From 3aee2fd43e3059a699af2b63c6f2395e5a55e515 Mon Sep 17 00:00:00 2001 From: KatolaZ Date: Wed, 27 Sep 2017 15:06:31 +0100 Subject: First commit on github -- NetBunch 1.0 --- src/Makefile.am | 5 + src/Makefile.in | 580 +++++++++++++++++++++++++ src/TODO | 24 ++ src/ba/Makefile.am | 3 + src/ba/Makefile.in | 564 ++++++++++++++++++++++++ src/ba/ba.c | 185 ++++++++ src/bb_fitness/Makefile.am | 5 + src/bb_fitness/Makefile.in | 584 +++++++++++++++++++++++++ src/bb_fitness/bb_fitness.c | 241 +++++++++++ src/bbv/Makefile.am | 4 + src/bbv/Makefile.in | 578 +++++++++++++++++++++++++ src/bbv/bbv.c | 335 +++++++++++++++ src/betweenness/Makefile.am | 7 + src/betweenness/Makefile.in | 590 +++++++++++++++++++++++++ src/betweenness/README | 8 + src/betweenness/bet_dependency.c | 224 ++++++++++ src/betweenness/betweenness.c | 316 ++++++++++++++ src/clust/Makefile.am | 6 + src/clust/Makefile.in | 588 +++++++++++++++++++++++++ src/clust/clust.c | 162 +++++++ src/clust/clust_w.c | 161 +++++++ src/cnm/Makefile.am | 7 + src/cnm/Makefile.in | 591 +++++++++++++++++++++++++ src/cnm/bst_pq.c | 808 +++++++++++++++++++++++++++++++++++ src/cnm/bst_pq.h | 159 +++++++ src/cnm/cnm.c | 480 +++++++++++++++++++++ src/cnm/cnm_bst_pq.c | 155 +++++++ src/cnm/cnm_bst_pq.h | 105 +++++ src/common.mk | 1 + src/components/Makefile.am | 10 + src/components/Makefile.in | 614 ++++++++++++++++++++++++++ src/components/components.c | 207 +++++++++ src/components/largest_component.c | 191 +++++++++ src/components/node_components.c | 442 +++++++++++++++++++ src/components/strong_conn.c | 277 ++++++++++++ src/conf/Makefile.am | 10 + src/conf/Makefile.in | 605 ++++++++++++++++++++++++++ src/conf/conf_model_deg.c | 259 +++++++++++ src/conf/conf_model_deg_nocheck.c | 182 ++++++++ src/deg_seq/Makefile.am | 6 + src/deg_seq/Makefile.in | 588 +++++++++++++++++++++++++ src/deg_seq/deg_seq.c | 115 +++++ src/deg_seq/deg_seq_w.c | 123 ++++++ src/dijkstra/Makefile.am | 7 + src/dijkstra/Makefile.in | 586 +++++++++++++++++++++++++ src/dijkstra/dijkstra.c | 242 +++++++++++ src/dijkstra/node_w_funs.c | 111 +++++ src/dijkstra/node_w_funs.h | 66 +++ src/dms/Makefile.am | 4 + src/dms/Makefile.in | 582 +++++++++++++++++++++++++ src/dms/dms.c | 211 +++++++++ src/er/Makefile.am | 9 + src/er/Makefile.in | 600 ++++++++++++++++++++++++++ src/er/er_A.c | 152 +++++++ src/er/er_B.c | 126 ++++++ src/f3m/Makefile.am | 5 + src/f3m/Makefile.in | 578 +++++++++++++++++++++++++ src/f3m/f3m.c | 657 ++++++++++++++++++++++++++++ src/fitmle/Makefile.am | 5 + src/fitmle/Makefile.in | 578 +++++++++++++++++++++++++ src/fitmle/fitmle.c | 479 +++++++++++++++++++++ src/gn/Makefile.am | 5 + src/gn/Makefile.in | 578 +++++++++++++++++++++++++ src/gn/gn.c | 495 +++++++++++++++++++++ src/graph_info/Makefile.am | 4 + src/graph_info/Makefile.in | 578 +++++++++++++++++++++++++ src/graph_info/graph_info.c | 130 ++++++ src/hidden/Makefile.am | 7 + src/hidden/Makefile.in | 585 +++++++++++++++++++++++++ src/hidden/hv_net.c | 337 +++++++++++++++ src/include/cum_distr.h | 60 +++ src/include/dset.h | 65 +++ src/include/gen_heap.h | 84 ++++ src/include/gen_pqueue.h | 108 +++++ src/include/gen_stack.h | 54 +++ src/include/iltree.h | 93 ++++ src/include/iltree_double.h | 62 +++ src/include/utils.h | 138 ++++++ src/johnson/Makefile.am | 6 + src/johnson/Makefile.in | 582 +++++++++++++++++++++++++ src/johnson/johnson_cycles.c | 328 ++++++++++++++ src/johnson/stack.c | 96 +++++ src/johnson/stack.h | 59 +++ src/knn/Makefile.am | 11 + src/knn/Makefile.in | 600 ++++++++++++++++++++++++++ src/knn/knn.c | 349 +++++++++++++++ src/knn/knn_w.c | 355 +++++++++++++++ src/knn/knntree.c | 95 ++++ src/knn/knntree.h | 54 +++ src/kruskal/Makefile.am | 6 + src/kruskal/Makefile.in | 590 +++++++++++++++++++++++++ src/kruskal/edge_w_funs.c | 73 ++++ src/kruskal/edge_w_funs.h | 54 +++ src/kruskal/kruskal.c | 215 ++++++++++ src/label_prop/Makefile.am | 5 + src/label_prop/Makefile.in | 578 +++++++++++++++++++++++++ src/label_prop/label_prop.c | 415 ++++++++++++++++++ src/modularity/Makefile.am | 5 + src/modularity/Makefile.in | 578 +++++++++++++++++++++++++ src/modularity/modularity.c | 220 ++++++++++ src/pm/Makefile.am | 5 + src/pm/Makefile.in | 578 +++++++++++++++++++++++++ src/pm/README | 1 + src/pm/pm.c | 231 ++++++++++ src/power_law/Makefile.am | 4 + src/power_law/Makefile.in | 578 +++++++++++++++++++++++++ src/power_law/power_law.c | 146 +++++++ src/shortest/Makefile.am | 6 + src/shortest/Makefile.in | 589 +++++++++++++++++++++++++ src/shortest/shortest.c | 259 +++++++++++ src/shortest/shortest_avg_max_hist.c | 223 ++++++++++ src/utils/cum_distr.c | 134 ++++++ src/utils/dset.c | 128 ++++++ src/utils/gen_heap.c | 302 +++++++++++++ src/utils/gen_pqueue.c | 359 ++++++++++++++++ src/utils/gen_stack.c | 87 ++++ src/utils/iltree.c | 291 +++++++++++++ src/utils/iltree_double.c | 102 +++++ src/utils/utils.c | 785 ++++++++++++++++++++++++++++++++++ src/ws/Makefile.am | 5 + src/ws/Makefile.in | 578 +++++++++++++++++++++++++ src/ws/ws.c | 204 +++++++++ 122 files changed, 30355 insertions(+) create mode 100644 src/Makefile.am create mode 100644 src/Makefile.in create mode 100644 src/TODO create mode 100644 src/ba/Makefile.am create mode 100644 src/ba/Makefile.in create mode 100644 src/ba/ba.c create mode 100644 src/bb_fitness/Makefile.am create mode 100644 src/bb_fitness/Makefile.in create mode 100644 src/bb_fitness/bb_fitness.c create mode 100644 src/bbv/Makefile.am create mode 100644 src/bbv/Makefile.in create mode 100644 src/bbv/bbv.c create mode 100644 src/betweenness/Makefile.am create mode 100644 src/betweenness/Makefile.in create mode 100644 src/betweenness/README create mode 100644 src/betweenness/bet_dependency.c create mode 100644 src/betweenness/betweenness.c create mode 100644 src/clust/Makefile.am create mode 100644 src/clust/Makefile.in create mode 100644 src/clust/clust.c create mode 100644 src/clust/clust_w.c create mode 100644 src/cnm/Makefile.am create mode 100644 src/cnm/Makefile.in create mode 100644 src/cnm/bst_pq.c create mode 100644 src/cnm/bst_pq.h create mode 100644 src/cnm/cnm.c create mode 100644 src/cnm/cnm_bst_pq.c create mode 100644 src/cnm/cnm_bst_pq.h create mode 100644 src/common.mk create mode 100644 src/components/Makefile.am create mode 100644 src/components/Makefile.in create mode 100644 src/components/components.c create mode 100644 src/components/largest_component.c create mode 100644 src/components/node_components.c create mode 100644 src/components/strong_conn.c create mode 100644 src/conf/Makefile.am create mode 100644 src/conf/Makefile.in create mode 100644 src/conf/conf_model_deg.c create mode 100644 src/conf/conf_model_deg_nocheck.c create mode 100644 src/deg_seq/Makefile.am create mode 100644 src/deg_seq/Makefile.in create mode 100644 src/deg_seq/deg_seq.c create mode 100644 src/deg_seq/deg_seq_w.c create mode 100644 src/dijkstra/Makefile.am create mode 100644 src/dijkstra/Makefile.in create mode 100644 src/dijkstra/dijkstra.c create mode 100644 src/dijkstra/node_w_funs.c create mode 100644 src/dijkstra/node_w_funs.h create mode 100644 src/dms/Makefile.am create mode 100644 src/dms/Makefile.in create mode 100644 src/dms/dms.c create mode 100644 src/er/Makefile.am create mode 100644 src/er/Makefile.in create mode 100644 src/er/er_A.c create mode 100644 src/er/er_B.c create mode 100644 src/f3m/Makefile.am create mode 100644 src/f3m/Makefile.in create mode 100644 src/f3m/f3m.c create mode 100644 src/fitmle/Makefile.am create mode 100644 src/fitmle/Makefile.in create mode 100644 src/fitmle/fitmle.c create mode 100644 src/gn/Makefile.am create mode 100644 src/gn/Makefile.in create mode 100644 src/gn/gn.c create mode 100644 src/graph_info/Makefile.am create mode 100644 src/graph_info/Makefile.in create mode 100644 src/graph_info/graph_info.c create mode 100644 src/hidden/Makefile.am create mode 100644 src/hidden/Makefile.in create mode 100644 src/hidden/hv_net.c create mode 100644 src/include/cum_distr.h create mode 100644 src/include/dset.h create mode 100644 src/include/gen_heap.h create mode 100644 src/include/gen_pqueue.h create mode 100644 src/include/gen_stack.h create mode 100644 src/include/iltree.h create mode 100644 src/include/iltree_double.h create mode 100644 src/include/utils.h create mode 100644 src/johnson/Makefile.am create mode 100644 src/johnson/Makefile.in create mode 100644 src/johnson/johnson_cycles.c create mode 100644 src/johnson/stack.c create mode 100644 src/johnson/stack.h create mode 100644 src/knn/Makefile.am create mode 100644 src/knn/Makefile.in create mode 100644 src/knn/knn.c create mode 100644 src/knn/knn_w.c create mode 100644 src/knn/knntree.c create mode 100644 src/knn/knntree.h create mode 100644 src/kruskal/Makefile.am create mode 100644 src/kruskal/Makefile.in create mode 100644 src/kruskal/edge_w_funs.c create mode 100644 src/kruskal/edge_w_funs.h create mode 100644 src/kruskal/kruskal.c create mode 100644 src/label_prop/Makefile.am create mode 100644 src/label_prop/Makefile.in create mode 100644 src/label_prop/label_prop.c create mode 100644 src/modularity/Makefile.am create mode 100644 src/modularity/Makefile.in create mode 100644 src/modularity/modularity.c create mode 100644 src/pm/Makefile.am create mode 100644 src/pm/Makefile.in create mode 100644 src/pm/README create mode 100644 src/pm/pm.c create mode 100644 src/power_law/Makefile.am create mode 100644 src/power_law/Makefile.in create mode 100644 src/power_law/power_law.c create mode 100644 src/shortest/Makefile.am create mode 100644 src/shortest/Makefile.in create mode 100644 src/shortest/shortest.c create mode 100644 src/shortest/shortest_avg_max_hist.c create mode 100644 src/utils/cum_distr.c create mode 100644 src/utils/dset.c create mode 100644 src/utils/gen_heap.c create mode 100644 src/utils/gen_pqueue.c create mode 100644 src/utils/gen_stack.c create mode 100644 src/utils/iltree.c create mode 100644 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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 + * . + * + * (c) Vincenzo Nicosia 2009-2017 -- + * + * 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 grows a network with N nodes using the linear + * preferential attachment model proposed by Barabasi and + * Albert. Each new node creates m links, and the initial (seed) + * network is a ring of n0>=m nodes. + * + * + * References: + * + * [1] A.-L. Barabasi, R. Albert, "Emergence of scaling in random + * networks", Science 286, 509-512 (1999). + * + */ + +#include +#include +#include +#include + +void usage(char *argv[]){ + printf("********************************************************************\n" + "** **\n" + "** -*- ba -*- **\n" + "** **\n" + "** Grow a scale-free network of 'N' nodes using the linear **\n" + "** preferential attachment model (Barabasi-Albert). **\n" + "** The initial network is a ring of 'n0' nodes, and each new **\n" + "** node creates 'm' edges. **\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 2010-2017 (v.nicosia@qmul.ac.uk)\n\n" + "********************************************************************\n\n" + ); + printf("Usage: %s \n", argv[0]); + +} + + + +int init_network(unsigned int **S, unsigned int n0){ + + int n; + + for(n=0; n 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); + } + + S = malloc(2 * sizeof(unsigned int*)); + S[0] = malloc(S_size * sizeof(unsigned int)); + S[1] = malloc(S_size * sizeof(unsigned int)); + + S_num = init_network(S, n0); + S_num = grow_ba_network(S, N, m, n0, S_num); + for(i=0; i&2; \ + exit 1;; \ + esac; \ + has_opt=no; \ + sane_makeflags=$$MAKEFLAGS; \ + if $(am__is_gnu_make); then \ + sane_makeflags=$$MFLAGS; \ + else \ + case $$MAKEFLAGS in \ + *\\[\ \ ]*) \ + bs=\\; \ + sane_makeflags=`printf '%s\n' "$$MAKEFLAGS" \ + | sed "s/$$bs$$bs[$$bs $$bs ]*//g"`;; \ + esac; \ + fi; \ + skip_next=no; \ + strip_trailopt () \ + { \ + flg=`printf '%s\n' "$$flg" | sed "s/$$1.*$$//"`; \ + }; \ + for flg in $$sane_makeflags; 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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 + * . + * + * (c) Vincenzo Nicosia 2009-2017 -- + * + * 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 fitness model proposed by Bianconi and + * Barabasi, where the attachment probability is: + * + * \Pi_{i->j} \propto a_j * k_j + * + * where a_j is the actractiveness of node j. + * + * + * References: + * + * [1] G. Bianconi, A.