First commit on github -- NetBunch 1.0

3 files changed, 797 insertions, 0 deletions

diff --git a/src/dms/Makefile.am b/src/dms/Makefile.am
new file mode 100644
index 0000000..935680c
--- /dev/null
+++ b/src/dms/Makefile.am
@@ -0,0 +1,4 @@
+include ../common.mk 
+bin_PROGRAMS = dms 
+dms_SOURCES = dms.c ../utils/utils.c ../utils/cum_distr.c ../include/utils.h ../include/cum_distr.h
+dms_LDADD = -lm
diff --git a/src/dms/Makefile.in b/src/dms/Makefile.in
new file mode 100644
index 0000000..046e4c8
--- /dev/null
+++ b/src/dms/Makefile.in
@@ -0,0 +1,582 @@
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+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:
+
+ps: ps-am
+
+ps-am:
+
+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/dms/dms.c b/src/dms/dms.c
new file mode 100644
index 0000000..da3ab63
--- /dev/null
+++ b/src/dms/dms.c
@@ -0,0 +1,211 @@
+/**
+ *  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 implements the Dorogovtsev-Samukhin-Mendes preferential
+ * attachment, where the attachment probability is:
+ *
+ * \Pi_{i->j} \propto k_j + a
+ *
+ * Here a > -m is a tunable parameter. The resulting network has a
+ * powerlaw degree distribution with exponent:
+ *
+ * \gamma = 3 + a/m
+ *
+ *  References:
+ *  
+ * [1] S. N. Dorogovtsev, J. F. F. Mendes, A. N. Samukhin. "Structure
+ *     of Growing Networks with Preferential Linking".
+ *     Phys. Rev. Lett. 85 (2000), 4633-4636. 
+ *
+ */
+
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <time.h>
+
+#include "cum_distr.h"
+
+
+void usage(char *argv[]){
+  printf("********************************************************************\n"
+         "**                                                                **\n"
+         "**                        -*-    dms    -*-                       **\n"
+         "**                                                                **\n"
+         "**   Grow a scale-free network of 'N' nodes using the modified    **\n"
+         "**   linear preferential attachment model proposed by             **\n"
+         "**   Dorogovtsev-Mendes-Samukhin.                                 **\n"
+         "**                                                                **\n"
+         "**   The initial network is a clique of 'n0' nodes, and each new  **\n"
+         "**   node creates 'm' edges. The attachment probability is of     **\n"
+         "**   the form:                                                    **\n"
+         "**                                                                **\n"
+         "**            P(i->j) ~ k_j + a                                   **\n"
+         "**                                                                **\n"
+         "**   where a > -m is the fourth parameter. The resulting          **\n"
+         "**   network will have a power-law degree distribution with       **\n"
+         "**   exponent                                                     **\n"
+         "**                                                                **\n"
+         "**       gamma = 3 + a/m                                          **\n"
+         "**                                                                **\n"
+         "**   The program prints on STDOUT the edge-list of the final      **\n"
+         "**   graph.                                                       **\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"
+         " (c) Vincenzo Nicosia 2009-2017 (v.nicosia@qmul.ac.uk)\n\n"
+         "********************************************************************\n\n"
+         );
+  printf("Usage: %s <N> <m> <n0> <a>\n", argv[0]);
+
+}
+
+
+
+int init_network(unsigned int *I, unsigned int *J, int n0, 
+                 double a, cum_distr_t *d){
+  
+  unsigned int n, i,  S_num;
+  
+  S_num = 0;
+  for(n=0; n<n0; n++){
+    for(i=n+1; i<n0; i++){
+      I[S_num] = n;
+      J[S_num] = i % n0;
+      S_num += 1;
+    }
+    cum_distr_add(d, n, n0+a);
+  }
+  return S_num;
+}
+
+int already_neighbour(unsigned int *J, int S_num, int j, int dest){
+
+   int i;
+
+   for(i=S_num; i< S_num + j; i ++){
+     if (J[i] == dest)
+       return 1;
+   }
+   return 0;
+}
+
+
+
+int dms(unsigned int *I, unsigned int *J, unsigned int N, 
+         unsigned int m, unsigned int n0,  double a){
+  
+  cum_distr_t *d = NULL;
+  unsigned int n, j, dest, S_num;
+  
+  d = cum_distr_init(N * m);
+  
+  S_num = init_network(I, J, n0, a, d);
+  
+  
+  n = n0;
+  while (n<N){
+    for(j=0; j<m; j++){
+      I[S_num+j] = n;
+      dest = cum_distr_sample(d);
+      while(already_neighbour(J, S_num, j, dest)){
+        dest = cum_distr_sample(d);
+      }
+      J[S_num + j] = dest;
+    }
+    cum_distr_add(d, n, m + a);
+    for (j=0; j<m; j++){
+      cum_distr_add(d, J[S_num + j], 1);
+    }
+    S_num += m;
+    n += 1;
+  }
+  cum_distr_destroy(d);
+  return S_num;
+}
+
+
+
+int main(int argc, char *argv[]){
+  
+  int N, m, n0, K, i;
+  unsigned int *I, *J;
+  double a;
+  
+  if (argc < 5){
+    usage(argv);
+    exit(1);
+  }
+  
+  N = atoi(argv[1]);
+  m = atoi(argv[2]);
+  n0 = atoi(argv[3]);
+  a = atof(argv[4]);
+
+  srand(time(NULL));
+
+  if (N < 1){
+    fprintf(stderr, "N must be positive\n");
+    exit(1);
+  }
+  if(m > n0){
+    fprintf(stderr, "n0 cannot be smaller than m\n");
+    exit(1);
+
+  }
+  if (n0<1){
+    fprintf(stderr, "n0 must be positive\n");
+    exit(1);
+  }
+  
+  if (m < 1){
+    fprintf(stderr, "m must be positive\n");
+    exit(1);
+  }
+
+  if (a < -m){
+    fprintf(stderr, "a must be larger than -m\n");
+    exit(1);
+  }
+  
+  
+  I = malloc(N * m * sizeof(unsigned int));
+  J = malloc(N * m * sizeof(unsigned int));
+  
+  K = dms(I, J, N, m, n0, a);
+  
+  for(i=0; i<K; i++){
+    printf("%d %d\n", J[i], I[i]);
+  }
+  free(I);
+  free(J);
+}