First commit on github -- NetBunch 1.0

4 files changed, 1056 insertions, 0 deletions

diff --git a/src/conf/Makefile.am b/src/conf/Makefile.am
new file mode 100644
index 0000000..b70fa7c
--- /dev/null
+++ b/src/conf/Makefile.am
@@ -0,0 +1,10 @@
+include ../common.mk 
+bin_PROGRAMS = conf_model_deg conf_model_deg_nocheck
+conf_model_deg_SOURCES = conf_model_deg.c ../utils/utils.c ../utils/iltree.c \
+	../utils/iltree_double.c ../include/utils.h ../include/iltree.h \
+../include/iltree_double.h ../include/utils.h
+conf_model_deg_LDADD = -lm
+conf_model_deg_nocheck_SOURCES = conf_model_deg_nocheck.c ../utils/utils.c \
+	../utils/iltree.c ../utils/iltree_double.c ../include/iltree.h \
+../include/iltree_double.h 
+conf_model_deg_nocheck_LDADD = -lm
diff --git a/src/conf/Makefile.in b/src/conf/Makefile.in
new file mode 100644
index 0000000..eaec7dc
--- /dev/null
+++ b/src/conf/Makefile.in
@@ -0,0 +1,605 @@
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+	    if test -d "$(distdir)/$$file"; then \
+	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
+	    fi; \
+	    if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
+	      cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
+	      find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
+	    fi; \
+	    cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
+	  else \
+	    test -f "$(distdir)/$$file" \
+	    || cp -p $$d/$$file "$(distdir)/$$file" \
+	    || exit 1; \
+	  fi; \
+	done
+check-am: all-am
+check: check-am
+all-am: Makefile $(PROGRAMS)
+installdirs:
+	for dir in "$(DESTDIR)$(bindir)"; do \
+	  test -z "$$dir" || $(MKDIR_P) "$$dir"; \
+	done
+install: install-am
+install-exec: install-exec-am
+install-data: install-data-am
+uninstall: uninstall-am
+
+install-am: all-am
+	@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
+
+installcheck: installcheck-am
+install-strip:
+	if test -z '$(STRIP)'; then \
+	  $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
+	    install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
+	      install; \
+	else \
+	  $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
+	    install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
+	    "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'" install; \
+	fi
+mostlyclean-generic:
+
+clean-generic:
+
+distclean-generic:
+	-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
+	-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
+	-rm -f ../utils/$(DEPDIR)/$(am__dirstamp)
+	-rm -f ../utils/$(am__dirstamp)
+
+maintainer-clean-generic:
+	@echo "This command is intended for maintainers to use"
+	@echo "it deletes files that may require special tools to rebuild."
+clean: clean-am
+
+clean-am: clean-binPROGRAMS clean-generic mostlyclean-am
+
+distclean: distclean-am
+	-rm -rf ../utils/$(DEPDIR) ./$(DEPDIR)
+	-rm -f Makefile
+distclean-am: clean-am distclean-compile distclean-generic \
+	distclean-tags
+
+dvi: dvi-am
+
+dvi-am:
+
+html: html-am
+
+html-am:
+
+info: info-am
+
+info-am:
+
+install-data-am:
+
+install-dvi: install-dvi-am
+
+install-dvi-am:
+
+install-exec-am: install-binPROGRAMS
+
+install-html: install-html-am
+
+install-html-am:
+
+install-info: install-info-am
+
+install-info-am:
+
+install-man:
+
+install-pdf: install-pdf-am
+
+install-pdf-am:
+
+install-ps: install-ps-am
+
+install-ps-am:
+
+installcheck-am:
+
+maintainer-clean: maintainer-clean-am
+	-rm -rf ../utils/$(DEPDIR) ./$(DEPDIR)
+	-rm -f Makefile
+maintainer-clean-am: distclean-am maintainer-clean-generic
+
+mostlyclean: mostlyclean-am
+
+mostlyclean-am: mostlyclean-compile mostlyclean-generic
+
+pdf: pdf-am
+
+pdf-am:
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+ps: ps-am
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+ps-am:
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+uninstall-am: uninstall-binPROGRAMS
+
+.MAKE: install-am install-strip
+
+.PHONY: CTAGS GTAGS TAGS all all-am check check-am clean \
+	clean-binPROGRAMS clean-generic cscopelist-am ctags ctags-am \
+	distclean distclean-compile distclean-generic distclean-tags \
+	distdir dvi dvi-am html html-am info info-am install \
+	install-am install-binPROGRAMS install-data install-data-am \
+	install-dvi install-dvi-am install-exec install-exec-am \
+	install-html install-html-am install-info install-info-am \
+	install-man install-pdf install-pdf-am install-ps \
+	install-ps-am install-strip installcheck installcheck-am \
+	installdirs maintainer-clean maintainer-clean-generic \
+	mostlyclean mostlyclean-compile mostlyclean-generic pdf pdf-am \
+	ps ps-am tags tags-am uninstall uninstall-am \
+	uninstall-binPROGRAMS
+
+.PRECIOUS: Makefile
+
+
+# Tell versions [3.59,3.63) of GNU make to not export all variables.