-L. Barabasi, " Competition and multiscaling in + * evolving networks". EPL-Europhys. Lett. 54 (2001), 436. + * + */ + + +#include +#include +#include + +#include "utils.h" +#include "cum_distr.h" + + +void usage(char *argv[]){ + printf("********************************************************************\n" + "** **\n" + "** -*- bb_fitness -*- **\n" + "** **\n" + "** Grow a network of 'N' nodes using the fitness model proposed **\n" + "** by Bianconi and Barabasi. **\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) ~ a_j * k_j **\n" + "** **\n" + "** where a_j is the attractiveness of node j. The values of **\n" + "** node attractiveness are sampled uniformly at random in **\n" + "** [0,1]. **\n" + "** **\n" + "** The program prints on STDOUT the edge-list of the final **\n" + "** graph. **\n" + "** **\n" + "** If 'FIT' is specified as a fourth parameter, the values **\n" + "** of node attractiveness are printed on STDERR. **\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 [SHOW]\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){ + 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); + } + + I = malloc(N * m * sizeof(unsigned int)); + J = malloc(N * m * sizeof(unsigned int)); + a = malloc(N * sizeof(double)); + + init_fitness_uniform(a, N); + + K = bb_fitness(I, J, N, m, n0, a); + + dump_graph(I, J, K); + if (argc > 4 && !my_strcasecmp(argv[4], "SHOW")){ + dump_fitness(a, N); + } + free(a); + free(I); + free(J); + +} diff --git a/src/bbv/Makefile.am b/src/bbv/Makefile.am new file mode 100644 index 0000000..0ed1800 --- /dev/null +++ b/src/bbv/Makefile.am @@ -0,0 +1,4 @@ +include ../common.mk +bin_PROGRAMS = bbv +bbv_SOURCES = bbv.c ../utils/cum_distr.c ../include/cum_distr.h +bbv_LDADD = -lm diff --git a/src/bbv/Makefile.in b/src/bbv/Makefile.in new file mode 100644 index 0000000..3f19d0c --- /dev/null +++ b/src/bbv/Makefile.in @@ -0,0 +1,578 @@ +# Makefile.in generated by automake 1.15 from Makefile.am. +# @configure_input@ + +# Copyright (C) 1994-2014 Free Software Foundation, Inc. + +# This Makefile.in is free software; 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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 + * . + * + * (c) Vincenzo Nicosia 2009-2017 -- + * + * 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 grows a weighted network using the model proposed by + * Barrat, Barthelemy, and Vespignani. + * + * References: + * + * [1] A. Barrat, M. Barthelemy, and A. Vespignani. "Weighted + * Evolving Networks: Coupling Topology and Weight + * Dynamics". Phys. Rev. Lett. 92 (2004), 228701. + * + * [2] A. Barrat, M. Barthelemy, and A. Vespignani. "Modeling the + * evolution of weighted networks". Phys. Rev. E 70 (2004), + * 066149. + * + */ + +#include +#include +#include +#include + +#include "cum_distr.h" + +void usage(char *argv[]){ + printf("********************************************************************\n" + "** **\n" + "** -*- bbv -*- **\n" + "** **\n" + "** Grow a weighted network of 'N' nodes using the model **\n" + "** proposed by Barrat-Barthelemy-Vespignani. **\n" + "** **\n" + "** The initial network is a clique of 'n0' nodes, and each new **\n" + "** node creates 'm' edges. All edges have an initial weight **\n" + "** equal to 'w0', and the attachment probability in of the **\n" + "** form: **\n" + "** **\n" + "** P(i->j) ~ s_j **\n" + "** **\n" + "** where s_j is the strength of node j. The parameter 'delta' **\n" + "** tunes the rearrangement of edge weights due to the **\n" + "** addition of a new edge. The degree, strength, and weight **\n" + "** distributions of the created graphs are power-laws, **\n" + "** whose esponents depend on the values of 'w0' and 'delta'. **\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", argv[0]); +} + + +typedef struct{ + int id; + double w; + double delta_w; +} link_t; + + +typedef struct { + int id; + int size; + int deg; + double s; + link_t *neighs; +} node_t; + + +/* create the initial graph as a clique of n0 nodes */ +void init_seed(node_t *G, int n0, double w0, cum_distr_t *d){ + + int i, j, n; + + for(i=0; i< n0; i++){ + G[i].neighs = malloc((n0-1) * sizeof(link_t)); + G[i].size = n0-1; + G[i].deg = n0-1; + n= 0; + for (j=0; j i){ + tot_w += G[i].neighs[j].w; + printf("%d %d %g\n", i, G[i].neighs[j].id, G[i].neighs[j].w); + } + } + } +} + + +/* grow a weighted graph using the BBV model */ +node_t* bbv(unsigned int N, unsigned int n0, unsigned int m, double w0, double delta){ + + node_t *G; + int t, i, j; + cum_distr_t *distr = NULL; + int *tmp_neighs; + + distr = cum_distr_init(N * m); + + + G = malloc(N * sizeof(node_t)); + tmp_neighs = malloc(m * sizeof(int)); + + init_seed(G, n0, w0, distr); + + + for(t=n0; t 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 (w0 <= 0.0){ + fprintf(stderr, "w0 must be positive\n"); + exit(1); + } + + if (delta < 0.0){ + fprintf(stderr, "delta must be positive\n"); + exit(1); + } + + + net = bbv(N, n0, m, w0, delta); + dump_net(net, N); + + for(i=0; i&2; \ + exit 1;; \ + esac; \ + has_opt=no; 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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 + * . + * + * (c) Vincenzo Nicosia 2009-2017 -- + * + * 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 computes the betweenness dependency of all the nodes + * of a graph, using Brandes' algorithm, and counting all the + * shortest paths originating from a set of nodes (potentially the + * whole set of vertices). + * + * References: + * U. Brandes. "A Faster Algorithm for Betweenness + * Centrality". J. Math. Sociol. 25 (2001), 163-177. + * + */ + + +#include +#include +#include + +#include "utils.h" + + +void usage(char *argv[]){ + printf("********************************************************************\n" + "** **\n" + "** -*- bet_dependency -*- **\n" + "** **\n" + "** Compute the betweenness dependency of all the nodes of a **\n" + "** network due to the shortest paths originating from a set **\n" + "** of initial nodes. If no start node is specified, compute **\n" + "** the dependency due to all the nodes of the graph. If no end **\n" + "** node is specified, compute the dependency due to the nodes **\n" + "** between node_start and the last node of the graph. **\n" + "** **\n" + "** The dependency of each node is printed on standard output. **\n" + "** **\n" + "** **\n" + "********************************************************************\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 (katolaz@yahoo.it)\n\n"); + printf("Usage: %s [ []]\n\n" , argv[0]); +} + +void add_predecessor(unsigned int **pred, unsigned int k){ + + (*pred)[0] += 1; + *pred = realloc(*pred, ((*pred)[0] + 1) * sizeof(unsigned int)); + (*pred)[ (*pred)[0] ] = k; +} + + + +/* + * Returns a list of dependencies + */ +double* compute_bet_dependency(unsigned int N, unsigned int *J_slap, unsigned int *r_slap, + unsigned int n_start, unsigned int n_end){ + + int i, j, k, w, idx, cur_node; + unsigned int *marked, **preds, *dist, *nj; + double *delta, *cB; + unsigned int d; + unsigned int n, nd, ndp; + + dist = malloc(N * sizeof(unsigned int)); + marked = malloc(N * sizeof(unsigned int)); + preds = malloc(N * sizeof(unsigned int *)); + + nj = malloc(N * sizeof(unsigned int)); + delta = malloc(N * sizeof(double)); + cB = malloc(N * sizeof(double)); + + for (i=0; i 0){ + for(i = n; i< n+nd; i ++){ + cur_node = marked[i]; + for (k=r_slap[cur_node]; k=1; k--){ + w = marked[k]; + for (idx=1; idx <= preds[w][0]; idx ++ ){ + i = preds[w][idx]; + delta[i] += 1.0 * nj[i] / nj[w] * (1 + delta[w]); + } + cB[w] += delta[w]; + } + } + free(dist); + free(marked); + for (i=0; i. + * + * (c) Vincenzo Nicosia 2009-2017 -- + * + * 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 computes the betweenness of all the nodes of a graph, + * using Brandes' algorithm, and counting all the shortest paths + * originating from a set of nodes (potentially the whole set of + * vertices). + * + * References: + * U. Brandes. "A Faster Algorithm for Betweenness + * Centrality". J. Math. Sociol. 25 (2001), 163-177. + * + */ + + +#include +#include +#include + +#include + +#include "utils.h" + + +void usage(char *argv[]){ + printf("********************************************************************\n" + "** **\n" + "** -*- betweenness -*- **\n" + "** **\n" + "** Compute the betweenness of all the nodes and edges of a **\n" + "** network due to the shortest paths originating from a set **\n" + "** of initial nodes. The set can be either a sequence of **\n" + "** nodes (if the second argument is 'SEQ') or a random sample **\n" + "** from the set of all the nodes (if it is 'RND'). **\n" + "** **\n" + "** The input file is an edge-list (use '-' to read from STDIN). **\n" + "** **\n" + "** With 'SEQ': **\n" + "** If is not specified, computes the betweenness **\n" + "** using shortest paths from *all* the nodes (WARNING: This can **\n" + "** be slow for large graphs!). If is not specified, **\n" + "** use shortest paths from all the nodes between **\n" + "** and the node with the largest label. **\n" + "** **\n" + "** With 'RND': **\n" + "** Compute the betweenness based on the shortest paths from **\n" + "** nodes sampled uniformly at random. **\n" + "** **\n" + "** When called with just , use all the nodes. **\n" + "** **\n" + "** The betweenness of all the nodes is printed on standard **\n" + "** output (STDOUT), while the edge betweenness is printed on **\n" + "** standard error (STDERR) **\n" + "** **\n" + "********************************************************************\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"); + printf("Usage: %s [SEQ []]\n" , argv[0]); + printf("Usage: %s [RND ]\n" , argv[0]); + +} + +/* + * Add a node the a list of predecessors + */ + +void add_predecessor(unsigned int **pred, unsigned int k){ + + (*pred)[0] += 1; + *pred = realloc(*pred, ((*pred)[0] + 1) * sizeof(unsigned int)); + (*pred)[ (*pred)[0] ] = k; +} + + + +/* + * + * Compute node and edge betweenness, based on shortest paths + * originating on the "num" nodes specified in "nlist". "edge_bet" + * should be an appropriately allocated (and initialised to zero!!!!) + * vector of length equal to J_slap, and will contain the values of + * edge betweenness. + * + */ +double* compute_bet_dependency(unsigned int N, unsigned int *J_slap, unsigned int *r_slap, + unsigned int *nlist, unsigned int num, double *edge_bet){ + + int i, j, k, w, idx, cur_node, m; + unsigned int *marked, **preds, *dist, *nj; + double *delta, *cB, val; + unsigned int d; + unsigned int n, nd, ndp; + unsigned int edge_pos; + + dist = malloc(N * sizeof(unsigned int)); + marked = malloc(N * sizeof(unsigned int)); + preds = malloc(N * sizeof(unsigned int *)); + + nj = malloc(N * sizeof(unsigned int)); + delta = malloc(N * sizeof(double)); + cB = malloc(N * sizeof(double)); + + for (i=0; i 0){ + for(i = n; i< n+nd; i ++){ + cur_node = marked[i]; + for (k=r_slap[cur_node]; k=1; k--){ + w = marked[k]; + for (idx=1; idx <= preds[w][0]; idx ++ ){ + i = preds[w][idx]; + val = 1.0 * nj[i] / nj[w] * (1 + delta[w]); + delta[i] += val; + /* Now we should update the betweenness of the edge (i,w) in + the appropriate position of the vector edge_bet*/ + find_neigh_in_Jslap(J_slap, r_slap, N, i, w, &edge_pos); + edge_bet[edge_pos] += val; + find_neigh_in_Jslap(J_slap, r_slap, N, w, i, &edge_pos); + edge_bet[edge_pos] += val; + } + cB[w] += delta[w]; + } + } + free(dist); + free(marked); + for (i=0; i 3){ + if(!my_strcasecmp(argv[2], "SEQ")){ + n_start = atoi(argv[3]); + if (n_start > N-1) + n_start = 0; + if (argc > 4){ + n_end = atoi(argv[4]); + } + else{ + n_end = N-1; + } + num = n_end - n_start + 1; + } + else if (!my_strcasecmp(argv[2], "RND")){ + num = atoi(argv[3]); + n_start = 0; + n_end = num-1; + if (num > N || num < 1) + num = N; + shuffle_vector(nlist, N); + } + } + + sort_neighbours(J_slap, r_slap, N); + edge_bet = malloc(K * sizeof(double)); + memset(edge_bet, 0, K * sizeof(double)); + cB = compute_bet_dependency(N, J_slap, r_slap, nlist+n_start, num, edge_bet); + + dump_cB(cB, N); + dump_edge_bet(J_slap, r_slap, N, edge_bet, stderr); + + free(cB); + free(J_slap); + free(r_slap); + free(edge_bet); + free(nlist); + +} diff --git a/src/clust/Makefile.am b/src/clust/Makefile.am new file mode 100644 index 0000000..676c6bf --- /dev/null +++ b/src/clust/Makefile.am @@ -0,0 +1,6 @@ +include ../common.mk +bin_PROGRAMS = clust clust_w +clust_SOURCES = clust.c ../utils/utils.c ../include/utils.h +clust_LDADD = -lm +clust_w_SOURCES = clust_w.c ../utils/utils.c ../include/utils.h +clust_w_LDADD = -lm diff --git a/src/clust/Makefile.in b/src/clust/Makefile.in new file mode 100644 index 0000000..3a891bb --- /dev/null +++ b/src/clust/Makefile.in @@ -0,0 +1,588 @@ +# Makefile.in generated by automake 1.15 from Makefile.am. +# @configure_input@ + +# Copyright (C) 1994-2014 Free Software Foundation, Inc. + +# This Makefile.in is free software; the Free Software Foundation +# gives unlimited permission to copy and/or distribute it, +# with or without modifications, as long as this notice is preserved. + +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY, to the extent permitted by law; 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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 + * . + * + * (c) Vincenzo Nicosia 2009-2017 -- + * + * 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 computes the clustering coefficient of a graph and of + * each node. + * + * + */ + + +#include +#include +#include +#include "utils.h" + + +void usage(char *argv[]){ + + printf("********************************************************************\n" + "** **\n" + "** -*- clust -*- **\n" + "** **\n" + "** Compute the graph clustering coefficient and, optionally, **\n" + "** also the node clustering coefficient of all the nodes in **\n" + "** the graph 'graph_in'. **\n" + "** **\n" + "** The input file 'graph_in' is an edge-list: **\n" + "** **\n" + "** I_1 J_1 **\n" + "** I_2 J_2 **\n" + "** I_3 J_3 **\n" + "** ... ... **\n" + "** I_K J_K **\n" + "** **\n" + "** If 'graph_in' is equal to '-' (dash), read the file from **\n" + "** the standard input (STDIN). **\n" + "** **\n" + "** The output is a single line containing the value of the **\n" + "** graph clustering coefficient of 'graph_in'. **\n" + "** **\n" + "** If 'SHOW' is provided as second argument, the program **\n" + "** on the standard error (STDERR) the label, degree, and **\n" + "** node clustering coefficient of all the nodes of 'graph_in' **\n" + "** in the format: **\n" + "** **\n" + "** node_1 k_1 c_1 **\n" + "** node_2 k_2 c_2 **\n" + "** node_3 k_3 c_3 **\n" + "** node_4 k_4 c_4 **\n" + "** ..... **\n" + "** **\n" + "** where 'k_1' is the degree of 'node_1' and 'c_1' is its **\n" + "** node clustering coefficient. If a node has degree smaller **\n" + "** than 2, its clustering coefficient is equal to zero. **\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 2009-2017 (v.nicosia@qmul.ac.uk)\n" + "********************************************************************\n\n" + ); + + printf("Usage: %s [SHOW]\n", argv[0]); +} + + + +double avg_clust(unsigned int *J_slap, unsigned int *r_slap, unsigned int N, int show){ + + double