First commit of MAMMULT code

1 files changed, 494 insertions, 0 deletions

diff --git a/dynamics/randomwalks/utils.c b/dynamics/randomwalks/utils.c
new file mode 100755
index 0000000..952fcd7
--- /dev/null
+++ b/dynamics/randomwalks/utils.c
@@ -0,0 +1,494 @@
+#include "iltree.h"
+#include <stdlib.h>
+#include <math.h>
+#include <stdio.h>
+#include <string.h>
+
+#include "utils.h"
+
+void* alloc_double(){
+  return malloc(sizeof(long double));
+}
+
+void dealloc_double(void *elem){
+  free(elem);
+}
+
+void copy_double(void *elem1, void *elem2){
+  *((long double*)elem2) = *((long double*)elem1);
+}
+
+int compare_double(void *elem1, void *elem2){
+  return *((long double*)elem1) - *((long double*)elem2);
+}
+
+void print_double(void *elem, void *fileout){
+  
+  long double k, i, j;
+  long double x;
+
+  k = *((long double*)elem);
+
+  x = (1 + sqrtl(1 + 8 * (k-1))) / 2;
+  i = floorl(x) + 1;
+  j = k - ( (i-1)*1.0 * (i-2) ) /2;
+  //printf("x: %Lf\n i: %0.0Lf j: %0.0Lf\n", x, i, j);
+  fprintf((FILE*)fileout, "%0.0Lf %0.0Lf\n", i-1, j-1);
+}
+
+iltree_t init_tree(iltree_t t, void *fileout){
+  
+  ilfunc_t funs= {
+    .alloc = alloc_double,
+    .dealloc = dealloc_double, 
+    .copy = copy_double,
+    .compare = compare_double, 
+    .print = print_double,
+    .fileout = fileout
+  };
+  
+  t = iltree_create(t);
+  iltree_set_funs(t, &funs);
+  return t;
+}
+
+
+/* @@@@ CAMBIARE IL PRIMO PARAMETRO IN UN FILE* PER RENDERLA COERENTE
+   ALLE ALTRE FUNZIONI DI READ!!!!*/
+int read_deg_distr(FILE *filein, unsigned int **degs, unsigned int **Nk, double **p){
+  
+  int n_degs = 0;
+  int size = 10;
+  char *line;
+  char buff[256];
+  int k_i, num_i;
+  double p_i;
+  char *ptr;
+
+  line = NULL;
+
+  *degs = realloc(*degs, size*sizeof(unsigned int));
+  *Nk = realloc(*Nk, size*sizeof(unsigned int));
+  *p = realloc(*p, size*sizeof(double));
+  
+
+  while(fgets(buff, 256, filein)){
+    ptr = strtok(buff, " ");
+    if (ptr[0] == '#')
+      continue;
+    k_i = atoi(ptr);
+    ptr = strtok(NULL, " " );
+    num_i = atoi(ptr);
+    ptr = strtok(NULL, " \n");
+    p_i = atof(ptr);
+    if (n_degs == size){
+      size += 10;
+      *degs = realloc(*degs, size*sizeof(unsigned int));
+      *Nk = realloc(*Nk, size*sizeof(unsigned int));
+      *p = realloc(*p, size*sizeof(double));
+    }
+    (*degs)[n_degs] = k_i;
+    (*Nk)[n_degs] = num_i;
+    (*p)[n_degs] = p_i;
+    n_degs += 1;
+  }
+  *degs = realloc(*degs, n_degs*sizeof(unsigned int));
+  *Nk = realloc(*Nk, n_degs*sizeof(unsigned int));
+  *p = realloc(*p, n_degs*sizeof(double));
+  return n_degs;
+}
+
+
+int read_deg_seq(FILE *filein, unsigned int **nodes){
+
+  int size, N, k;
+  char buff[256];
+  char *ptr;
+
+  N = 0;
+  size = 10;
+  
+  *nodes = (unsigned int*)malloc(size * sizeof(unsigned int));
+
+  while(fgets(buff, 256, filein)){
+    ptr = strtok(buff, " ");
+    if (ptr[0] == '#')
+      continue;