+# Otherwise a system limit (for SysV at least) may be exceeded.
+.NOEXPORT:
diff --git a/src/conf/conf_model_deg.c b/src/conf/conf_model_deg.c
new file mode 100644
index 0000000..70df8a9
--- /dev/null
+++ b/src/conf/conf_model_deg.c
@@ -0,0 +1,259 @@
+/**
+ *  This program 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 program 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.
+ *
+ *  You should have received a copy of the GNU General Public License
+ *  along with this program.  If not, see
+ *  <http://www.gnu.org/licenses/>.
+ *
+ *  (c) Vincenzo Nicosia 2009-2017 -- <v.nicosia@qmul.ac.uk>
+ * 
+ *  This file is part of NetBunch, a package for complex network
+ *  analysis and modelling. For more information please visit:
+ *
+ *             http://www.complex-networks.net/
+ *
+ *  If you use this software, please add a reference to 
+ *
+ *               V. Latora, V. Nicosia, G. Russo             
+ *   "Complex Networks: Principles, Methods and Applications"
+ *              Cambridge University Press (2017) 
+ *                ISBN: 9781107103184
+ *
+ ***********************************************************************
+ *
+ *  This program samples a simple graph (i.e., without self-loops
+ *  and/or multiple edges) from the configuration model, using the
+ *  degree sequence provided as input.
+ *
+ */
+
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <time.h>
+#include "utils.h"
+#include "iltree_double.h"
+
+
+#define MAXREJECTS 1000000
+
+
+/* Usage */
+void usage(char *argv[]){
+  printf("********************************************************************\n"
+         "**                                                                **\n"
+         "**                   -*-  conf_model_deg  -*-                     **\n"
+         "**                                                                **\n"
+         "**  Sample a simple graph from the configuration model associated **\n"
+         "**  to the degree sequence provided as input.                     **\n"
+         "**                                                                **\n"
+         "**  The degree sequence is a file with format:                    **\n"
+         "**                                                                **\n"
+         "**                           k_1                                  **\n"
+         "**                           k_2                                  **\n"
+         "**                           k_3                                  **\n"
+         "**                           ....                                 **\n"
+         "**                           k_N                                  **\n"
+         "**                                                                **\n"
+         "**   where 'k_i' is the degree of the i-th node. The program      **\n"
+         "**   prints on output the edge-list of the resulting graph.       **\n"
+         "**                                                                **\n"
+         "**   The second (optional) parameter 'threshold' indicates the    **\n"
+         "**   number of edge stubs that are allowed to remain unmatched    **\n"
+         "**   in the final graph. This parameter might be used to          **\n"
+         "**   obtain a graph from a too-constrained degree sequence, e.g., **\n"
+         "**   a power-law sequence whose maximum degree is larger than     **\n"
+         "**   the structural cut-off.                                      **\n"
+         "**                                                                **\n"
+         "********************************************************************\n"
+         " This is Free Software - You can use and distribute it under \n"
+         " the terms of the GNU General Public License, version 3 or later\n\n"
+         " Please visit http://www.complex-networks.net for more information\n\n"
+         " (c) Vincenzo Nicosia 2010-2017 (v.nicosia@qmul.ac.uk)\n"
+         "********************************************************************\n\n"
+         );
+  printf("Usage: %s <degs> [<threshold>]\n\n" , argv[0]);
+}
+
+
+unsigned int count_stubs(unsigned int *nodes, int N){
+  
+  int i;
+  unsigned int cnt;
+
+  cnt = 0;
+  for (i=0; i<N; i ++){
+    cnt += nodes[i];
+  }
+  return cnt;
+}
+
+
+void sample_graph_conf(unsigned int *nodes, int N, iltree_t *t, 
+                           unsigned int thresh){
+  
+  unsigned int S;
+  unsigned int i, j;
+  unsigned int n_stubs;
+  unsigned int *stubs;
+  unsigned int countreject;
+  unsigned int L1, L2, I1, I2, tmp;
+  long double k;
+  FILE *tmp_file;
+  
+  n_stubs = count_stubs(nodes, N);
+  
+  if (n_stubs %2){
+    fprintf(stderr, "The sequence is not even!\n");
+    exit(3);
+  }
+  /* ind = malloc(n_stubs * sizeof(unsigned int)); */
+  /* stub2node = malloc(n_stubs * sizeof(unsigned int)); */
+  
+  stubs = malloc(n_stubs * sizeof(unsigned int));
+  
+  
+  do{
+    countreject = 0;
+    S = 0;
+    /*
+     * We first initialize the stubs
+     *
+     * This is needed only before the first iteration, indeed.... 
