/*========================================================       file : initial.c       purpose : create initial population and initialize parameters   developed : 1991     author : Kalyanmoy Deb   modified : Alex Kosorukoff (AK)==========================================================*/#include "mga.ext"void get_input()/* read and set input parameters */{	register int i;	FILE *fp, *finput, *fopen();	long clock, time();	char *ctime(), msg[PAGEWIDTH];	gen_file("Parameters",         Inputfilename,    "parameters");	gen_file("Era",                Erafilename,      "era");	gen_file("Objective function", Objfilename,      "subfunc");	gen_file("Template",           Templatefilename, "template");	gen_file("Partition input",    Partinfilename,   "partitions");	gen_file("Pop record input",   Poprinfilename,   "poprecin");	gen_file("Extra members",      Extrafilename,    "extra");	gen_file("Output",             Outputfilename,   "output");	gen_file("Pop record output",  Poproutfilename,  "poprecout");	gen_file("Partition output",   Partoutfilename,  "partout");	gen_file("Plotting",           Plotfilename,     "plot");	/*  check input files  */	check_input_file(Inputfilename);	/*  read input parameters  */	finput = fopen(Inputfilename, "r");	if (fscanf(finput, FORMAT_1, VARS_1) != 17) {		sprintf(msg,"Error in the input file: parameters.\n");		print_error(msg);	}	check_input_file(Erafilename);	check_input_file(Objfilename);	if (extrapopflag)		check_input_file(Extrafilename);	/*  open output files  */	scratch_file(Outputfilename);	if (plotstatflag)		scratch_file(Plotfilename);	if (popprintflag) {		check_input_file(Poprinfilename);		scratch_file(Poproutfilename);	}	if (partitionflag) {		check_input_file(Partinfilename);		scratch_file(Partoutfilename);	}	/*  set up the clock  */	fp = fopen(Outputfilename, "a");	time(&clock);	fprintf(fp,"Start-up time is : %s\n",ctime(&clock));	fclose(fp);	/*  generate random numbers  */	randomize();	/*  get the template  */	get_template();	fscanf(finput,"Copies (10 1 1) =");	if(!(copies = (int *)malloc((max_era+1) * sizeof(int))))	{		sprintf(msg,"Insufficient memory for variable, copies.\n");		print_error(msg);	}	for (i = era; i <= max_era; i++) {		copies[i] = 1;     /* default */		fscanf(finput,"%d",&copies[i]);	}	fclose(finput);	/*  get the objective function information  */	function_evaluations = 0.0;	objfunc_info();	/*  get the auxiliary information for report  */	if (partitionflag)  		partition_info();	if (popprintflag)		poprec_info();	/* writes the problem information */	problem_rep();}void initialize()/* initialize parameters */{	char msg[PAGEWIDTH];	if (thresholdingflag)		shuffle_num = problem_length;	if (popprintflag)	{		/* set the counter to the first generation */		nextpopstatgen = sortpopstatgen[0];	}	/*  get other input parameters  */	if (fscanf(fin, FORMAT_2, VARS_2) != 2) {		sprintf(msg,"Error in input file era.\n");		print_error(msg);	}	/*  generate initial population, get stats, and write report  */	initialize_pop();	statistics(oldpop);	/*  set up the population sizing in primordial phase  */	setup_popsize();	initreport();}void initialize_pop()/* setup parameters for initial population */{	register int i;	long member_id = 0;	int temp_order, allele_combo;	long max_size, total_size = 0, population_size[MAX_ORDER];	char msg[PAGEWIDTH];	gen = 0;	stopmgaflag = 0;	/* reset the population size array */	for (i=0; i <= era; i++) population_size[i] = 0;	/* only order era strings are created */	order = temp_order = era;	/* but if tiebreaking is on, 	   all strings of order less than era are created */	if (tiebreakingflag) {		order = temp_order = 1;	}	while (order <= era) {	 	/* if reduction in initpop is desired */		if (r_initpop_flag)			allele_combo = 1;		else			allele_combo = power(2,order);		max_size = copies[order] * allele_combo * \				choose(problem_length,order);		population_size[order] = max_size;		total_size += max_size;		order++;	}	/*  storage allocation for */	/*  population array  */	popsize=total_size;	/* AK */	if(!(newpop=(struct INDIVIDUAL *)malloc(total_size * \				sizeof(struct INDIVIDUAL))))	{		sprintf(msg,"Insufficient memory for newpop.\n");		print_error(msg);	}	if(!(oldpop=(struct INDIVIDUAL *)malloc(total_size * \				sizeof(struct INDIVIDUAL))))	{		sprintf(msg,"Insufficient memory for oldpop.\n");		print_error(msg);	}	/*  storage for shuffle array  */	if (!(shuffle = (int *)malloc(total_size*sizeof(int *))))	{		sprintf(msg,"Insufficient memory for shuffle array.