c = 0, ci=0; + unsigned int i, j, l, ki; + + for(i=0; i 1) + ci /= ki * (ki-1); + else + ci = 0; + if (show) + fprintf(stderr, "%d %d %g\n", i, ki, ci); + c += ci; + } + c /= N; + return c; +} + + + + +int main(int argc, char *argv[]){ + + unsigned int *J_slap=NULL, *r_slap=NULL; + unsigned int K, N; + FILE *filein; + double c; + int show = 0; + + if (argc < 2){ + usage(argv); + exit(1); + } + + if (argc >2 && !my_strcasecmp("SHOW", argv[2])){ + show = 1; + } + + if (!strcmp(argv[1], "-")){ + /* take the input from STDIN */ + filein = stdin; + } + else { + filein = openfile_or_exit(argv[1], "r", 2); + } + + read_slap(filein, &K, &N, &J_slap, &r_slap); + fclose(filein); + + c = avg_clust(J_slap, r_slap, N, show); + printf("%2.8lf\n", c); + free(J_slap); + free(r_slap); +} diff --git a/src/clust/clust_w.c b/src/clust/clust_w.c new file mode 100644 index 0000000..dcf14ed --- /dev/null +++ b/src/clust/clust_w.c @@ -0,0 +1,161 @@ +/** + * 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 + * . + * + * (c) Vincenzo Nicosia 2009-2017 -- + * + * 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 computes the weighted clustering coefficient as + * defined in Barrat, Barthelemy, Pastor-Satorras, Vespignani, PNAS + * 101, 3747 (2004). + * + */ + +#include +#include +#include +#include "utils.h" + +void usage(char *argv[]){ + + printf("********************************************************************\n" + "** **\n" + "** -*- clust_w -*- **\n" + "** **\n" + "** Compute the weighted clustering coefficient of 'graph_in' **\n" + "** using the definition proposed by Barrayt, Barthelemy, **\n" + "** Pastor-Satorras and Vespignani. **\n" + "** **\n" + "** The input file 'graph_in' is an edge-list, in the format: **\n" + "** **\n" + "** I_1 J_1 W_1 **\n" + "** I_2 J_2 W_2 **\n" + "** **\n" + "** where W_i is the weight if the edge (I_i, J_i). **\n" + "** **\n" + "** If 'graph_in' is equal to '-' (dash), read the file from **\n" + "** the standard input (STDIN). **\n" + "** **\n" + "** The output is a single line containing the value of the **\n" + "** graph clustering coefficient of 'graph_in'. **\n" + "** **\n" + "** If 'SHOW' is provided as second argument, the program **\n" + "** on the standard error (STDERR) the label, degree, and **\n" + "** node clustering coefficient of all the nodes of 'graph_in' **\n" + "** in the format: **\n" + "** **\n" + "** node_1 k_1 c_1 **\n" + "** node_2 k_2 c_2 **\n" + "** node_3 k_3 c_3 **\n" + "** node_4 k_4 c_4 **\n" + "** ..... **\n" + "** **\n" + "** where 'k_1' is the degree of 'node_1' and 'c_1' is its **\n" + "** node clustering coefficient. If a node has degree smaller **\n" + "** than 2, its clustering coefficient is equal to zero. **\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 2009-2017 (v.nicosia@qmul.ac.uk)\n" + "********************************************************************\n\n" + ); + + printf("Usage: %s [SHOW]\n", argv[0]); +} + + + + +double avg_clust_w(unsigned int *J_slap, unsigned int *r_slap, double *W_slap, + unsigned int N, int show){ + + double c = 0, ci=0, w=0.0; + unsigned int i, j, l, ki; + + for(i=0; i 0.0){ + ci += (W_slap[j] + w) / 2.0; + } + } + } + if(ki > 1) + ci /= strength(r_slap, W_slap, i) * (ki-1); + else + ci = 0; + if (show) + fprintf(stderr, "%d %d %0.14g\n", i, ki, ci); + c += ci; + } + c /= N; + return c; +} + + + + +int main(int argc, char *argv[]){ + + unsigned int *J_slap=NULL, *r_slap=NULL; + double *W_slap = NULL; + unsigned int K, N; + FILE *filein; + double c; + int show = 0; + + if (argc < 2){ + printf("Usage: %s [SHOW]\n", argv[0]); + exit(1); + } + if (argc >2 ){ + show = 1; + } + + if (!strcmp(argv[1], "-")){ + /* take the input from STDIN */ + filein = stdin; + } + else { + filein = openfile_or_exit(argv[1], "r", 2); + } + + + read_slap_w(filein, &K, &N, &J_slap, &r_slap, &W_slap); + fclose(filein); + c = avg_clust_w(J_slap, r_slap, W_slap, N, show); + printf("%2.8lf\n", c); + free(J_slap); + free(r_slap); + free(W_slap); +} diff --git a/src/cnm/Makefile.am b/src/cnm/Makefile.am new file mode 100644 index 0000000..b036fac --- /dev/null +++ b/src/cnm/Makefile.am @@ -0,0 +1,7 @@ +include ../common.mk +bin_PROGRAMS = cnm +cnm_SOURCES = cnm.c bst_pq.c cnm_bst_pq.c bst_pq.h cnm_bst_pq.h \ +../utils/utils.c ../utils/gen_stack.c ../utils/dset.c \ +../include/utils.h ../include/gen_stack.h ../include/dset.h +cnm_LDADD = -lm + diff --git a/src/cnm/Makefile.in b/src/cnm/Makefile.in new file mode 100644 index 0000000..74cd719 --- /dev/null +++ b/src/cnm/Makefile.in @@ -0,0 +1,591 @@ +# Makefile.in generated by automake 1.15 from Makefile.am. +# @configure_input@ + +# Copyright (C) 1994-2014 Free Software Foundation, Inc. + +# This Makefile.in is free software; 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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 + * . + * + * (c) Vincenzo Nicosia 2009-2017 -- + * + * 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 is an implementation of a Binary Search Tree augmented by a + * Priority Queue. This data structure is central to the + * implementation of the Clauset-Newman-Moore greedy modularity + * optimisation algorithm + * + */ + +#include +#include +#include +#include + +#include "utils.h" +#include "bst_pq.h" + + + +/* BST-related functions */ + + +void __recursive_preorder(node_t *cur, ilfunc_t *funs){ + + if(cur->left){ + __recursive_preorder(cur->left, funs); + } + if(cur -> active) + funs->print(cur->info, funs->fileout); + if(cur->right){ + __recursive_preorder(cur->right, funs); + } +} + +/* + * + * Recursive push of nodes in the nodecache :-) + * + */ + +void __recursive_destroy(node_t *cur, ilfunc_t *funs){ + if(cur->left){ + __recursive_destroy(cur->left, funs); + cur->left = NULL; + } + if(cur->right){ + __recursive_destroy(cur->right, funs); + cur->right = NULL; + } +} + + +int __recursive_insert(node_t *cur, node_t *elem, ilfunc_t *f){ + + int res ; + res = f->compare(cur->info, elem->info); + /* printf("res: %d\n", res); */ + assert(res != 0); + if ( res > 0){ + if (cur->left){ + return __recursive_insert(cur->left, elem, f); + } + else{ + cur->left = elem; + elem->parent = cur; + return 0; + } + } + else if (res < 0){ + if (cur->right){ + return __recursive_insert(cur->right, elem, f); + } + else{ + cur->right = elem; + elem->parent = cur; + return 0; + } + } + if (cur -> active){ + printf("warning!!!!! duplicate entry!!!!!!\n\n"); + exit(1); + } + else + cur->active = 1; + return -1; +} + + + +void* __recursive_lookup(node_t *cur, int v, ilfunc_t *f){ + + int res; + + res = f->compare(cur->info, v); + + if (res > 0){ + if(cur->left) + return __recursive_lookup(cur->left, v, f); + else + return NULL; + + } + else if (res < 0){ + if(cur->right) + return __recursive_lookup(cur->right, v, f); + else + return NULL; + } + else{ /* res == 0, we found the element we were looking for */ + return cur; + } +} + + + +node_t* __recursive_getmin(node_t *cur){ + + if(cur->left){ + return __recursive_getmin(cur->left); + } + else{ + return cur; + } + +} + + +node_t* __tree_getmin(node_t *n){ + + if (!n){ + return NULL; + } + else{ + return __recursive_getmin(n); + } + +} + + +/* This is used by __tree__delete to put another tree v in place of + the current node u */ + + +void __tree_transplant(bst_pq_t t, node_t *u, node_t * v){ + + if (u->parent == NULL){ + t->root = v; + } + else if(u == u->parent->left){ + u->parent->left = v; + } + else{ + u->parent->right = v; + } + if (v != NULL){ + v->parent = u->parent; + } + +} + + +void __tree_delete(bst_pq_t t, node_t *z){ + + node_t *y; + + if (z == NULL) + return; + + if (z->left == NULL){ + __tree_transplant(t, z, z->right); + } + else if(z->right == NULL){ + __tree_transplant(t, z, z->left); + } + else{ + y = __tree_getmin(z->right); + if (y->parent != z){ + __tree_transplant(t, y, y->right); + y->right = z->right; + y->right->parent = y; + } + __tree_transplant(t, z, y); + y->left = z->left; + y->left->parent = y; + } +} + + + + +void bst_pq_tree_destroy(bst_pq_t t){ + + if(t->root) + __recursive_destroy(t->root, & (t->bst_funs)); + free(t); +} + + + + +void __bst_pq_tree_view_pre(bst_pq_t t){ + + if (t->root){ + printf("----\n"); + __recursive_preorder(t->root, & (t->bst_funs)); + printf("\n----\n"); + } + else + printf("----- Empty tree!!!! -----\n"); + +} + + + +void* __bst_pq_tree_lookup(bst_pq_t t , int elem){ + + if(t->root) + return __recursive_lookup(t->root, elem, & (t->bst_funs) ); + else + return NULL; +} + + + + + +/* void bst_pq_tree_map(bst_pq_t t, void (*func)(void*)){ */ + +/* __recursive_map(t->root, func); */ + +/* } */ + + +/* void bst_pq_tree_map_args(bst_pq_t t, void (*func)(void*, void*), void *args){ */ + +/* __recursive_map_args(t->root, func, args); */ + +/* } */ + +void* bst_pq_tree_get_fileout(bst_pq_t t){ + + return t->bst_funs.fileout; +} + +void bst_pq_tree_set_fileout(bst_pq_t t, void *f){ + + t->bst_funs.fileout = f; +} + + + +node_t* __recursive_getmax(node_t *cur){ + + if(cur->right){ + return __recursive_getmax(cur->right); + } + else{ + return cur; + } + +} + + +void* bst_pq_tree_getmax(bst_pq_t t){ + + if (!t){ + return NULL; + } + else{ + return __recursive_getmax(t->root); + } + +} + + +/************************ + * PQ-related functions * + ************************/ + +void __update_handle(bst_pq_t q, int idx){ + + node_t *n; + n = (node_t*) q->v[idx]; + n->index = idx; + //q->handles[q->pq_funs.get_id(q->v[idx])] = idx; +} + + + +void __bst_pq_queue_sift_up(bst_pq_t q, int i){ + + int idx, parent; + void *tmp; + + if ( q->last < 0) + return; /* no sifting if the PQ is empty!!! */ + + idx = i; + parent = PARENT(idx); + + switch(q->qtype){ + case MAX_QUEUE: + while ( idx >0 && q->pq_funs.compare(q->v[idx]->key, q->v[parent]->key) > 0){ + tmp = q->v[idx]; + q->v[idx] = q->v[parent]; + q->v[parent] = tmp; + __update_handle(q, idx); + __update_handle(q, parent); + idx = parent; + parent = PARENT(idx); + } + break; + case MIN_QUEUE: + while ( idx >0 && q-> pq_funs.compare(q->v[idx]->key, q->v[parent]->key) < 0){ + tmp = q->v[idx]; + q->v[idx] = q->v[parent]; + q->v[parent] = tmp; + __update_handle(q, idx); + __update_handle(q, parent); + idx = parent; + parent = PARENT(idx); + } + break; + } +} + + +void __bst_pq_queue_sift_down(bst_pq_t q, int i){ + + int left, right, largest, smallest; + void *tmp; + + if ( q->last < 0) + return; /* no sifting if the PQ is empty!!! */ + if( i > q->last) + return; /* no sifting if the index i is beyond the end of the PQ */ + + switch(q->qtype){ + case MAX_QUEUE: + largest = i; + left = 2 * i + 1; + right = 2 * i + 2; + + if (left <= q->last && q->pq_funs.compare(q->v[left]->key, q->v[largest]->key) > 0){ + largest = left; + } + if (right <= q->last && q->pq_funs.compare(q->v[right]->key, q->v[largest]->key) > 0){ + largest = right; + } + if (largest != i){ + tmp = q->v[i]; + q->v[i] = q->v[largest]; + q->v[largest] = tmp; + __update_handle(q, i); + __update_handle(q, largest); + __bst_pq_queue_sift_down(q, largest); + } + else{ + __update_handle(q, i); + } + break; + + case MIN_QUEUE: + smallest = i; + left = 2 * i + 1; + right = 2 * i + 2; + + if (left <= q->last && q->pq_funs.compare(q->v[left]->key, q->v[smallest]->key) < 0){ + smallest = left; + } + if (right <= q->last && q->pq_funs.compare(q->v[right]->key, q->v[smallest]->key) < 0){ + smallest = right; + } + if (smallest != i){ + tmp = q->v[i]; + q->v[i] = q->v[smallest]; + q->v[smallest] = tmp; + __update_handle(q, i); + __update_handle(q, smallest); + __bst_pq_queue_sift_down(q, smallest); + } + else{ + __update_handle(q, i); + } + break; + } +} + + +void __bst_pq_queue_insert(bst_pq_t q, void *elem){ + + //void *tmp; + + if (q->last == q->N-1){ + /* reallocate the array to arrange a few new elements */ + q->N += 10; + q->v = realloc(q->v, (q->N) * sizeof(void*)); + VALID_PTR_OR_EXIT(q->v, 17); + //q->v = tmp; + } + + q->last += 1; + q->v[q->last] = elem; + __update_handle(q, q->last); + __bst_pq_queue_sift_up(q, q->last); + +} + + + +int __bst_pq_queue_delete_index(bst_pq_t q, int index){ + + if (q->last >=0 && index <= q->last){ + //*val = q->v[0]; + q->v[index] = q->v[q->last]; + q->last -= 1; + __bst_pq_queue_sift_down(q, index); + return 0; + } + else{ + return 1; + } +} + + + +void* __bst_pq_queue_peek(bst_pq_t q){ + + if (q->last >= 0) + return q->v[0]; + else + return NULL; +} + + + +int __bst_pq_queue_force_key(bst_pq_t q, unsigned int idx, double key){ + + switch(q->qtype){ + case MAX_QUEUE: + if (q->pq_funs.compare_to_key(q->v[idx], key) > 0){ + //q->pq_funs.set_key(q->v[idx], key); + q->v[idx]->key = key; + __bst_pq_queue_sift_down(q, idx); + } + else{ + //q->pq_funs.set_key(q->v[idx], key); + q->v[idx]->key = key; + __bst_pq_queue_sift_up(q, idx); + } + break; + case MIN_QUEUE: + if (q->pq_funs.compare_to_key(q->v[idx], key) < 0){ + //q->pq_funs.set_key(q->v[idx], key); + q->v[idx]->key = key; + __bst_pq_queue_sift_down(q, idx); + } + else{ + //q->pq_funs.set_key(q->v[idx], key); + q->v[idx]->key = key; + __bst_pq_queue_sift_up(q, idx); + } + break; + } + return 0; +} + + + +void __bst_pq_queue_dump(bst_pq_t q){ + + int i; + + unsigned int N; + + N = q->last+1; + + printf("N: %d last:%d root:", q->N, q->last); + if (q->last >=0) + q->pq_funs.print_elem(q->v[0]); + else + printf("NULL"); + printf("\n"); + + for(i=0; ipq_funs.print_elem(q->v[i]); + printf(" ("); + q->pq_funs.print_elem(q->v[2*i+1]); + printf(", "); + q->pq_funs.print_elem(q->v[2*i+2]); + printf(")\n"); + } + else{ + printf("%d: ", i); + q->pq_funs.print_elem(q->v[i]); + printf(" ("); + q->pq_funs.print_elem(q->v[2*i+1]); + printf(", NULL)\n"); + } + else{ + printf("%d: ", i); + q->pq_funs.print_elem(q->v[i]); + printf(" (NULL, NULL)\n"); + } + } + else{ + printf("%d: ", i); + q->pq_funs.print_elem(q->v[i]); + printf(" (NULL, NULL)\n"); + } + } + printf("\n"); +} + + + + +/* bst_pq