+     *
+     */
+    for(i=0; i<N; i ++){
+      for(j=0; j<nodes[i]; j ++){
+        stubs[S] = i;
+        S += 1;
+      }
+    }
+    while (S > 0 && countreject < MAXREJECTS){
+      /* sample the first stub */
+      L1 = rand() % S;
+      I1 = stubs[L1];
+      S -= 1;
+
+      /* sample the second stub */
+      L2 = rand() % S;
+      I2 = stubs[L2];
+      S -= 1;
+
+      if (L1 == L2){/* If L1 and L2 are the same element, discard the
+                       sample */
+        /* reset S to the value it had before */
+        S += 2;
+        continue;
+      }
+      
+      if (I1 == I2){
+        /* reject the pair: it's the same node! */
+        countreject += 1;
+        /* reset S to the value it had before */
+        S += 2;
+        continue;
+      }
+      
+    
+      if (I1 > I2){ /* we require that I1 < I2 */
+        tmp = I2;
+        I2 = I1;
+        I1 = tmp;
+      }
+      k = 1.0 * (I2)* (I2-1) / 2 + I1 + 1; /* This number represents the
+                                        couple I1, I2 (I1 < I2)*/
+      if (!iltree_lookup(*t, &k)){ /* The element "k" is not yet present in the BST*/
+        /* We can accept the new pair... */
+        /* ...so we insert it into the tree */
+        iltree_insert(*t, &k);
+        /* remove the two stubs */
+        tmp = stubs[L1];
+        stubs[L1] = stubs[S+1];
+        stubs[S+1] = tmp;
+
+        tmp = stubs[L2];
+        stubs[L2] = stubs[S];
+        stubs[S] = tmp;
+      }
+      else{/* reject the pair */
+        /* reset S to the value it had before */
+        countreject += 1;
+        S += 2;
+      }
+    }
+    
+    /* Let's check if we got a graph....*/
+    if (countreject >= MAXREJECTS){
+      if (S <= thresh){
+        fprintf(stderr, "Found a graph (unmatched stubs: %d <= threshold: %d)\n", 
+                S, thresh);
+        break;
+      }
+      else{
+        fprintf(stderr, "Graph not found (unmatched stubs: %d > threshold: %d)\n", 
+                S, thresh);
+        S = 0;
+        countreject = 0;
+        tmp_file = iltree_get_fileout(*t);
+        iltree_destroy(*t);
+        *t = NULL;
+        *t = iltree_double_init(*t, tmp_file);
+      }
+    }
+    else{
+      fprintf(stderr, "Found a graph!\n");
+      break;
+    }
+  } while(1);
+  free(stubs);
+}
+
+
+
+int main(int argc, char *argv[]){
+  
+  unsigned int  *nodes= NULL;
+  int N;
+  iltree_t t = NULL;
+  FILE *filein;
+  unsigned int thresh;
+
+  if (argc < 2){
+    usage(argv);
+    exit(1);
+  }
+  
+  srand(time(NULL));
+
+  if (!strcmp(argv[1], "-")){
+    /* take the input from STDIN */
+    filein = stdin;
+  }
+  else {
+    filein = openfile_or_exit(argv[1], "r", 2);
+  }
+  
+  if (argc > 2) /* Set the threshold */
+    thresh = atoi(argv[2]);
+  else
+    thresh = 0;
+  
+  
+  t = iltree_double_init(t, stdout);
+  
+  N = read_deg_seq(filein, &nodes);
+  sample_graph_conf(nodes, N, &t, thresh);
+  iltree_double_dump_edges(t);
+  fclose(filein);
+  free(nodes);
+  iltree_destroy(t);
+}
diff --git a/src/conf/conf_model_deg_nocheck.c b/src/conf/conf_model_deg_nocheck.c
new file mode 100644
index 0000000..26f89d1
--- /dev/null
+++ b/src/conf/conf_model_deg_nocheck.c
@@ -0,0 +1,182 @@
+/**
+ *  This program 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 program 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.
+ *
+ *  You should have received a copy of the GNU General Public License
+ *  along with this program.  If not, see
+ *  <http://www.gnu.org/licenses/>.