+    k = atoi(ptr);
+    
+    if (N == size){
+      size += 10;
+      *nodes = realloc(*nodes, size*sizeof(unsigned int));
+    }
+    (*nodes)[N] = k;
+    N += 1;
+  }
+  *nodes = realloc(*nodes, N * sizeof(unsigned int));
+  return N;
+}
+
+int read_stubs(FILE *filein, unsigned int **S){
+  
+  int size, K;
+  char buff[256];
+  char *ptr;
+  
+  K=0;
+  size = 20;
+  *S = malloc(size * sizeof(unsigned int));
+  
+  while(fgets(buff, 256, filein)){
+    if (K == size){
+      size += 20;
+      *S = realloc(*S, size*sizeof(unsigned int));
+    }
+    ptr = strtok(buff, " "); /* read the first node */
+    (*S)[K++] = atoi(ptr);
+    ptr = strtok(NULL, " "); /* read the second node */
+    (*S)[K++] = atoi(ptr);
+  }
+  *S = realloc(*S, K * sizeof(unsigned int));
+  return K;
+}
+
+/*
+ * Read a file in ij format 
+ */
+int read_ij(FILE *filein, unsigned int **I, unsigned int **J){
+  
+  unsigned int size, K;
+  char buff[256];
+  char *ptr;
+  
+  size = 20;
+  K = 0;
+  
+  *I = malloc(size * sizeof(unsigned int));
+  *J = malloc(size * sizeof(unsigned int));
+  while(fgets(buff, 256, filein)){
+    if (buff[0] == '#')
+      continue;
+    if (K == size){
+      size += 20;
+      *I = realloc(*I, size*sizeof(unsigned int));
+      *J = realloc(*J, size*sizeof(unsigned int));
+    }
+    ptr = strtok(buff, " "); /* read the first node */
+    (*I)[K] = atoi(ptr);
+    ptr = strtok(NULL, " "); /* read the second node */
+    (*J)[K] = atoi(ptr);
+    K += 1;
+  }
+  
+  *I = realloc(*I, K * sizeof(unsigned int));
+  *J = realloc(*J, K * sizeof(unsigned int));
+  return K;
+}
+
+/*funzione pesata di moreno*/
+
+int read_ij_w(FILE *filein, unsigned int **I, unsigned int **J , double **W){
+  
+  unsigned int size, K;
+  char buff[256];
+  char *ptr;
+  
+  size = 20;
+  K = 0;
+  
+  *I = malloc(size * sizeof(unsigned int));
+  *J = malloc(size * sizeof(unsigned int));
+  *W = malloc(size * sizeof(double));
+  
+  while(fgets(buff, 256, filein)){
+    if (buff[0] == '#')
+      continue;
+    if (K == size){
+      size += 20;
+      *I = realloc(*I, size*sizeof(unsigned int));
+      *J = realloc(*J, size*sizeof(unsigned int));
+      *W = realloc(*W, size*sizeof(double));
+      if (*W==NULL) {
+	printf ("Errore");
+	exit(-1);
+	}
+    }
+    ptr = strtok(buff, " "); /* read the first node */
+    (*I)[K] = atoi(ptr);
+    ptr = strtok(NULL, " "); /* read the second node */
+    (*J)[K] = atoi(ptr);
+    ptr = strtok(NULL, " "); /* read the weight  */
+    (*W)[K] = atof(ptr);    
+    K += 1;
+  }
+  
+  *I = realloc(*I, K * sizeof(unsigned int));
+  *J = realloc(*J, K * sizeof(unsigned int));
+  *W = realloc(*W, K * sizeof(double));
+  return K;
+}
+
+
+
+void read_slap(FILE *filein, unsigned int *K, unsigned int *N, 
+              unsigned int **J_slap, unsigned int **r_slap){
+  
+  unsigned int *I=NULL, *J=NULL;
+  unsigned int i, k;
+  
+  k = read_ij(filein, &I, &J);