interface */ + +/* init the BST_PQ -- TESTED --*/ + +bst_pq_t bst_pq_create(ilfunc_t *bst_funs, gen_pqueue_func_t *pq_funs, char qtype, + unsigned int N, gen_stack_t *node_cache){ + + bst_pq_t b; + + b = (bst_pq_t)malloc(sizeof(bst_pq_struct_t)); + b->root = NULL; + b->bst_funs = *bst_funs; + + b->bst_funs.fileout = stdout; + b->qtype = qtype; + b->N = N; + b->last = -1; + b->pq_funs = *pq_funs; + b->v = b->pq_funs.alloc_vector(N); + if (node_cache == NULL){ + b->node_cache = malloc(sizeof(gen_stack_t)); + gen_stack_create(b->node_cache); + } + else{ + b->node_cache = node_cache; + } + return b; +} + + + + + + + +/* insert a new element in the BST_PQ -- TESTED */ +void bst_pq_insert(bst_pq_t b, unsigned int elem_info, double elem_key){ + + /* insert the element in the tree first */ + node_t *n; + int err; + + n = __bst_pq_tree_lookup(b, elem_info); + + /* The following assert should fail ONLY if there is an auto-loop */ + assert(n == NULL); + + if (gen_stack_empty(b->node_cache)){ + n = (node_t*)malloc(sizeof(node_t)); + //n->info = b->bst_funs.alloc(); + //n->key = b->pq_funs.alloc_key(); + } + else{ + err = gen_stack_pop(b->node_cache, (void**) &n); + if (err){ + n = malloc(sizeof(node_t)); + //n->info = b->bst_funs.alloc(); + //n->key = b->pq_funs.alloc_key(); + } + } + //b->bst_funs.copy(elem_info, n->info); + n->info = elem_info; + n->left = n->right = NULL; + if (b->root == NULL){ + b->root = n; + n->parent = NULL; + } + else{ + err = __recursive_insert(b->root, n, & (b->bst_funs)); + if(err){ + fprintf(stderr, "Error during insert into BST!!! (%s: %d)\n", + __FILE__, __LINE__); + exit(23); + } + } + n->active = 1; + n->index = -1; + /* set the key as needed */ + //b->pq_funs.copy_key(elem_key, n->key); + n->key = elem_key; + + /* then, insert the pointer to the element in the PQ */ + __bst_pq_queue_insert(b, n); + +} + +/* delete (or deactivate) the element associated to a given info -- TESTED --*/ +int bst_pq_delete(bst_pq_t b, unsigned int info){ + + node_t *n; + + n = __bst_pq_tree_lookup(b, info); + + if (n != NULL){ + __tree_delete(b, n); + n->active = 0; /* deactivate the node */ + /* After the node has been deleted from the tree, we add it to + the node cache */ + gen_stack_push(b->node_cache, n); + __bst_pq_queue_delete_index(b, n->index); /* remove the reference form the PQ */ + return 0; /* No problem */ + } + return 1; /* the element does not exist */ +} + +/* change the key of an element in the BST_PQ -- TESTED --*/ +int bst_pq_change_key(bst_pq_t b, unsigned int info, double key){ + + node_t *n; + int idx; + + n = __bst_pq_tree_lookup(b, info); + if (n != NULL){ + /* the element exists. We should just force its key and sift as required */ + idx = n->index; + __bst_pq_queue_force_key(b, idx, key); + return 0; /* No problem */ + } + else{ + return 1; /* The element does not exist */ + } + +} + +/* return the head of the PQ -- TESTED --*/ +void* bst_pq_peek(bst_pq_t q){ + + return __bst_pq_queue_peek(q); +} + + +/* Read the key of a given node of the BST */ +double bst_pq_get_key(bst_pq_t b, unsigned int info){ + + node_t *n; + + n = __bst_pq_tree_lookup(b, info); + if (n != NULL){ + return n->key; + } + else{ + return -100000; + } +} + + +/* Read the key of the element of index "index" in the PQ */ +double bst_pq_get_key_from_index(bst_pq_t b, int index){ + + node_t *n; + + n = (node_t *)b->v[index]; + + return n->key; +} + + +/* Dump the BST -- TESTED -- */ +void bst_pq_dump_bst(bst_pq_t b){ + + __bst_pq_tree_view_pre(b); + +} + +/* Show the PQ -- TESTED -- */ +void bst_pq_dump_pq(bst_pq_t b){ + + __bst_pq_queue_dump(b); + +} + +/* Perform a lookup of an element in the BST_PQ -- TESTED-- */ +node_t* bst_pq_lookup(bst_pq_t b, unsigned int info){ + + return __bst_pq_tree_lookup(b, info); +} + + +node_t* bst_pq_lookup_active(bst_pq_t b, unsigned int info){ + + node_t *ptr; + + ptr = __bst_pq_tree_lookup(b, info); + + if(ptr) + assert(ptr->active != 0); + + if (ptr != NULL && ptr->active){ + return ptr; + } + + return NULL; +} + + +/* void bst_pq_insert_existing(bst_pq_t b, node_t *n){ */ + +/* /\* insert the element in the tree first *\/ */ +/* if (n == NULL){ */ +/* fprintf(stderr, "Error!!!! Attempt to insert a NULL existing element (%s: %d)\n", */ +/* __FILE__, __LINE__); */ +/* exit(37); */ +/* } */ +/* /\* n->info = b->bst_funs.alloc(); *\/ */ +/* /\* n->key = b->pq_funs.alloc_key(); *\/ */ +/* /\* b->bst_funs.copy(elem_info, n->info); *\/ */ +/* n->left = n->right = NULL; */ +/* if (b->root == NULL){ */ +/* b->root = n; */ +/* n->parent = NULL; */ +/* } */ +/* else{ */ +/* __recursive_insert(b->root, n, & (b->bst_funs)); */ +/* } */ + +/* n->active = 1; */ +/* /\* set the key as needed *\/ */ +/* //b->pq_funs.copy_key(elem_key, n->key); */ + +/* /\* then, insert the pointer to the element in the PQ *\/ */ +/* __bst_pq_queue_insert(b, n); */ + +/* } */ + + + + + + +void bst_pq_destroy(bst_pq_t b, char destroy_cache){ + + int i; + node_t *n; + + if (b == NULL) + return; + + if(destroy_cache && b->node_cache != NULL ){ + while(!gen_stack_pop(b->node_cache, (void**) &n)){ + //b->bst_funs.dealloc(n->info); + //free(n->key); + free(n); + } + free(b->node_cache->v); + free(b->node_cache); + } + + for(i=b->last; i>=0; i--){ + __tree_delete(b, b->v[i]); + __bst_pq_queue_delete_index(b, i); /* remove the reference form the PQ */ + //bst_pq_delete(b, b->v[i]->info); + //b->bst_funs.dealloc(b->v[i]->info); + //free(b->v[i]->key); + free(b->v[i]); + } + free(b->v); + free(b); +} diff --git a/src/cnm/bst_pq.h b/src/cnm/bst_pq.h new file mode 100644 index 0000000..892eef0 --- /dev/null +++ b/src/cnm/bst_pq.h @@ -0,0 +1,159 @@ +/** + * 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 + * . + * + * (c) Vincenzo Nicosia 2009-2017 -- + * + * 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 is an implementation of a Binary Search Tree augmented by a + * Priority Queue. This data structure is central to the + * implementation of the Clauset-Newman-Moore greedy modularity + * optimisation algorithm + * + */ + +#ifndef __BST_PQ_H__ +#define __BST_PQ_H__ + +#include "gen_stack.h" + + +/** + * + * This is an implementation of a Binary Search Tree augmented by a + * Priority Queue. + * + */ + +#define PARENT(i) (int)(floor((i-1)/2)) + +#define MIN_QUEUE 0x01 +#define MAX_QUEUE 0x02 + +typedef struct node{ + unsigned int info; /* This is the ID of the neighbour used in the BST */ + double key; /* This is the \DeltaQ values used as a key in the + PQ */ + struct node* left; /* left child of the current element in the BST */ + struct node* right; /* right child of the current element in the BST */ + int index; /* Index of the current node in the PQ */ + struct node *parent; /* Parent of the current node in the BST */ + char active; /* indicates whether the node is active or not */ +} node_t; + + +typedef struct{ + void* (*alloc)(); + void (*dealloc)(void*); + //void (*copy)(void *src, void *dst); + int (*compare)(unsigned int e1, unsigned int e2); + void (*print)(unsigned int, void*); + void *fileout; +} ilfunc_t; + + +typedef struct{ + int (*compare)(double e1, double e2); /* compare two elements (standard comparator) */ + void* (*alloc_vector)(unsigned int N); /* */ + void (*dealloc_vector)(void *v); /* */ + void* (*alloc_key)(void); /* Allocate an element for the key */ + void (*copy_key)(void *src, void *dst); /* copy into key */ + void (*print_elem)(void *e); /* print an element */ + void (*set_key)(void *e, double k); /* set a new key to element e */ + int (*compare_to_key)(void *e, double key); /* compare a key with the one of element e */ +} gen_pqueue_func_t; + + +typedef struct { + node_t* root; /* root of the BST */ + int N; /* Maximum size of the PQ */ + int last; /* last element in the PQ */ + node_t **v; /* vector of pointers to the nodes of the BST */ + char qtype; /* type of PQ, either MIN_QUEUE or MAX_QUEUE */ + ilfunc_t bst_funs; + gen_pqueue_func_t pq_funs; + gen_stack_t *node_cache; /* this is a pointer to a cache of + allocated nodes, implemented as a stack */ +} bst_pq_struct_t; + + +typedef bst_pq_struct_t* bst_pq_t; + + + + + +/* bst_pq interface */ + +/* init the BST_PQ */ + +bst_pq_t bst_pq_create(ilfunc_t* bst_funs, gen_pqueue_func_t* pq_funs, char qtype, + unsigned int N, gen_stack_t *node_cache); + +/* Destroy an existing BST_PQ */ +void bst_pq_destroy(bst_pq_t b, char clear_cache); + +/* lookup an element in the BST */ +node_t* bst_pq_lookup(bst_pq_t b, unsigned int info); + +/* insert a new element in the BST_PQ */ +void bst_pq_insert(bst_pq_t b, unsigned int info, double key); + +/* delete (or deactivate) an element in the BST_PQ */ +int bst_pq_delete(bst_pq_t b, unsigned int info); + +/* change the key of an element in the BST_PQ */ +int bst_pq_change_key(bst_pq_t b, unsigned int info, double key); + +/* return the head of the PQ */ +void* bst_pq_peek(bst_pq_t); + +/* Read the key of a given node of the BST */ +double bst_pq_get_key(bst_pq_t b, unsigned int info); + +/* Read the key of the element of index "index" in the PQ */ +double bst_pq_get_key_from_index(bst_pq_t b, int index); + +/* Dump the BST */ +void bst_pq_dump_bst(bst_pq_t b); + +/* Show the PQ */ +void bst_pq_dump_pq(bst_pq_t b); + +/* See if a node is in the BST, either active or inactive */ +node_t* bst_pq_lookup(bst_pq_t b, unsigned int info); + +/* See if a node is in the BST and is ACTIVE */ +node_t* bst_pq_lookup_active(bst_pq_t b, unsigned int info); + + +/* Insert a pre-allocated node_t in the BST_PQ */ +//void bst_pq_insert_existing(bst_pq_t b, node_t *n); + + + +#endif /*__BST_PQ_H__*/ diff --git a/src/cnm/cnm.c b/src/cnm/cnm.c new file mode 100644 index 0000000..d1afb3f --- /dev/null +++ b/src/cnm/cnm.c @@ -0,0 +1,480 @@ +/** + * 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 + * . + * + * (c) Vincenzo Nicosia 2009-2017 -- + * + * 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 finds the communities in a graph using the greedy + * modularity optimisation algorithm proposed by Clauset, Newman, and + * Moore. + * + * References: + * + * [1] A. Clauset, M. E. J. Newman, and C. Moore. "Finding community + * structure in very large networks". Phys. Rev. E 70 (2004), + * 066111. + * + */ + +#include +#include +#include +#include +#include + +#include "utils.h" +#include "cnm_bst_pq.h" +#include "dset.h" + + +void usage(char *argv[]){ + + printf("********************************************************************\n" + "** **\n" + "** -*- cnm -*- **\n" + "** **\n" + "** Find the communities of the input graph 'graph_in' using **\n" + "** the greedy modularity optimisation algorithm proposed by **\n" + "** Clauset, Newman, and Moore. **\n" + "** **\n" + "** The input file 'graph_in' is an edge-list. **\n" + "** If 'graph_in' is equal to '-' (dash), read the file from **\n" + "** the standard input (STDIN). **\n" + "** **\n" + "** The program prints on STDOUT the partition corresponding **\n" + "** to the largest value of modularity, in the format: **\n" + "** **\n" + "** node_1 comm_1 **\n" + "** node_2 comm_2 **\n" + "** node_3 comm_3 **\n" + "** ..... **\n" + "** **\n" + "** where 'comm_1' is the community to which 'node_1' belongs. **\n" + "** **\n" + "** The program prints on STDERR the number of communities and **\n" + "** the value of modularity obtained at each step, in the **\n" + "** format: **\n" + "** **\n" + "** ## nc: NUM_COMM Q_max: Q_MAX **\n" + "** nc_1 Q_1 **\n" + "** nc_2 Q_2 **\n" + "** nc_3 Q_3 **\n" + "** ... **\n" + "** **\n" + "** where 'nc_1', 'nc_2', 'nc_3', etc. is the number of **\n" + "** communities at the 1st, 2nd, 3rd step etc., and 'Q_1', **\n" + "** 'Q_2', 'Q_3', etc. are the value of the modularity **\n" + "** function of the corresponding node partition. The first **\n" + "** output line reports the number of communities NUM_COMM **\n" + "** and corresponding value of modularity Q_MAX of the best **\n" + "** partition found. **\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 2009-2017 (v.nicosia@qmul.ac.uk)\n" + "********************************************************************\n\n" + ); + printf("Usage: %s \n", argv[0]); + exit(1); +} + + +/* shuffle a vector in-place */ +void shuffle_vector_ptr(unsigned int **v, unsigned int N){ + + int i, pos; + void *tmp; + + for(i=N-1; i>=0; i--){ + pos = rand() % N; + if (pos != i){ + tmp = v[i]; + v[i] = v[pos]; + v[pos] = tmp; + } + } +} + + + + +/* initialise BST-related functions */ +void set_bst_funs(ilfunc_t *f){ + + f->alloc = cnm_bst_alloc; + f->dealloc = cnm_bst_dealloc; + f->compare = cnm_bst_compare; + f->print = cnm_bst_print; + +} + +/* Initialise priority-queue-related functions */ +void set_pq_funs(gen_pqueue_func_t *f){ + + f->compare = cnm_pq_compare; + f->alloc_vector = cnm_pq_alloc_vector; + f->dealloc_vector = cnm_pq_dealloc_vector; + f->alloc_key = cnm_pq_alloc_key; + f->copy_key = cnm_pq_copy_key; + f->print_elem = cnm_pq_print_elem; + f->set_key = cnm_pq_set_key; + f->compare_to_key = cnm_pq_compare_to_key; +} + + + +void init_bsts(unsigned int *J_slap, unsigned int *r_slap, unsigned int N, + bst_pq_t *b, bst_pq_t *H, gen_stack_t *node_cache){ + + unsigned int i, j, n, m, deg_i, deg_j; + //struct_key_t dQ; + double dQ; + //struct_neigh_t ith, jth; + unsigned int K; + node_t *node_ptr; + + ilfunc_t bst_funs; + gen_pqueue_func_t pq_funs; + unsigned int *nodes; + + set_bst_funs(&bst_funs); + set_pq_funs(&pq_funs); + + K = r_slap[N]/2; + *H = bst_pq_create(&bst_funs, &pq_funs, MAX_QUEUE, N, node_cache); + nodes = malloc(N * sizeof(unsigned int)); + for (i=0; iv, (b[i]->last + 1) * sizeof(node_t *)); + num_neighs = b[i]->last + 1; + shuffle_vector_ptr((void*)neighs, num_neighs); + + for(m=0; mv, (b[j]->last + 1) * sizeof(node_t *)); + num_neighs = b[j]->last + 1; + shuffle_vector_ptr((void*)neighs, num_neighs); + + for(m=0; mQ_max){ + Q_max = Q; + N_max = N-l-1; + } + } + fprintf(stdout, "### nc: %d Q_max: %g\n", N_max, Q_max); + free(a); + free(neighs); + + return comms; +} + + +void dump_communities(dset_t *comms, unsigned int N){ + + int i; + + for(i=0; i. + * + * (c) Vincenzo Nicosia 2009-2017 -- + * + * 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 + * + *********************************************************************** + * + * Functions used to manage the special BST-augmented priority queue + * used in the Clauset-Newman-Moore greedy modularity optimisation + * algorithm. + * + */ + + +#include +#include + +#include "cnm_bst_pq.h" + + +/* Prototypes for BST-related functions */ + +void* cnm_bst_alloc(){ + + /* nothing to be done, actually*/ + return NULL; // malloc(sizeof(struct_neigh_t)); +} + +void cnm_bst_dealloc(void *info){ + + /* Nothing to be done, actually */ + return; +} + + +int cnm_bst_compare(unsigned int e1, unsigned int e2){ + + //struct_neigh_t *i1, *i2; + + /* i1 = (struct_neigh_t*)e1; */ + /* i2 = (struct_neigh_t*)e2; */ + + //return (((struct_neigh_t*)e1)->neigh - ((struct_neigh_t*)e2)->neigh); + return e1 - e2; +} + +void cnm_bst_print(unsigned int elem, void *fout){ + fprintf(fout, " %d ", elem); +} + + +/* Prototypes for PQ-related functions */ + +int cnm_pq_compare(double e1, double e2){ + + return (e1 - e2) > 0 ? 