\n");		print_error(msg);	}	order = temp_order;	while (order <= era) {		initpop(&member_id, population_size[order]);		order++;	}	if (extrapopflag)		extra_pop(&member_id);	order--;	storepop(&best_indv,era);	copy_chrom(oldpop[0],&best_indv);	popsize = member_id;	templatefitness = objfunc(template);}void extra_pop(last_member)long *last_member;/*  creates extra population members  */{	register int i,j,k,m;	int flag=0, count=0, extra_size=0;	long size, cnt;	int patsize[MAX_PARTITIONS], extra_copies[MAX_PARTITIONS];	GENE_ID pattern[MAX_PARTITIONS][MAX_ORDER];	ALLELES allele_list[MAX_ORDER];	struct GENE *tailold;	char dummy[PAGEWIDTH];	FILE *fp, *fopen();	fp = fopen(Extrafilename,"r");	get_string(fp, dummy, PAGEWIDTH);	/* read gene information */	while (fscanf(fp,"%d",&patsize[count]) == 1) {		for (i=0; i<patsize[count]; i++)			fscanf(fp,"%d",&pattern[count][i]);		fscanf(fp,"%d\n",&extra_copies[count]);		extra_size += extra_copies[count] * power(2,patsize[count]);		count++;        }	fclose(fp);	size = (*last_member) + extra_size;	/* reallocate memory size and allocate memory for extra individuals */	reallocate_memory(size);	cnt = (*last_member);	for (i=0; i<count; i++) {		for (j=0; j<patsize[i]; j++)			allele_list[j] = 0;		for (j=0; j<power(2,patsize[i]); j++) {                        if (j != 0)				next_allele_comb(allele_list,patsize[i],patsize[i]);			for (k=0; k<extra_copies[i]; k++) {				storepop(&(oldpop[cnt]),patsize[i]);				storepop(&(newpop[cnt]),patsize[i]);				tailold = oldpop[cnt].firstgene;				tailold->genenumber = pattern[i][0];				tailold->allele = allele_list[0];				for (m=1; m<patsize[i]; m++) {					tailold = tailold->nextgene;					tailold->genenumber = pattern[i][m];					tailold->allele = allele_list[m];				}				fill_chrom(&(oldpop[cnt]));				oldpop[cnt].fitness = \					objfunc(oldpop[cnt].fullchrom);				cnt++;			}		}	}        *last_member = cnt;}void randomtemplate(temp)unsigned *temp;/*  create a random template  */{	register int i,j;	unsigned mask = 1;	for (i = 0; i < bytesize; i++)	{		temp[i] = 0;		for (j = 0; j < bytelimit[i]; j++)		{			if (flip(0.5))				temp[i] |= mask;			if (j < bytelimit[i]-1)				temp[i] <<= 1;		}	}}void next_genic_comb(list, n)GENE_ID *list;int n;/*    calculates the next gene combination  */{	register int j, s, k;	BOOLEAN exitflag = 0;	int pos;	pos = n-1;	if (list[pos] < problem_length - 1)		(list[pos])++;	else	{		for (j = pos; j > 0 && !exitflag; j--)		{			if (list[j-1] < problem_length - pos + j - 2)			{				(list[j-1])++;				for (s = j; s <= pos; s++)				{					list[s] = list[j-1] + s - j + 1;					exitflag = 1;				}			}		}	}}void next_allele_comb(list,size,len)ALLELES *list;int size, len;/*  calculates the next bit combination  */{	register int i;	int total=0, pos;	ALLELES allele_max = 1;	pos = size-1;	for (i = 0; i < pos+1; i++)	{		if (list[i])  total++;	}	if (list[pos] < allele_max)		(list[pos])++;	else if (total == pos+1)		reset_list(list,size);	else if ((list[pos-1] >= allele_max) && (list[pos] >= allele_max))		next_allele_comb(list, pos, len);	else if (list[pos] >= allele_max)	{		for (i = pos; i < len; i++)			list[i] = 0;		(list[pos-1])++;	}}void storepop(pop, n)struct INDIVIDUAL *pop;int n;/*  allocates memory for an individual */{	register int j;	struct GENE *tail;	char msg[PAGEWIDTH];	/*  storage allocation for */	/*  genes */	if(!((*pop).firstgene = (struct GENE *)malloc(sizeof(struct GENE))))	{		sprintf(msg,"Insufficient memory for firstgene.\n");		print_error(msg);	}	/*  initialize genes  */	tail = (*pop).firstgene;	/*  for each gene  */	for (j = 1; j < n; j++)	{		if (!(tail->nextgene = (struct GENE *)malloc(sizeof(struct GENE))))		{			sprintf(msg,"Insufficient memory for making a gene.\n");			print_error(msg);		}		tail = tail->nextgene;	}	/*  assign last gene pointer and chromosome length */	(*pop).lastgene = tail;	tail->nextgene = NIL;	(*pop).chromlen = n;	(*pop).genelen  = n;	/*  allocate storage for fullchrom  */	if(!((*pop).fullchrom = (unsigned *)malloc(bytesize*sizeof(unsigned))))	{		sprintf(msg,"Insufficient memory for fullchrom.\n");		print_error(msg);	}	/*  allocate storage for fullgene  */	if(!((*pop).fullgene = (unsigned *)malloc(bytesize*sizeof(unsigned))))	{		sprintf(msg,"Insufficient memory for fullgene.\n");		print_error(msg);	}}void initpop(last_member, n)long *last_member;long n;/*  generates initial population  */{	register int i, j, m, count;	long current_size;	int allele_combo;	GENE_ID genenumber_list[MAX_ORDER];	ALLELES allele_list[MAX_ORDER];	struct GENE *tailold;	char msg[PAGEWIDTH];        sprintf(msg,"   Initpop entered for order %d",order);	TRACE(msg);        /* check if reduced population is desired */	if (r_initpop_flag) 		allele_combo = 1;	else