+  *K = 2 * k;
+  I = realloc(I, 2*k * sizeof(unsigned int));
+  J = realloc(J, 2*k * sizeof(unsigned int));
+  for (i=k; i<2*k; i ++){
+    I[i] = J[i-k];
+    J[i] = I[i-k];
+  }
+  
+  *N = convert_ij2slap(I, J, 2*k, r_slap, J_slap);
+  free(I);
+  free(J);
+  return;
+}
+
+/*funzione pesata di moreno*/
+
+void read_slap_w(FILE *filein, unsigned int *K, unsigned int *N, 
+              unsigned int **J_slap, unsigned int **r_slap, double **w_slap){
+  
+  unsigned int *I=NULL, *J=NULL;
+  double *W=NULL;
+  unsigned int i, k;
+  
+  k = read_ij_w(filein, &I, &J, &W);
+  *K = 2 * k;
+  I = realloc(I, 2*k * sizeof(unsigned int));
+  J = realloc(J, 2*k * sizeof(unsigned int));
+  W = realloc(W, 2*k * sizeof(double));
+  
+  for (i=k; i<2*k; i ++){
+    I[i] = J[i-k];
+    J[i] = I[i-k];
+    W[i] = W[i-k];
+  }
+  
+  *N = convert_ij2slap_w(I, J, W, 2*k, r_slap, J_slap, w_slap);
+  free(I);
+  free(J);
+  free(W);
+  return;
+}
+
+unsigned int find_max(unsigned int *v, unsigned int N){
+
+  unsigned int i, max;
+  
+  max = v[0];
+  i = 0;
+  while(++i < N){
+    if (v[i] > max)
+      max = v[i];
+  }
+  return max;
+}
+
+
+int convert_ij2slap(unsigned int *I, unsigned int *J, unsigned int K, 
+                    unsigned int ** r_slap, unsigned int **J_slap){
+  
+  unsigned int tmp, max;
+  unsigned int N;
+  unsigned int i, pos;
+  unsigned int *p;
+
+  max = find_max(I, K) + 1;
+  tmp = find_max(J, K) + 1;
+  if (tmp > max){
+    max = tmp ;
+  }
+  
+  *r_slap = malloc( (max+1) * sizeof(unsigned int));
+  p = malloc(max * sizeof(unsigned int));
+  
+  *J_slap = malloc(K * sizeof(unsigned int));
+  
+  memset(*r_slap, 0, (max+1) * sizeof(unsigned int));
+  for(i=0; i<max + 1; i++)
+    (*r_slap)[i] = 0;
+  memset(p, 0, max * sizeof(unsigned int));
+  (*r_slap)[0] = 0;
+  //fprintf(stderr, "WARNING!!!! R_SLAP[0] NOW IS SET TO ZERO!!!!!\n");
+  for(i=0; i<K; i++){
+    (*r_slap)[ I[i] + 1] += 1;
+  }
+  for(i=1; i<=max; i++){
+    (*r_slap)[i] += (*r_slap)[i-1];
+  }
+  for(i=0; i<K; i++){
+    pos = (*r_slap) [ I[i] ] + p[ I[i] ];
+    (*J_slap)[pos] = J[i];
+    p[ I[i] ] += 1;
+  }
+  free(p);
+  return max;
+}
+
+/*funzione pesata di moreno*/
+int convert_ij2slap_w(unsigned int *I, unsigned int *J, double *W, unsigned int K, 
+                    unsigned int ** r_slap, unsigned int **J_slap,double **w_slap){
+  
+  unsigned int tmp, max;
+  unsigned int N;
+  unsigned int i, pos;
+  unsigned int *p;
+
+  max = find_max(I, K) + 1;
+  tmp = find_max(J, K) + 1;
+  if (tmp > max){
+    max = tmp ;
+  }
+  
+  *r_slap = malloc( (max+1) * sizeof(unsigned int));
+  p = malloc(max * sizeof(unsigned int));
+  
+  *J_slap = malloc(K * sizeof(unsigned int));
+  *w_slap = malloc(K * sizeof(double));
+  
+  memset(*r_slap, 0, (max+1) * sizeof(unsigned int));
+  for(i=0; i<max + 1; i++)
+    (*r_slap)[i] = 0;
+  memset(p, 0, max * sizeof(unsigned int));
+  (*r_slap)[0] = 0;