1 : (e1 - e2) < 0 ? -1 : 0; +} + +void* cnm_pq_alloc_vector(unsigned int N){ + + return malloc(N * sizeof(node_t*)); +} + +void cnm_pq_dealloc_vector(void *v){ + + free (v); +} + +void* cnm_pq_alloc_key(void){ + + + //return malloc(sizeof(struct_key_t)); + return NULL; +} + +void cnm_pq_copy_key(void *src, void *dst){ + + struct_key_t *k1 = (struct_key_t *)src; + struct_key_t *k2 = (struct_key_t *)dst; + + k2->deltaQ = k1->deltaQ; + +} + +void cnm_pq_print_elem(void *e){ + + node_t *n = (node_t*)e; + printf("%g{%d [%d]}", n->key, n->info, n->index); + +} + + +double cnm_pq_get_key(void *e){ + + node_t *n; + + n = (node_t *)e; + return n->key; +} + +void cnm_pq_set_key(void *e, double k){ + + node_t *n; + + n = (node_t *)e; + n->key = k; +} + +int cnm_pq_compare_to_key(void *e, double key){ + + double d1; + d1 = ((node_t*)e)->key; + + return (d1 - key) > 0 ? 1 : (d1 - key) < 0 ? -1 : 0; +} + + + +unsigned int cnm_get_id(node_t *n){ + + return n->info; +} + + +double cnm_get_Q(node_t *n){ + + if (n) + return n->key; + else + return 0; +} diff --git a/src/cnm/cnm_bst_pq.h b/src/cnm/cnm_bst_pq.h new file mode 100644 index 0000000..f49687a --- /dev/null +++ b/src/cnm/cnm_bst_pq.h @@ -0,0 +1,105 @@ +/** + * 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 + * . + * + * (c) Vincenzo Nicosia 2009-2017 -- + * + * 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 + * + *********************************************************************** + * + * Functions used to manage the special BST-augmented priority queue + * used in the Clauset-Newman-Moore greedy modularity optimisation + * algorithm. + * + */ + +#ifndef __CNM_BST_PQ_H__ +#define __CNM_BST_PQ_H__ + +#include "bst_pq.h" + +/** + * + * Specific functions needed for the management of the BST_PQ used in + * the implementation of CNM + * + * (c) Vincenzo Nicosia (KatolaZ) -- 2016 + */ + +/* data structure for the id, to be used by the BST */ +typedef struct{ + int neigh; /* This is the label of a neighbour */ +} struct_neigh_t; + + +/* data structure for the key, to be used by the PQ */ +typedef struct{ + double deltaQ; /* This is the variation in modularity associated to + the join with neighbour contained in info */ +} struct_key_t; + + +/* Prototypes for BST-related functions */ + +void* cnm_bst_alloc(); + +void cnm_bst_dealloc(void*); + +//void cnm_bst_copy(unsigned int src, unsigned int dst); + +int cnm_bst_compare(unsigned int, unsigned int ); + +void cnm_bst_print(unsigned int, void*); + + +/* Prototypes for PQ-related functions */ + +int cnm_pq_compare(double e1, double e2); + +void* cnm_pq_alloc_vector(unsigned int N); + +void cnm_pq_dealloc_vector(void *v); + +void* cnm_pq_alloc_key(void); + +void cnm_pq_copy_key(void *src, void *dst); + +void cnm_pq_print_elem(void *e); + +double cnm_pq_get_key(void *e); + +void cnm_pq_set_key(void *e, double k); + +int cnm_pq_compare_to_key(void *e, double key); + +unsigned int cnm_get_id(node_t *); + +double cnm_get_Q(node_t *); + + + + +#endif /*__CNM_BST_PQ_H__*/ + diff --git a/src/common.mk b/src/common.mk new file mode 100644 index 0000000..69414e6 --- /dev/null +++ b/src/common.mk @@ -0,0 +1 @@ +AM_CFLAGS= -I../include -O2 -std=c99 -Wall diff --git a/src/components/Makefile.am b/src/components/Makefile.am new file mode 100644 index 0000000..df629ab --- /dev/null +++ b/src/components/Makefile.am @@ -0,0 +1,10 @@ +include ../common.mk +bin_PROGRAMS = components largest_component strong_conn node_components +components_SOURCES = components.c ../utils/utils.c ../include/utils.h +components_LDADD = -lm +largest_component_SOURCES = largest_component.c ../utils/utils.c ../include/utils.h +largest_component_LDADD = -lm +strong_conn_SOURCES = strong_conn.c ../utils/utils.c ../include/utils.h +strong_conn_LDADD = -lm +node_components_SOURCES = node_components.c ../utils/utils.c ../include/utils.h +node_components_LDADD = -lm diff --git a/src/components/Makefile.in b/src/components/Makefile.in new file mode 100644 index 0000000..a36407b --- /dev/null +++ b/src/components/Makefile.in @@ -0,0 +1,614 @@ +# Makefile.in generated by automake 1.15 from Makefile.am. +# @configure_input@ + +# Copyright (C) 1994-2014 Free Software Foundation, Inc. + +# This Makefile.in is free software; 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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 + * . + * + * (c) Vincenzo Nicosia 2009-2017 -- + * + * 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 Depth-First Search algorithm to find + * the connected components of a graph provided as input. + * + */ + +#include +#include +#include + +#include "utils.h" + + + +void usage(char *argv[]){ + printf("********************************************************************\n" + "** **\n" + "** -*- components -*- **\n" + "** **\n" + "** Find the connected components of an undirected graph **\n" + "** and print on output their size and/or the list of nodes **\n" + "** belonging to each component. The first parameter 'graph_in' **\n" + "** is the name of the file containing the edge list of the **\n" + "** graph. **\n" + "** **\n" + "** If 'graph_in' is equal to '-' (dash), read the edge list **\n" + "** from standard input (STDIN). **\n" + "** **\n" + "** The program prints on output the SIZE of each connected **\n" + "** component of the graph, one per line: **\n" + "** **\n" + "** size_1 **\n" + "** size_2 **\n" + "** size_3 **\n" + "** **\n" + "** The sizes are in no particular order. **\n" + "** **\n" + "** If 'SHOW' is given as second argument, the list of nodes **\n" + "** belonging to each component is printed as well, in the **\n" + "** format: **\n" + "** **\n" + "** size_1: node_1 node_2 node_3 .... **\n" + "** size_2: node_1 node_2 node_3 .... **\n" + "** size_3: node_1 node_2 node_3 .... **\n" + "** **\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 [SHOW]\n\n" , argv[0]); +} + + + +/** + * + * Depth-First search on node i.... + * + */ +int dfs(unsigned int i, unsigned int *J_slap, unsigned int *r_slap, + unsigned int N, unsigned int nc, + unsigned int *ic, unsigned int *f, + char reset){ + + static unsigned int time; + unsigned int j, s; + + if(reset){ + time = 0; + } + + ic[i] = nc; + s = 1; + time += 1; + + for(j=r_slap[i]; j2 && !my_strcasecmp("SHOW", argv[2])){ + show = 1; + } + + if (!strcmp(argv[1], "-")){ + /* take the input from STDIN */ + filein = stdin; + } + else { + filein = openfile_or_exit(argv[1], "r", 2); + } + + read_slap(filein, &K, &N, &J_slap, &r_slap); + fclose(filein); + + nc = components(J_slap, r_slap, N, &ic, &f, &sizes); + for(i=1; i<=nc; i++){ + printf("%d", sizes[i]); + if (show){ + printf(":"); + for(j=0; j. + * + * (c) Vincenzo Nicosia 2009-2017 -- + * + * 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 + * + *********************************************************************** + * + * Compute the largest connected component of a graph (i.e., the + * connected component that contains the largest number of nodes). + * + * + */ + + +#include +#include +#include + +#include "utils.h" + + +void usage(char *argv[]){ + printf("********************************************************************\n" + "** **\n" + "** -*- largest_component -*- **\n" + "** **\n" + "** Find the largest connected component of 'graph_in'. **\n" + "** **\n" + "** The input file 'graph_in' is an edge-list: **\n" + "** **\n" + "** I_1 J_1 **\n" + "** I_2 J_2 **\n" + "** I_3 J_3 **\n" + "** ... ... **\n" + "** I_K J_K **\n" + "** **\n" + "** If 'graph_in' is equal to '-' (dash), read the file from **\n" + "** the standard input (STDIN). **\n" + "** **\n" + "** The program prints on STDOUT the edge list of the largest **\n" + "** connected component of 'graph_in'. **\n" + "** **\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 2009-2017 (v.nicosia@qmul.ac.uk)\n" + "********************************************************************\n\n" + ); + + printf("Usage: %s \n", argv[0]); +} + + + +/** + * + * Depth-First search on the node i.... + * + */ +int dfs(unsigned int i, unsigned int *J_slap, unsigned int *r_slap, + unsigned int N, unsigned int nc, + unsigned int *ic, unsigned int *f, + char reset){ + + static unsigned int time; + unsigned int j, s; + + if(reset){ + time = 0; + } + + ic[i] = nc; + s = 1; + time += 1; + + for(j=r_slap[i]; j sizes[max_c]) + max_c = i; + } + for(i=0; i i) + fprintf(stdout, "%d %d\n", i, J_slap[j]); + } + } + } + free(J_slap); + free(r_slap); + free(ic); + free(f); + free(sizes); +} diff --git a/src/components/node_components.c b/src/components/node_components.c new file mode 100644 index 0000000..33477f6 --- /dev/null +++ b/src/components/node_components.c @@ -0,0 +1,442 @@ +/** + * 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 + * . + * + * (c) Vincenzo Nicosia 2009-2017 -- + * + * 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 computes (the size of) all the components associated + * to a node, namely the OUT-, IN-, SCC (strongly connected + * component), and the WCC (weekly connected component). + * + * + */ + +#include +#include +#include + +#include "utils.h" + +#define COMP_IN 0x01 +#define COMP_OUT 0x02 +#define COMP_WCC 0x04 +#define COMP_SCC 0x08 +#define COMP_ALL (COMP_IN | COMP_OUT | COMP_WCC | COMP_SCC) + + +void usage(char *argv[]){ + printf("********************************************************************\n" + "** **\n" + "** -*- node_components -*- **\n" + "** **\n" + "** Find all the components associated to a node of a directed **\n" + "** graph, namely the IN-, OUT-, SCC, and WCC, and print on **\n" + "** output their size and/or the list of nodes belonging to **\n" + "** each component. The first parameter 'graph_in' is the name **\n" + "** of the file containing the edge list of the graph. **\n" + "** **\n" + "** The second parameter 'node' is the label of the node whose **\n" + "** components we are interested in. The (optional) third **\n" + "** parameter can be one of 'IN', 'OUT', 'INOUT', **\n" + "** 'SCC', 'WCC', respectively corresponding to the IN-, OUT-, **\n" + "** IN- and OUT-, strongly connected and weakly connected **\n" + "** component to which 'node' belongs. If the is **\n" + "** 'ALL', the program computes all the components to which **\n" + "** 'node' belongs. If no third parameter is provided, all **\n" + "** the components are computed by default. **\n" + "** **\n" + "** If SHOW is given as fourth argument, the list nodes in each **\n" + "** component is dumped on output as well. **\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 [ [SHOW]]\n\n" , argv[0]); +} + +int dfs(unsigned int i, unsigned int *J_slap, unsigned int *r_slap, + unsigned int N, unsigned int nc, + unsigned int *ic, unsigned int *f, + char reset){ + + static unsigned int time = 0; + unsigned int j, s; + + if(reset){ + time = 0; + } + + ic[i] = nc; + s = 1; + + for(j=r_slap[i]; j=0; i--){ + idx = f[i]; + while( (*ic) [idx] != 0 && i > 0 ){ + i -= 1; + idx = f[i]; + } + if (i == 0) + break; + nc += 1; + if (nc == 1){ + s = dfs(idx, J_slap, r_slap, N, nc, *ic, *f_T, 1); + } + else{ + s = dfs(idx, J_slap, r_slap, N, nc, *ic, *f_T, 1); + } + (*sizes)[nc] = s; + } + return nc; +} + + +void compute_comp_out(FILE *filein, unsigned int node, char show){ + + unsigned int N, K, size, i; + unsigned int *J_slap, *r_slap, *ic, *f, *I, *J; + + I = J = NULL; + K = read_ij(filein, &I, &J); + rewind(filein); + + J_slap = NULL; + r_slap = NULL; + /* obtain the SLAP representation of the graph */ + N = convert_ij2slap(I, J, K, &r_slap, &J_slap); + + ic = malloc(N * sizeof(unsigned int)); + f = malloc(N * sizeof(unsigned int)); + for(i=0; i= N2 ? N1 : N2; + + components(J_slap, r_slap, N, &ic, &f, &sizes); + components_rev(J_slap_T, r_slap_T, N, &ic_T, f, &f_T, &sizes_T); + + node_comp = ic_T[node]; + + + printf("SCC: %d", sizes_T[node_comp]); + if (show){ + for(j=0; j 4 && !my_strcasecmp("SHOW", argv[4])){ + show = 1; + } + + + switch(mode){ + case COMP_IN: + compute_comp_in(filein, node, show); + break; + case COMP_OUT: + compute_comp_out(filein, node, show); + break; + case COMP_IN | COMP_OUT: + compute_comp_in(filein, node, show); + compute_comp_out(filein, node, show); + break; + case COMP_WCC: + compute_wcc(filein, node, show); + break; + case COMP_SCC: + compute_scc(filein, node, show); + break; + default: + compute_comp_in(filein, node, show); + compute_comp_out(filein, node, show); + compute_wcc(filein, node, show); + compute_scc(filein, node, show); + }; + fclose(filein); + +} diff --git a/src/components/strong_conn.c b/src/components/strong_conn.c new file mode 100644 index 0000000..4c0f80d --- /dev/null +++ b/src/components/strong_conn.c @@ -0,0 +1,277 @@ +/** + * 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 + * . + * + * (c) Vincenzo Nicosia 2009-2017 -- + * + * 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 finds the (size of the) strongly connected components + * of a directed graph given as input. We use the Kosaraju-Sharir + * algorithm, which performs two DFS scans of the graph, the first + * time using the original DFS algorithm on the graph, and the second + * time using the transposed graph and a slightly modified version of + * "components", which traverses the nodes of the graph in descending + * order of finishing time. + * + * + * + */ + + +#include +#include +#include + +#include "utils.h" + + +void usage(char *argv[]){ + printf("********************************************************************\n" + "** **\n" + "** -*- strong_conn -*- **\n" + "** **\n" + "** Find the strongly connected components of a directed graph **\n" + "** and print on output their size and/or the list of nodes **\n" + "** belonging to each component. The first parameter 'graph_in' **\n" + "** is the name of the file containing the edge list of the **\n" + "** graph. **\n" + "** **\n" + "** If 'graph_in' is equal to '-' (dash), read the edge list **\n" + "** from standard input (STDIN). **\n" + "** **\n" + "** The program prints on output the SIZE of each strongly **\n" + "** connected component of the graph, one per line: **\n" + "** **\n" + "** size_1 **\n" + "** size_2 **\n" + "** size_3 **\n" + "** **\n" + "** The sizes are in no particular order. **\n" + "** **\n" + "** If 'SHOW' is given as second argument, the list of nodes **\n" + "** belonging to each component is printed as well, in the **\n" + "** format: **\n" + "** **\n" + "** size_1: node_1 node_2 node_3 .... **\n" + "** size_2: node_1 node_2 node_3 .... **\n" + "** size_3: node_1 node_2 node_3 .... **\n" + "** **\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 [SHOW]\n\n" , argv[0]); +} + +int dfs(unsigned int i, unsigned int *J_slap, unsigned int *r_slap, + unsigned int N, unsigned int nc, + unsigned int *ic, unsigned int *f, + char reset){ + + static unsigned int time = 0; + unsigned int j, s; + + if(reset){ + time = 0; + } + + ic[i] = nc; + s = 1; + + for(j=r_slap[i]; j=0; i--){ + idx = f[i]; + while( i >0 && (*ic) [idx] != 0 ){ + i -= 1; + idx = f[i]; + } + if (i < 0) + break; + nc += 1; + if (nc == 1){ + s = dfs(idx, J_slap, r_slap, N, nc, *ic, *f_T, 1); + } + else{ + s = dfs(idx, J_slap, r_slap, N, nc, *ic, *f_T, 1); + } + (*sizes)[nc] = s; + } + return nc; +} + + + +int main(int argc, char *argv[]){ + + + FILE *filein; + unsigned int N, K, N1, N2; + unsigned int *I, *J, *J_slap, *r_slap, *J_slap_T, *r_slap_T; + unsigned int *ic, *f, *sizes, *ic_T, *f_T, *sizes_T; + unsigned int i, j, nc_T; + char show = 0; + + if (argc < 2){ + usage(argv); + exit(1); + } + if (argc == 3 && !my_strcasecmp("SHOW", argv[2])){ + show = 1; + } + + if (!strcmp(argv[1], "-")){ + /* take the input from STDIN */ + filein = stdin; + } + else { + filein = openfile_or_exit(argv[1], "r", 2); + } + + + I = J = NULL; + K = read_ij(filein, &I, &J); + J_slap = J_slap_T = NULL; + r_slap = r_slap_T = NULL; + /* obtain the SLAP representation of the graph */ + N1 = convert_ij2slap(I, J, K, &r_slap, &J_slap); + /* obtain the SLAP representation of the transposed graph */ + N2 = convert_ij2slap(J, I, K, &r_slap_T, &J_slap_T); + N = N1 >= N2 ? 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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 + * . + * + * (c) Vincenzo Nicosia 2009-2017 -- + * + * 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 +#include +#include +#include +#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 []\n\n" , argv[0]); +} + + +unsigned int count_stubs(unsigned int *nodes, int N){ + + int i; + unsigned int cnt; + + cnt = 0; + for (i=0; i 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 + * . + * + * (c) Vincenzo Nicosia 2009-2017 -- + * + * 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 +#include +#include +#include +#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 \n\n" , argv[0]); +} + + +unsigned int count_stubs(unsigned int *nodes, int N){ + + int i; + unsigned int cnt; + + cnt = 0; + for (i=0; i 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); +} diff --git a/src/deg_seq/Makefile.am b/src/deg_seq/Makefile.am new file mode 100644 index 0000000..f8bbb07 --- /dev/null +++ b/src/deg_seq/Makefile.am @@ -0,0 +1,6 @@ +include ../common.mk +bin_PROGRAMS = deg_seq deg_seq_w +deg_seq_SOURCES = deg_seq.c ../utils/utils.c ../include/utils.h +deg_seq_LDADD = -lm +deg_seq_w_SOURCES = deg_seq_w.c ../utils/utils.c ../include/utils.h +deg_seq_w_LDADD = -lm diff --git a/src/deg_seq/Makefile.in b/src/deg_seq/Makefile.in new file mode 100644 index 0000000..c8dfb25 --- /dev/null +++ b/src/deg_seq/Makefile.in @@ -0,0 +1,588 @@ +# Makefile.in generated by automake 1.15 from Makefile.am. +# @configure_input@ + +# Copyright (C) 1994-2014 Free Software Foundation, Inc. + +# This Makefile.in is free software; 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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 + * . + * + * (c) Vincenzo Nicosia 2009-2017 -- + * + * 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 prints the degree sequence of a graph given as input + * + */ + + +#include +#include +#include + +#include "utils.h" + + +#define DISTR_ONLY 0x01 +#define SEQ_ONLY 0x02 +#define BOTH 0x04 + + +void usage(char *argv[]){ + printf("********************************************************************\n" + "** **\n" + "** -*- deg_seq -*- **\n" + "** **\n" + "** Compute the degree sequence of a graph given as input. **\n" + "** **\n" + "** The input file 'graph_in' is an edge-list: **\n" + "** **\n" + "** I_1 J_1 **\n" + "** I_2 J_2 **\n" + "** I_3 J_3 **\n" + "** ... ... **\n" + "** I_K J_K **\n" + "** **\n" + "** If 'graph_in' is equal to '-' (dash), read the file from **\n" + "** the standard input (STDIN). **\n" + "** **\n" + "** The program prints on output the degree of each node, one **\n" + "** on each line. **\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 2009-2017 (v.nicosia@qmul.ac.uk)\n" + "********************************************************************\n\n" + ); + printf("Usage: %s \n" , argv[0]); +} + + +void print_deg_seq(FILE *fileout, unsigned int *r, unsigned int N){ + + int i; + + for(i=1; i. + * + * (c) Vincenzo Nicosia 2009-2017 -- + * + * 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 prints the degree and the strength sequence of a + * graph given as input. + * + */ + +#include +#include +#include + +#include "utils.h" + + + +void usage(char *argv[]){ + printf("********************************************************************\n" + "** **\n" + "** -*- deg_seq_w -*- **\n" + "** **\n" + "** Compute the degree and the strength sequence of a graph. **\n" + "** **\n" + "** The input file 'graph_in' is an edge-list: **\n" + "** **\n" + "** I_1 J_1 W_1 **\n" + "** I_2 J_2 W_2 **\n" + "** I_3 J_3 W_3 **\n" + "** ... ... **\n" + "** I_K J_K W_K **\n" + "** **\n" + "** If 'graph_in' is equal to '-' (dash), read the file from **\n" + "** the standard input (STDIN). **\n" + "** **\n" + "** The program prints on output the degree and strength of **\n" + "** all the nodes, in the format: **\n" + "** **\n" + "** k_1 s_1 **\n" + "** k_2 s_2 **\n" + "** ..... **\n" + "** **\n" + "** where 'k_i' is the degree of the i-th node, and 's_i' is **\n" + "** its strength (sum of the weights of incident 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 2009-2017 (v.nicosia@qmul.ac.uk)\n" + "********************************************************************\n\n" + ); 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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 + * . + * + * (c) Vincenzo Nicosia 2009-2017 -- + * + * 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 Dijkstra's algorithm to find the + * shortest paths from a given node (source) to all the other nodes + * of a weighted graph given as input. + * + * References: + * + * [1] E. W. Dijkstra. "A Note on Two Problems in Connexion with + * Graphs". Num. Math. 1 (1959), 269-271. + * + */ + + +#include +#include +#include +#include + +#include "utils.h" +#include "gen_pqueue.h" + +#include "node_w_funs.h" + +#define INFINITY DBL_MAX + + +void usage(char *argv[]){ + printf("********************************************************************\n" + "** **\n" + "** -*- dijkstra -*- **\n" + "** **\n" + "** Compute the distance from the given 'node' to all the other **\n" + "** nodes of a weighted graph. The first parameter 'graph_in' **\n" + "** is the name of the file containing the edge list of the **\n" + "** graph. The second parameter 'node' is the label of the node **\n" + "** for which we want to compute the distances to all the other **\n" + "** nodes. **\n" + "** **\n" + "** If 'graph_in' is equal to '-' (dash), read the edge list **\n" + "** from standard input (STDIN) **\n" + "** **\n" + "** The program prints on output a row of values: **\n" + "** **\n" + "** d0 d1 d2 d3 d4...... **\n" + "** **\n" + "** where d0 is the distance between 'node' and '0', 'd1' is the **\n" + "** distance between 'node' and '1', and so on. If a node is **\n" + "** not reachable from , the corresponding distance is set **\n" + "** to 'inf'. **\n" + "** **\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 \n\n" , argv[0]); +} + + + +void init_prio_queue(gen_pqueue_t **q, unsigned int N){ + + gen_pqueue_func_t *funs; + + funs = malloc(sizeof(gen_pqueue_func_t)); + (*funs).compare = compare_node_w; + (*funs).alloc_vector = alloc_vector_node_w; + (*funs).dealloc_vector = dealloc_vector_node_w; + (*funs).dealloc_elem = dealloc_elem_node_w; + (*funs).print_elem = print_elem_node_w; + (*funs).get_id = get_id_node_w; + (*funs).set_key = set_key_node_w; + (*funs).get_key = get_key_node_w; + (*funs).compare_to_key = compare_to_key_node_w; + + *q = gen_pqueue_init(N, MIN_QUEUE, funs); + free(funs); +} + +void flatten_pqueue_to_array(gen_pqueue_t *q, double *v, unsigned int N){ + + int i; + double *val; + + for(i=0; ii = i; + if (i != s) + elem->w = INFINITY; + else + elem->w = 0.0; + gen_pqueue_insert(qdist, elem); + prev[i] = -1; + dist[i] = INFINITY; + } + + + while (!gen_pqueue_delete(qdist, (void**)&elem)){ /* get the node with minimum distance */ + cur_node = qdist->funs.get_id(elem); + dist_cur_node = *((double*) qdist->funs.get_key(elem)); + if (dist_cur_node == INFINITY){ /* No more nodes are reachable from the origin */ + free(elem); + gen_pqueue_destroy(qdist); + return; + } + dist[cur_node] = dist_cur_node; + for(i=r_slap[cur_node]; i= dist_neigh_node){ + /* now we call gen_pqueue_change_key, which updates the key of node n */ + gen_pqueue_change_key(qdist, gen_pqueue_get_handle(qdist, n), &dist_neigh_node); + prev[n] = cur_node; + } + } + free(elem); + } + gen_pqueue_destroy(qdist); +} + + +void dump_dists(double *v, unsigned int N){ + + int i; + + for(i=0; i= N){ + fprintf(stderr, "Error!!! Source node index should be in the range [0:%d]\n", + N-1); + exit(3); + } + + dists = malloc(N * sizeof(double)); + prev = malloc(N * sizeof(int)); + + dijkstra(N, K, r_slap, J_slap, W_slap, s, dists, prev); + dump_dists(dists, N); + free(J_slap); + free(r_slap); + free(W_slap); + free(dists); + free(prev); +} diff --git a/src/dijkstra/node_w_funs.c b/src/dijkstra/node_w_funs.c new file mode 100644 index 0000000..112140f --- /dev/null +++ b/src/dijkstra/node_w_funs.c @@ -0,0 +1,111 @@ +/** + * 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 + * . + * + * (c) Vincenzo Nicosia 2009-2017 -- + * + * 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 + * + *********************************************************************** + * + * Definition of the functions to be used with the Priority Queue + * + */ +#include +#include + +#include "gen_pqueue.h" +#include "node_w_funs.h" + + +int compare_node_w(const void *e1, const void *e2){ + + node_w_t *n1, *n2; + + n1 = (node_w_t*) e1; + n2 = (node_w_t*) e2; + + return (n1->w == n2->w ? 0 : (n1->w < n2->w ? -1 : 1)); +} + + +void* alloc_vector_node_w(unsigned int N){ + + return malloc(N * sizeof(node_w_t)); +} + +void dealloc_vector_node_w(void *v){ + free(v); +} + + +void dealloc_elem_node_w(void *e){ + + free(e); +} + +void print_elem_node_w(void *e){ + + node_w_t *elem; + + elem = (node_w_t*)e; + + printf("[%d, %2.8g]", elem->i, elem->w); +} + +int get_id_node_w(void *e){ + + node_w_t *elem; + + elem = (node_w_t*)e; + return elem->i; +} + +void set_key_node_w(void *e, void *k){ + + node_w_t *elem; + + + elem = (node_w_t*)e; + elem-> w = *((double*)(k)); +} + +int compare_to_key_node_w(void *e, void *k){ + + node_w_t *elem; + double d; + + elem = (node_w_t*)e; + d = *((double*)k); + + return (elem->w == d ? 