+ *
+ *  (c) Vincenzo Nicosia 2009-2017 -- <v.nicosia@qmul.ac.uk>
+ * 
+ *  This file is part of NetBunch, a package for complex network
+ *  analysis and modelling. For more information please visit:
+ *
+ *             http://www.complex-networks.net/
+ *
+ *  If you use this software, please add a reference to 
+ *
+ *               V. Latora, V. Nicosia, G. Russo             
+ *   "Complex Networks: Principles, Methods and Applications"
+ *              Cambridge University Press (2017) 
+ *                ISBN: 9781107103184
+ *
+ ***********************************************************************
+ *
+ *  This program samples a multigraph (i.e., a graph that might
+ *  contain self-loops and/or multiple edges) from the configuration
+ *  model, using the degree sequence provided as input.
+ *
+ */
+
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <time.h>
+#include "utils.h"
+#include "iltree.h"
+
+
+
+/* Usage*/
+void usage(char *argv[]){
+  printf("********************************************************************\n"
+         "**                                                                **\n"
+         "**                -*-  conf_model_deg_nocheck  -*-                **\n"
+         "**                                                                **\n"
+         "**  Sample a multigraph from the configuration model associated   **\n"
+         "**  to the degree sequence provided as input.                     **\n"
+         "**                                                                **\n"
+         "**  The degree sequence is a file with format:                    **\n"
+         "**                                                                **\n"
+         "**                           k_1                                  **\n"
+         "**                           k_2                                  **\n"
+         "**                           k_3                                  **\n"
+         "**                           ....                                 **\n"
+         "**                           k_N                                  **\n"
+         "**                                                                **\n"
+         "**   where 'k_i' is the degree of the i-th node. The program      **\n"
+         "**   prints on output the edge-list of the resulting graph. The   **\n"
+         "**   final graph might contain self-loops and multiple edges.     **\n"
+         "**                                                                **\n"
+         "********************************************************************\n"
+         " This is Free Software - You can use and distribute it under \n"
+         " the terms of the GNU General Public License, version 3 or later\n\n"
+         " Please visit http://www.complex-networks.net for more information\n\n"
+         " (c) Vincenzo Nicosia 2010-2017 (v.nicosia@qmul.ac.uk)\n"
+         "********************************************************************\n\n"
+         );
+  printf("Usage: %s <degs>\n\n" , argv[0]);
+}
+
+
+unsigned int count_stubs(unsigned int *nodes, int N){
+  
+  int i;
+  unsigned int cnt;
+
+  cnt = 0;
+  for (i=0; i<N; i ++){
+    cnt += nodes[i];
+  }
+  return cnt;
+}
+
+
+/* sample a multigraph from the configuration model */
+
+void sample_graph_conf_nocheck(unsigned int *nodes, int N){
+  
+  unsigned int S;
+  unsigned int i, j;
+  unsigned int n_stubs;
+  unsigned int *stubs;
+  unsigned int L1, L2, I1, I2, tmp;
+  
+  n_stubs = count_stubs(nodes, N);
+  
+  if (n_stubs %2){
+    fprintf(stderr, "The sequence is not even!\n");
+    exit(3);
+  }
+
+  stubs = malloc(n_stubs * sizeof(unsigned int));
+  
+  /*
+   * We first initialize the stubs
+   */
+  
+  S = 0;
+  for(i=0; i<N; i ++){
+    for(j=0; j<nodes[i]; j ++){
+      stubs[S] = i;
+      S += 1;
+    }
+  }
+  while (S > 0){
+    /* sample the first stub */
+    L1 = rand() % S;
+    I1 = stubs[L1];
+    S -= 1;
+
+    /* sample the second stub */
+    L2 = rand() % S;
+    I2 = stubs[L2];
+    S -= 1;
+    
+    if (L1 == L2){/* If L1 and L2 are the same element, discard the
+                     sample */
+      /* reset S to the value it had before */
+      S += 2;
+      continue;
+    }
+
+    if (I1 > I2){
+      tmp = I2;
+      I2 = I1;
+      I1 = tmp;
+    }
+    
+    printf("%d %d\n", I1, I2);
+    /* And then we remove the two stubs */
+    stubs[L1] = stubs[S+1];
+    stubs[L2] = stubs[S];
+  }
+  free(stubs);
+}
+
+
+
+int main(int argc, char *argv[]){
+  
+  unsigned int  *nodes= NULL;
+  int N;
+  FILE *filein;
+
+  if (argc < 2){
+    usage(argv);
+    exit(1);
+  }
+  
+  srand(time(NULL));
+
+  if (!strcmp(argv[1], "-")){
+    /* take the input from STDIN */
+    filein = stdin;
+  }
+  else {
+    filein = openfile_or_exit(argv[1], "r", 2);
+  }
+  
+  N = read_deg_seq(filein, &nodes);
+  fclose(filein);
+  sample_graph_conf_nocheck(nodes, N);
+  free(nodes);
+}