+  //fprintf(stderr, "WARNING!!!! R_SLAP[0] NOW IS SET TO ZERO!!!!!\n");
+  for(i=0; i<K; i++){
+    (*r_slap)[ I[i] + 1] += 1;
+  }
+  for(i=1; i<=max; i++){
+    (*r_slap)[i] += (*r_slap)[i-1];
+  }
+  for(i=0; i<K; i++){
+    pos = (*r_slap) [ I[i] ] + p[ I[i] ];
+    (*J_slap)[pos] = J[i];
+    
+    (*w_slap)[pos] = W[i];
+    
+    p[ I[i] ] += 1;
+  }
+  free(p);
+  return max;
+}
+
+
+
+int convert_ij2slap_N(unsigned int *I, unsigned int *J, unsigned int K,   
+                      unsigned int N, unsigned int ** r_slap, 
+                      unsigned int **J_slap){
+  
+  unsigned int tmp, max;
+  unsigned int i, pos;
+  unsigned int *p;
+
+  max = N;
+  
+  *r_slap = malloc( (max+1) * sizeof(unsigned int));
+  p = malloc(max * sizeof(unsigned int));
+  
+  *J_slap = malloc(K * sizeof(unsigned int));
+  
+  memset(*r_slap, 0, (max+1) * sizeof(unsigned int));
+  for(i=0; i<max + 1; i++)
+    (*r_slap)[i] = 0;
+  memset(p, 0, max * sizeof(unsigned int));
+  (*r_slap)[0] = 0;
+  //fprintf(stderr, "WARNING!!!! R_SLAP[0] NOW IS SET TO ZERO!!!!!\n");
+  for(i=0; i<K; i++){
+    (*r_slap)[ I[i] + 1] += 1;
+  }
+  for(i=1; i<=max; i++){
+    (*r_slap)[i] += (*r_slap)[i-1];
+  }
+  for(i=0; i<K; i++){
+    pos = (*r_slap) [ I[i] ] + p[ I[i] ];
+    (*J_slap)[pos] = J[i];
+    p[ I[i] ] += 1;
+  }
+  free(p);
+  return max;
+}
+
+
+
+/* RIVEDERE QUESTA  FUNZIONE...... PASSARE UN FILE COME ARGOMENTO E
+   USARE fprintf */
+void dump_deg_distr(unsigned int *degs, double *p, int n){
+
+  int i;
+
+  for(i=0; i<n; i++){
+    printf("%d %2.6f\n", degs[i], p[i]);
+  }
+}
+
+
+
+/* RIVEDERE QUESTA  FUNZIONE...... PASSARE UN FILE COME ARGOMENTO E
+   USARE fprintf */
+void dump_deg_seq(unsigned int *nodes, int N){
+
+  int i;
+  for(i=0; i<N; i++){
+    printf("%d: %d\n", i, nodes[i]);
+  }
+}
+
+void dump_edges(iltree_t t){
+
+  iltree_view_pre(t);
+}
+
+FILE* openfile_or_exit(char *filename, char *mode, int exitcode){
+  
+  FILE *fileout;
+  char error_str[256];
+  
+  fileout = fopen(filename, mode);
+  if (!fileout){
+    sprintf(error_str, "Error opening file %s", filename);
+    perror(error_str);
+    exit(exitcode);
+  }
+  return fileout;
+}
+
+inline int compare_int(const void *x1, const void *x2){
+  return *((unsigned int*)x1) - *((unsigned int*)x2);
+}
+
+void write_edges(FILE *fileout, unsigned int *J_slap, 
+                 unsigned int *r_slap, unsigned int N){
+  
+  unsigned int i, j;
+  
+  for(i=0; i<N; i++){
+    for (j=r_slap[i]; j<r_slap[i+1]; j++){
+      if (J_slap[j] > i){
+        fprintf(fileout, "%d %d\n", i, J_slap[j]);
+      }
+    }
+  }
+}
+  
+
+/* Check if j is a neighbour of i */
+int is_neigh(unsigned int *J_slap, unsigned int *r_slap, unsigned int N, 
+             unsigned int i, unsigned int j){
+  
+  unsigned int l;
+  unsigned int count;
+  count = 0;
+  for(l=r_slap[i]; l<r_slap[i+1]; l++){
+    if (J_slap[l] == j)
+      count ++;
+  }
+  return count;
+}