0 : (elem->w < d ? -1 : 1)); +} + +void* get_key_node_w(void *e){ + + node_w_t *n; + + n = (node_w_t*)e; + return &(n->w); +} diff --git a/src/dijkstra/node_w_funs.h b/src/dijkstra/node_w_funs.h new file mode 100644 index 0000000..3b670a1 --- /dev/null +++ b/src/dijkstra/node_w_funs.h @@ -0,0 +1,66 @@ +/** + * 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 + * . + * + * (c) Vincenzo Nicosia 2009-2017 -- + * + * 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 + * + *********************************************************************** + * + * Declaration of the functions to be used with the Priority Queue + * + */ +#ifndef __NODE_W_FUNS_H__ +#define __NODE_W_FUNS_H__ + + + +typedef struct{ + int i; + double w; +} node_w_t; + + +int compare_node_w(const void *e1, const void *e2); + +void* alloc_vector_node_w(unsigned int N); + +void dealloc_vector_node_w(void *v); + +void dealloc_elem_node_w(void *e); + +void print_elem_node_w(void *e); + +int get_id_node_w(void *e); + +void set_key_node_w(void *e, void *k); + +void* get_key_node_w(void *e); + +int compare_to_key_node_w(void *e, void *k); + + + +#endif //__NODE_W_FUNS_H__ 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 @@ +# Makefile.in generated by automake 1.15 from Makefile.am. +# @configure_input@ + +# Copyright (C) 1994-2014 Free Software Foundation, Inc. + +# This Makefile.in is free software; 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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 + * . + * + * (c) Vincenzo Nicosia 2009-2017 -- + * + * 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 +#include +#include + +#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", 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){ + 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"); 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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 + * . + * + * (c) Vincenzo Nicosia 2009-2017 -- + * + * 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 graph from the Erdos-Renyi random graph + * model A, i.e., the ensemble of graphs with N nodes and K edges. + * + * + * References: + * + * [1] Erdős, P. & Rényi, A. On Random Graphs I Publ. Math. Debrecen, + * 6, 290 (1959) + * + * [2] Erdos, P. & Renyi, A. On the evolution of random graphs + * Publ. Math. Inst. Hungary. Acad. Sci., 5, 17-61 (1960) + * + */ + + + +#include +#include +#include + +#include "iltree_double.h" + + + +void usage(char *argv[]){ + printf("********************************************************************\n" + "** **\n" + "** -*- er -*- **\n" + "** **\n" + "** sample an Erdos-Renyi graph of N nodes and K links **\n" + "** **\n" + "** the output is an I,J matrix: **\n" + "** I_1 J_1 **\n" + "** I_2 J_2 **\n" + "** I_3 J_3 **\n" + "** ... ... **\n" + "** I_K J_K **\n" + "** **\n" + "** (output is to stdout or to a file) **\n" + "** **\n" + "** If a filename is specified as fourth parameter then **\n" + "** the degree sequence is dumped out to that file **\n" + "** **\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 2010-2017 (v.nicosia@qmul.ac.uk)\n\n" + "********************************************************************\n\n" + ); + printf("Usage: %s []\n\n" , argv[0]); +} + + +void sample_edges(unsigned int N, double K, iltree_t t){ + + long double k; + double i, k1, k2, tmp; + + for(i=0; i k2){ + tmp = k2; + k2 = k1; + k1 = tmp; + } + k = 1.0 * (k2-1)* (k2-2) / 2 + k1; /* This number represents the couple k1, k2 (k1 < k2)*/ + if (!iltree_lookup(t, &k)){ /* The element "k" is not yet present in the BST*/ + /* So we insert into in the tree */ + iltree_insert(t, &k); + /* and then we increment the counter of inserted edges */ + i += 1; + } + } +} + + + +int main(int argc, char *argv[]){ + + iltree_t t = NULL; /* This is the insert-lookup BST */ + FILE *fileout; + char error_str [256]; + unsigned int N; + double K; + + if(argc < 3){ + usage(argv); + exit(1); + } + + N = atoi(argv[1]); + K = atof(argv[2]); + + + if (argc >3){ + fileout = fopen(argv[3], "w+"); + if (!fileout){ + sprintf(error_str, "Error opening file %s", argv[3]); + perror(error_str); + exit(2); + } + } + else{ + fileout = stdout; + } + + t = iltree_double_init(t, fileout); + + srand(time(NULL)); + /* Now we sample K integers without repetition (using the BST)*/ + sample_edges(N, K, t); + /* And then we dump out the edges in I,J format */ + iltree_view_pre(t); + iltree_destroy(t); +} diff --git a/src/er/er_B.c b/src/er/er_B.c new file mode 100644 index 0000000..84a0b4b --- /dev/null +++ b/src/er/er_B.c @@ -0,0 +1,126 @@ +/** + * 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 + * . + * + * (c) Vincenzo Nicosia 2009-2017 -- + * + * 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 graph from the Erdos-Renyi random graph + * model B, i.e., the ensemble of graphs with N nodes where each of + * the possible N(N-1)/2 edges is created with probability equal to + * p, and independently from all the other edges. + * + * + * References: + * + * [1] Erdős, P. & Rényi, A. On Random Graphs I Publ. Math. Debrecen, + * 6, 290 (1959) + * + * [2] Erdos, P. & Renyi, A. On the evolution of random graphs + * Publ. Math. Inst. Hungary. Acad. Sci., 5, 17-61 (1960) + * + */ + + + +#include +#include +#include + +void usage(char *argv[]){ + printf("********************************************************************\n" + "** **\n" + "** -*- er_B -*- **\n" + "** **\n" + "** sample an Erdos-Renyi graph of N nodes and edge probability p **\n" + "** **\n" + "** the output is an I,J matrix: **\n" + "** I_1 J_1 **\n" + "** I_2 J_2 **\n" + "** I_3 J_3 **\n" + "** ... ... **\n" + "** I_K J_K **\n" + "** **\n" + "** (output is to stdout or to a file) **\n" + "** **\n" + "** If a filename is specified as fourth parameter then **\n" + "** the degree sequence is dumped out to that file **\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 2010-2017 (v.nicosia@qmul.ac.uk)\n\n" + "********************************************************************\n\n" + ); + printf("Usage: %s

[]\n\n" , argv[0]); +} + + + +int main(int argc, char *argv[]){ + + unsigned int N, i, j;; + FILE *fileout; + double p, val; + char error_str [256]; + + if(argc < 3){ + usage(argv); + exit(1); + } + + N = atoi(argv[1]); + p = atof(argv[2]); + + + if (argc >3){ + fileout = fopen(argv[3], "w+"); + if (!fileout){ + sprintf(error_str, "Error opening file %s", argv[3]); + perror(error_str); + exit(2); + } + } + else{ + fileout = stdout; + } + + srand(time(NULL)); + + /* Loop over all nodes...*/ + for(i=0; i&2; \ + exit 1;; \ + esac; \ + has_opt=no; \ + sane_makeflags=$$MAKEFLAGS; \ + if $(am__is_gnu_make); then \ + sane_makeflags=$$MFLAGS; \ + else \ + case $$MAKEFLAGS in \ + *\\[\ \ ]*) \ + bs=\\; \ + sane_makeflags=`printf '%s\n' "$$MAKEFLAGS" \ + | sed "s/$$bs$$bs[$$bs $$bs ]*//g"`;; \ + esac; \ + fi; \ + skip_next=no; \ + strip_trailopt () \ + { \ + flg=`printf '%s\n' "$$flg" | sed "s/$$1.*$$//"`; \ + }; \ + for flg in $$sane_makeflags; do \ + test $$skip_next = yes && { skip_next=no; continue; }; \ + case $$flg in \ + *=*|--*) continue;; \ + -*I) strip_trailopt 'I'; skip_next=yes;; \ + -*I?*) strip_trailopt 'I';; \ + -*O) strip_trailopt 'O'; skip_next=yes;; \ + -*O?*) strip_trailopt 'O';; \ + -*l) strip_trailopt 'l'; skip_next=yes;; \ + -*l?*) strip_trailopt 'l';; \ + -[dEDm]) skip_next=yes;; \ + -[JT]) skip_next=yes;; \ + esac; \ + case $$flg in \ + *$$target_option*) has_opt=yes; break;; \ + esac; \ + done; \ + test $$has_opt = yes +am__make_dryrun = (target_option=n; $(am__make_running_with_option)) +am__make_keepgoing = (target_option=k; $(am__make_running_with_option)) +pkgdatadir = $(datadir)/@PACKAGE@ +pkgincludedir = $(includedir)/@PACKAGE@ +pkglibdir = $(libdir)/@PACKAGE@ +pkglibexecdir = $(libexecdir)/@PACKAGE@ +am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd +install_sh_DATA = $(install_sh) -c -m 644 +install_sh_PROGRAM = $(install_sh) -c +install_sh_SCRIPT = $(install_sh) -c +INSTALL_HEADER = $(INSTALL_DATA) +transform = $(program_transform_name) +NORMAL_INSTALL = : +PRE_INSTALL = : +POST_INSTALL = : +NORMAL_UNINSTALL = : +PRE_UNINSTALL = : +POST_UNINSTALL = : +bin_PROGRAMS = f3m$(EXEEXT) +subdir = src/f3m +ACLOCAL_M4 = $(top_srcdir)/aclocal.m4 +am__aclocal_m4_deps = $(top_srcdir)/configure.ac +am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ + $(ACLOCAL_M4) +DIST_COMMON = $(srcdir)/Makefile.am $(am__DIST_COMMON) +mkinstalldirs = $(install_sh) -d +CONFIG_HEADER = $(top_builddir)/config.h +CONFIG_CLEAN_FILES = +CONFIG_CLEAN_VPATH_FILES = +am__installdirs = "$(DESTDIR)$(bindir)" +PROGRAMS = $(bin_PROGRAMS) +am__dirstamp = $(am__leading_dot)dirstamp +am_f3m_OBJECTS = f3m.$(OBJEXT) ../utils/utils.$(OBJEXT) +f3m_OBJECTS = $(am_f3m_OBJECTS) +f3m_DEPENDENCIES = +AM_V_P = $(am__v_P_@AM_V@) +am__v_P_ = $(am__v_P_@AM_DEFAULT_V@) +am__v_P_0 = false +am__v_P_1 = : +AM_V_GEN = $(am__v_GEN_@AM_V@) +am__v_GEN_ = $(am__v_GEN_@AM_DEFAULT_V@) +am__v_GEN_0 = @echo " GEN " $@; +am__v_GEN_1 = +AM_V_at = $(am__v_at_@AM_V@) +am__v_at_ = $(am__v_at_@AM_DEFAULT_V@) +am__v_at_0 = @ +am__v_at_1 = +DEFAULT_INCLUDES = -I.@am__isrc@ -I$(top_builddir) +depcomp = $(SHELL) $(top_srcdir)/depcomp +am__depfiles_maybe = depfiles +am__mv = mv -f +COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \ + $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS) +AM_V_CC = $(am__v_CC_@AM_V@) +am__v_CC_ = $(am__v_CC_@AM_DEFAULT_V@) +am__v_CC_0 = @echo " CC " $@; +am__v_CC_1 = +CCLD = $(CC) +LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@ +AM_V_CCLD = $(am__v_CCLD_@AM_V@) +am__v_CCLD_ = $(am__v_CCLD_@AM_DEFAULT_V@) +am__v_CCLD_0 = @echo " CCLD " $@; +am__v_CCLD_1 = +SOURCES = $(f3m_SOURCES) +DIST_SOURCES = $(f3m_SOURCES) +am__can_run_installinfo = \ + case $$AM_UPDATE_INFO_DIR in \ + n|no|NO) false;; \ + *) (install-info --version) >/dev/null 2>&1;; \ + esac +am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) $(LISP) +# Read a list of newline-separated strings from the standard input, +# and print each of them once, without duplicates. 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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 + * . + * + * (c) Vincenzo Nicosia 2009-2017 -- + * + * 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 + * + *********************************************************************** + * + * Enumerate all the three-nodes subgraphs in a directed network, and + * compute the significance of their number with respect to the + * corresponding configuration model ensemble. + * + * References: + * + * [1] R. Milo et al. "Network Motifs: Simple Building Blocks of + * Complex Networks". Science 298 (2002), 824-827. + * + * [2] R. Milo et al. "Superfamilies of evolved and designed + * networks." Science 303 (2004), 1538-1542 + * + */ + +#include +#include +#include +#include +#include + +#include "utils.h" + + + +void usage(char *argv[]){ + + printf("********************************************************************\n" + "** **\n" + "** -*- f3m -*- **\n" + "** **\n" + "** Count all the 3-node subgraphs of a directed graph given as **\n" + "** input, and compute the relevance (z-score) of each motif **\n" + "** with respect to the corresponding configuration model graph **\n" + "** ensemble. **\n" + "** **\n" + "** The file 'graph_in' contains the edge list of the graph. **\n" + "** **\n" + "** The program prints on STDOUT one line for each of the 13 **\n" + "** motifs, in the format **\n" + "** **\n" + "** motif count mean_rnd std_rnd z-score **\n" + "** **\n" + "** where 'motif' is the motif number (an integer between 1 and **\n" + "** 13), 'count' is the number of subgraphs of that type found **\n" + "** in 'graph_in', 'mean_rnd' is the average number of those **\n" + "** subgraphs found in the randomised realisations of the graph, **\n" + "** 'std_rnd' is the standard deviation associated to 'avg_rnd', **\n" + "** and 'z-score' is the normalised deviation of 'count' from **\n" + "** 'mean_rnd'. **\n" + "** **\n" + "** If the (optional) parameter 'num_random' is provided, use **\n" + "** that number of random realisations to compute the z-score. **\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 2009-2017 (v.nicosia@qmul.ac.uk)\n" + "********************************************************************\n\n" + ); + printf("Usage: %s []\n", argv[0]); +} + + + + + + +#define MIN(x, y) ((x) < (y) ? (x) : (y)) + + +typedef struct{ + unsigned int N; + unsigned int K; + unsigned int *J_slap; + unsigned int *r_slap; +} graph_t; + + +typedef struct{ + double f_count_real[13]; + int num_rnd; + double **f_count_rnd; +} mstats_t; + + +char perm12[3][3] = {{0, 1, 0}, + {1, 0, 0}, + {0, 0, 1}}; + +char perm13[3][3] = {{0, 0, 1}, + {0, 1, 0}, + {1, 0, 0}}; + +char perm23[3][3] = {{1, 0, 0}, + {0, 0, 1}, + {0, 1, 0}}; + + + +void shuffle_list(unsigned int *v, unsigned int K){ + + int i, pos; + + for(i=K-1; i>=0; i--){ + pos = rand() % K; + if (pos != i){ + v[i] ^= v[pos]; + v[pos] ^= v[i]; + v[i] ^= v[pos]; + } + } +} + +int is_simple_graph(unsigned int *J_slap, unsigned int *r_slap, unsigned int K, + unsigned int N){ + + int i, j; + for(i=0; i r_slap[i] && J_slap[j] == J_slap[j-1]) /* or a double edge... */ + return 0; + } + } + return 1; +} + +int is_loop_free(unsigned int *J_slap, unsigned int *r_slap, unsigned int K, + unsigned int N){ + + int i, j; + for(i=0; i n2){ + n1 ^= n2; + n2 ^= n1; + n1 ^= n2; + } + + perm = n1 + (n2<<2); + + switch(perm){ + case (1 + (2<<2)): /* permute 1 with 2 */ + apply_perm_3(m, perm12); + break; + case (1 + (3<<2)): /* permute 1 with 3 */ + apply_perm_3(m, perm13); + break; + case (2 + (3<<2)): /* permute 2 with 3 */ + apply_perm_3(m, perm23); + break; + } +} + + + +/* Load the input graph. We construct two versions of the graph, + i.e. the directed versions G_out ( containing the list of + out-neighbours of each node) and the underlying undirected graph + G_u + + N.B.: This is quite inefficient at the moment, since it reads the + file twice, and could be replaced by one call to read_ij and two + appropriate calls to convert_ij2slap.... */ + +void load_graph(FILE *fin, graph_t *G_u, graph_t *G_out){ + + /*FIXME!!!! WE CANNOT REWIND THE STANDARD OUTPUT !!!!! */ + read_slap(fin, &(G_u->K), &(G_u->N), &(G_u->J_slap), &(G_u->r_slap)); + sort_neighbours(G_u->J_slap, G_u->r_slap, G_u->N); + rewind(fin); + read_slap_dir(fin, &(G_out->K), &(G_out->N), &(G_out->J_slap), &(G_out->r_slap)); + sort_neighbours(G_out->J_slap, G_out->r_slap, G_out->N); + rewind(fin); + +} + + +void