6,7} = 0;
k{6,8} = 0.58;
k{6,9} = 1;
k{6,10} = 0.06;
k{6,11} = 1;
k{6,12} = 2;
k{6,13} = 0.67;
k{6,14} = 0; 


/*********/
/* Sheep */
/*********/
k{7,1} = 1;
k{7,2} = 2;
k{7,3} = 8;
k{7,4} = 8;
k{7,5} = 0.75;
k{7,6} = 0; 
k{7,7} = 0.57;
k{7,8} = 0.15;
k{7,9} = 0;
k{7,10} = 0.03;
k{7,11} = 7;
k{7,12} = 14;
k{7,13} = 0.96;
k{7,14} = 0; 


/************************/
/* Initial populations  */
/************************/

/*******************/
/* Bearded Vulture */
/*******************/
q{1,0} = 0;
q{1,1} = 0;
q{1,2} = 0;
q{1,3} = 0;
q{1,4} = 0;
q{1,5} = 0;
q{1,6} = 0;
q{1,7} = 0;
q{1,8} = 2;
q{1,9} = 2;
q{1,10} = 2;
q{1,11} = 2;
q{1,12} = 2;
q{1,13} = 2;
q{1,14} = 1;
q{1,15} = 1;
q{1,16} = 1;
q{1,17} = 1;
q{1,18} = 1;
q{1,19} = 1;
q{1,20} = 1;
q{1,21} = 1;

/********************/
/* Pyrenean Chamois */
/********************/
q{2,0} = 0;
q{2,1} = 741;
q{2,2} = 740;
q{2,3} = 668;
q{2,4} = 667;
q{2,5} = 667;
q{2,6} = 596;
q{2,7} = 594;
q{2,8} = 518;
q{2,9} = 517;
q{2,10} = 444;
q{2,11} = 444;
q{2,12} = 444;
q{2,13} = 373;
q{2,14} = 373;
q{2,15} = 372;
q{2,16} = 296;
q{2,17} = 296;
q{2,18} = 252;
q{2,19} = 0;
q{2,20} = 0;
q{2,21} = 0;

/*******************/
/* Red Deer Female */
/*******************/
q{3,0} = 0;
q{3,1} = 167;
q{3,2} = 133;
q{3,3} = 107;
q{3,4} = 85;
q{3,5} = 68;
q{3,6} = 41;
q{3,7} = 33;
q{3,8} = 26;
q{3,9} = 21;
q{3,10} = 17;
q{3,11} = 13;
q{3,12} = 11;
q{3,13} = 9;
q{3,14} = 7;
q{3,15} = 5;
q{3,16} = 4;
q{3,17} = 3;
q{3,18} = 0;
q{3,19} = 0;
q{3,20} = 0;
q{3,21} = 0;

/******************/
/* Reed Deer Male */
/******************/
q{4,0} = 0;
q{4,1} = 58;
q{4,2} = 44;
q{4,3} = 35;
q{4,4} = 28;
q{4,5} = 23;
q{4,6} = 14;
q{4,7} = 11;
q{4,8} = 9;
q{4,9} = 7;
q{4,10} = 5;
q{4,11} = 5;
q{4,12} = 4;
q{4,13} = 3;
q{4,14} = 2;
q{4,15} = 2;
q{4,16} = 1;
q{4,17} = 1;
q{4,18} = 0;
q{4,19} = 0;
q{4,20} = 0;
q{4,21} = 0;

/***************/
/* Fallow Deer */
/***************/
q{5,0} = 0;
q{5,1} = 83;
q{5,2} = 73;
q{5,3} = 69;
q{5,4} = 63;
q{5,5} = 59;
q{5,6} = 55;
q{5,7} = 51;
q{5,8} = 47;
q{5,9} = 35;
q{5,10} = 33;
q{5,11} = 30;
q{5,12} = 0;
q{5,13} = 0;
q{5,14} = 0;
q{5,15} = 0;
q{5,16} = 0;
q{5,17} = 0;
q{5,18} = 0;
q{5,19} = 0;
q{5,20} = 0;
q{5,21} = 0;

/***************/
/* Roe Deer    */
/***************/
q{6,0} = 0;
q{6,1} = 121;
q{6,2} = 121;
q{6,3} = 121;
q{6,4} = 121;
q{6,5} = 109;
q{6,6} = 108;
q{6,7} = 108;
q{6,8} = 96;
q{6,9} = 96;
q{6,10} = 0;
q{6,11} = 0;
q{6,12} = 0;
q{6,13} = 0;
q{6,14} = 0;
q{6,15} = 0;
q{6,16} = 0;
q{6,17} = 0;
q{6,18} = 0;
q{6,19} = 0;
q{6,20} = 0;
q{6,21} = 0;


/*********/
/* Sheep */
/*********/
q{7,0} = 0;
q{7,1} = 20832;
q{7,2} = 20208;
q{7,3} = 19601;
q{7,4} = 19014;
q{7,5} = 18443;
q{7,6} = 17890;
q{7,7} = 17353;
q{7,8} = 16659;
q{7,9} = 0;
q{7,10} = 0;
q{7,11} = 0;
q{7,12} = 0;
q{7,13} = 0;
q{7,14} = 0;
q{7,15} = 0;
q{7,16} = 0;
q{7,17} = 0;
q{7,18} = 0;
q{7,19} = 0;
q{7,20} = 0;
q{7,21} = 0;


/* EOF */