dump_matrix_3(char m[3][3]){ + + int i, j; + + for(i=0; i<3; i++){ + for(j=0; j<3; j++){ + printf("%d ", m[i][j]); + } + printf("\n"); + } +} + + +int motif_number(char m[3][3]){ + + char m0[3][3]; + char m1[3][3]; + char m2[3][3]; + char m3[3][3]; + + int v, v0, v1, v2, v3, v4, v5; + int i,j; + + for(i=0; i<3; i++){ + for(j=0; j<3; j++){ + m0[i][j] = m[i][j]; + } + } + + if (row_value(m[0]) == 0){ + permute_matrix_3(m0, 1, 2); + } + if (row_value(m0[1]) == 0){ + permute_matrix_3(m0, 2, 3); + } + + + for(i=0; i<3; i++){ + for(j=0; j<3; j++){ + m1[i][j] = m0[i][j]; + m2[i][j] = m0[i][j]; + m3[i][j] = m0[i][j]; + } + } + + /* We consider here all the 6 possible permutations... */ + + /* {0, 1, 2} */ + v0 = matrix_value(m0); + /* {1, 0, 2} */ + permute_matrix_3(m1, 1, 2); + v1 = matrix_value(m1); + /* {2, 1, 0} */ + permute_matrix_3(m2, 1, 3); + v2 = matrix_value(m2); + /* {0, 2, 1} */ + permute_matrix_3(m3, 2, 3); + v3 = matrix_value(m3); + /* {1, 2, 0} */ + permute_matrix_3(m2, 1, 2); + v4 = matrix_value(m2); + /* {2, 0, 1} */ + permute_matrix_3(m3, 1, 2); + v5 = matrix_value(m3); + + v = MIN (MIN( MIN( MIN( MIN( v0, v1), v2), v3), v4), v5); + + switch(v){ + case 6: + return 0; + case 12: + return 1; + case 14: + return 2; + case 36: + return 3; + case 38: + return 4; + case 46: + return 5; + case 74: + return 6; + case 78: + return 7; + case 98: + return 8; + case 102: + return 9; + case 108: + return 10; + case 110: + return 11; + case 238: + return 12; + default: + fprintf(stderr, "No motif with number %d! Exiting\n", v); + dump_matrix_3(m); + exit(5); + } +} + +int get_motif_3(int n1, int n2, int n3, graph_t *G_out){ + + char m[3][3]; + unsigned int n[3] = {n1, n2, n3}; + + int i, j, v; + + for(i=0; i<3; i++){ + for (j=0; j<3; j++){ + if (is_neigh(G_out->J_slap, G_out->r_slap, G_out->N, + n[i], n[j])){ + m[i][j] = 1; + } + else{ + m[i][j] = 0; + } + } + } + v = motif_number(m); + return v; +} + + + +void find_subgraphs_3(graph_t *G_u, graph_t *G_out, double *f_cnt){ + + int i, j, k, n1, n2; + int val; + + for (i=0; iN; i++){ + for(n1 = G_u->r_slap[i]; n1r_slap[i+1]; n1++){ + /* j is a first-neighbour of i in G_u */ + j = G_u->J_slap[n1]; + /* avoid multiple entries in the J_slap vector */ + if (n1 > G_u->r_slap[i] && j == G_u->J_slap[n1-1]) + continue; + for(n2 = n1+1; n2 < G_u->r_slap[i+1]; n2++){ + /* and k is another first neighbour of i in G_u */ + k = G_u->J_slap[n2]; + /* avoid multiple entries in the J_slap vector */ + if (n2 > n1+1 && k == G_u->J_slap[n2-1]) + continue; + /* now, if j and k are connected by an edge, we consider this + triangle only if iJ_slap, G_u->r_slap, G_u->N, j, k) && + (j < i || k < j || k < i)) || (j==k)) + continue; + val = get_motif_3(i, j, k, G_out); + f_cnt[val] +=1; + } + } + } + +} + +void init_graph(graph_t *G1){ + G1->J_slap = G1->r_slap = NULL; +} + +void init_stats(mstats_t *st, int n_rand){ + int i; + + st->f_count_rnd = malloc(n_rand * sizeof(double*)); + + st->num_rnd = n_rand; + + for(i=0; i<13; i++){ + st->f_count_real[i] = 0; + } + + for(i=0; if_count_rnd[i] = malloc(13 * sizeof(double)); + memset(st->f_count_rnd[i], 0, 13 * sizeof(double)); + } +} + + +void compute_rnd_st_mean_std(mstats_t *st, double *mean, double *std){ + + double sum[13], sum2[13]; + double val, n; + + int i, j; + + + n = st->num_rnd; + + for (i=0; i<13; i++){ + sum[i] = sum2[i] = 0; + } + + if (n == 0) + return; + + for(i=0; if_count_rnd[i][j]; + sum[j] += val; + sum2[j] += val*val; + } + } + + for(i=0; i<13; i++){ + mean[i] = sum[i] / n; + if (sum2[i] > 0) + std[i] = sqrt(sum2[i] * 1.0/(n-1) - 1.0/( n * (n-1)) * sum[i]*sum[i]); + else + std[i] = 0.0; + } +} + + + + + +void dump_stats(mstats_t *st){ + + int i; + double v_mean[13], v_std[13], x; + + memset(v_mean, 0, 13 * sizeof(double)); + memset(v_std, 0, 13 * sizeof(double)); + + compute_rnd_st_mean_std(st, v_mean, v_std); + for(i=0; i<13; i++){ + x = st->f_count_real[i]; + if (v_std[i] > 0) + printf("%-2d %12.0f %15.2f %10.3f %+10.3f\n", i+1, x, + v_mean[i], v_std[i], 1.0 * (x - v_mean[i])/v_std[i] ); + else + printf("%-2d %12.0f %15.2f %10.3f %+10.3f\n", i+1, x, + v_mean[i], v_std[i], 0.0); + + } +} + +void randomise_graph(graph_t *G_out, graph_t *RNDG_out, graph_t *RNDG_u){ + + static unsigned int *I, *J; + static unsigned int I_size, J_size; + unsigned int *tmp; + + if (!I || I_size < 2*G_out->K){ + tmp = realloc(I, G_out -> K * 2 * sizeof(unsigned int)); + VALID_PTR_OR_EXIT(tmp, 3); + I = tmp; + I_size = 2*G_out->K; + } + + + if (!J || J_size < 2*G_out->K){ + tmp = realloc(J, G_out -> K * 2 * sizeof(unsigned int)); + VALID_PTR_OR_EXIT(tmp, 3); + J = tmp; + J_size = 2*G_out->K; + } + + if (RNDG_out->J_slap){ + free(RNDG_out->J_slap); + RNDG_out->J_slap = NULL; + } + + + RNDG_out->J_slap = sample_conf_model_smart(G_out->J_slap, G_out->r_slap, G_out->K, G_out->N); + + tmp = realloc(RNDG_out->r_slap, (G_out->N + 1) * sizeof(unsigned int)); + VALID_PTR_OR_EXIT(tmp, 19); + RNDG_out->r_slap = tmp; + memcpy(RNDG_out->r_slap, G_out->r_slap, (G_out->N + 1) * sizeof(unsigned int)); + RNDG_out->N = G_out->N; + RNDG_out->K = G_out->K; + + + convert_slap2ij(RNDG_out->J_slap, RNDG_out->r_slap, RNDG_out->N, I, J); + + /* copy J at the end of I */ + memcpy(&(I[G_out->K]), J, G_out->K * sizeof(unsigned int)); + /* copy I at the end of J */ + memcpy(&(J[G_out->K]), I, G_out->K * sizeof(unsigned int)); + + + RNDG_u->N = convert_ij2slap(I, J, 2*G_out->K, & (RNDG_u->r_slap), &(RNDG_u->J_slap)); + + RNDG_u->K = 2 * G_out->K; + + sort_neighbours(RNDG_u->J_slap, RNDG_u->r_slap, RNDG_u->N); + sort_neighbours(RNDG_out->J_slap, RNDG_out->r_slap, RNDG_out->N); + + if (!is_loop_free(RNDG_u->J_slap, RNDG_u->r_slap, RNDG_u->K, RNDG_u->N)){ + fprintf(stderr, "Error!!!! 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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 + * . + * + * (c) Vincenzo Nicosia 2009-2017 -- + * + * 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 fits a set of values provided as input with a + * power-law function using the Maximum-Likelihood Estimator (MLE). + * + * References: + * + * [1] A. Clauset, C. R. Shalizi, and M. E. J. Newman. "Power-law + * distributions in empirical data". SIAM Rev. 51, (2007), + * 661-703. + * + */ + + +#include +#include +#include +#include +#include + +#include "utils.h" + +void usage(char *argv[]){ + + printf("********************************************************************\n" + "** **\n" + "** -*- fitmle -*- **\n" + "** **\n" + "** Fit a set of values with a power-law function using the **\n" + "** Maximum-Likelihood Estimator (MLE). The program implements **\n" + "** the MLE for both continuous and discrete values, and **\n" + "** selects the appropriate one automatically. **\n" + "** **\n" + "** The input file 'data_in' contains one value on each row. **\n" + "** If 'data_in' is '-' (dash), read the values from the **\n" + "** standard input (STDIN). **\n" + "** **\n" + "** The program prints on output a single row, in the format: **\n" + "** **\n" + "** gamma x_min ks **\n" + "** **\n" + "** where 'gamma' is the exponent of the best fit, 'x_min' is **\n" + "** the smallest of the input values after which the power-law **\n" + "** hypothesis hold, and 'ks' is the value of the KS statistics **\n" + "** for the best fit. **\n" + "** **\n" + "** The second (optional) parameter 'tol' sets the tolerance **\n" + "** on the acceptable statistical error of the fit (set to **\n" + "** 0.1 if no value is provided). **\n" + "** **\n" + "** If the third parameter is 'TEST', the program uses the **\n" + "** the Kolmogorov-Smirnov test on a series of bootstrapped **\n" + "** power-law sequences to estimate the p-value of the fit, and **\n" + "** the output is in the format: **\n" + "** **\n" + "** gamma x_min ks p_value **\n" + "** **\n" + "** Higher values of 'p_value' correspond to better fits. **\n" + "** **\n" + "** If 'num_test' is provided, use that number of bootstrapped **\n" + "** sequences to compute the p-value. Otherwise, use 100 **\n" + "** sequences. **\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 2010-2017 (v.nicosia@qmul.ac.uk)\n\n" + "********************************************************************\n\n" + ); + printf("Usage: %s [ [ TEST []]]\n", argv[0]); +} + + +void load_data(char *fname, double **data, unsigned int *N, char sort){ + + FILE *fin; + char error_str[256]; + char buff[256]; + char *ptr; + double x; + unsigned int size; + + size = 10; + + *data = malloc(size * sizeof(double)); + + *N=0; + if (!strcmp(fname, "-")){ + fin = stdin; + } + else{ + fin = fopen(fname, "r"); + } + if (!fin){ + sprintf(error_str, "Error opening file %s", fname); + perror(error_str); + exit(3); + } + + while(fgets(buff, 256, fin)){ + ptr = strtok(buff, " "); + if (ptr[0] == '#') + continue; + x = atof(ptr); + if (*N == size){ + size += 10; + *data = realloc(*data, size*sizeof(double)); + } + (*data)[*N] = x; + *N += 1; + } + *data = realloc(*data, (*N)*sizeof(double)); + if (sort){ + qsort(*data, *N, sizeof(double), compare_double); + } + fclose(fin); + return; +} + +/** + * find the first position at which the element x appears in the + * "data" array using binary search (the array is sorted in + * increasing order of x) + */ +int find_pos_x(double x,double *data, unsigned int N){ + int H, L, M; + + L = 0; + H = N-1; + + while(L<=H){ + M = (H + L)/2; + if (x == data[M]){ + while(M >=0 && x == data[M]) M--; + if (M==-1){ + return 0; + } + return M+1; /* we return the index of the first appearance of element x*/ + } + else if (x < data[M]){ + H = M-1; + } + else if (x > data[M]){ + L = M+1; + } + } + return -1; /* the value is not present */ +} + +double fit_alpha(double *data, unsigned int N, double xmin, unsigned int idx){ + + double alpha = 0; + int i; + + for(i = idx; i < N; i++){ + alpha += log(data[i]*1.0/(xmin-0.5)); + } + alpha = 1 + (N - idx) * 1.0 / alpha; + return alpha; +} + + +double fit_alpha_continuous(double *data, unsigned int N, double xmin, unsigned int idx){ + + double alpha = 0; + int i; + + for(i = idx; i < N; i++){ + alpha += log(data[i]*1.0/(xmin)); + } + alpha = 1 + (N - idx) * 1.0 / alpha; + return alpha; +} + + +/* + * + * Kolmogorov-Smirnov test + * + */ + +double KS (double *data, unsigned int N, double alpha, int idx){ + + double c_data, c_theo, val; + double xmin, x; + double dist, max_dist = -1; + int i; + + c_data = c_theo = 0.0; + xmin = data[idx]; + + for (i=idx; i max_dist){ + max_dist = dist; + } + i++; + } + c_data = 1.0 * (i- idx)/(N-idx); + } + return max_dist; +} + +void dump_data_double(double *v, unsigned int N){ + int i; + + if (N < 1){ + return; + } + printf("%g",v[0]); + for(i=1; i ks){ + num += 1; + } + } + free(v); + return 1.0 * num / num_test; +} + +/* We assume that the data set has already been sorted in ascending + order */ +int is_continuous(double *data, int N){ + int i; + + for (i=0; i 2) + tol = atof(argv[2]); + else + tol = 0.1; + + if (argc > 3 && !my_strcasecmp(argv[3], "TEST")){ + test = 1; + } + + if(argc > 4){ + num_test = atoi(argv[4]); + } + else + num_test = 100; + + srand(time(NULL)); + + + + load_data(argv[1], &data, &N, 1); + + if(is_continuous(data, N)){ + fprintf(stderr, "Using continuous fit\n"); + fit_func = best_fit_continuous; + } + else{ + fprintf(stderr, "Using discrete fit\n"); + fit_func = best_fit; + } + + scaling_fact = 1.0; + + fit_func(data, N, &alpha, &xmin, tol); + i = find_pos_x(xmin, data, N); + ks = KS(data, N, alpha, i); + if (test){ + p_value = test_powerlaw(data, N, alpha, xmin, ks, num_test, fit_func); + printf("%g %g %g %g\n", alpha, xmin/scaling_fact, ks, p_value); + } + else{ + printf("%g %g %g\n", alpha, xmin / scaling_fact, ks); + } + free(data); +} diff --git a/src/gn/Makefile.am b/src/gn/Makefile.am new file mode 100644 index 0000000..77874be --- /dev/null +++ b/src/gn/Makefile.am @@ -0,0 +1,5 @@ +include ../common.mk +bin_PROGRAMS = gn +gn_SOURCES = gn.c ../utils/utils.c ../include/utils.h +gn_LDADD = -lm + diff --git a/src/gn/Makefile.in b/src/gn/Makefile.in new file mode 100644 index 0000000..85ffa4c --- /dev/null +++ b/src/gn/Makefile.in @@ -0,0 +1,578 @@ +# Makefile.in generated by automake 1.15 from Makefile.am. +# @configure_input@ + +# Copyright (C) 1994-2014 Free Software Foundation, Inc. + +# This Makefile.in is free software; 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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 + * . + * + * (c) Vincenzo Nicosia 2009-2017 -- + * + * 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 Girvan-Newman algorithm for community + * detection, based on the removal of edges with largest betweenness. + * + * + * References: + * + * [1] M. Girvan and M. E. J. Newman. "Community structure in social + * and biological networks". P. Natl. Acad. Sci. USA 99 (2002), + * 7821--7826. + * + */ + + +#include +#include +#include +#include +#include + +#include "utils.h" + +void usage(char *argv[]){ + + printf("********************************************************************\n" + "** **\n" + "** -*- gn -*- **\n" + "** **\n" + "** Find the communities of the input graph 'graph_in' using **\n" + "** the Girvan-Newman algorithm (successive removal of edges **\n" + "** with high betweeneess). **\n" + "** **\n" + "** The input file 'graph_in' is an edge-list: **\n" + "** **\n" + "** I_1 J_1 **\n" + "** I_2 J_2 **\n" + "** I_3 J_3 **\n" + "** ... ... **\n" + "** I_K J_K **\n" + "** **\n" + "** If 'graph_in' is equal to '-' (dash), read the file from **\n" + "** the standard input (STDIN). **\n" + "** **\n" + "** The program prints on STDOUT the partition corresponding **\n" + "** to the largest value of modularity, in the format: **\n" + "** **\n" + "** node_1 comm_1 **\n" + "** node_2 comm_2 **\n" + "** node_3 comm_3 **\n" + "** ..... **\n" + "** **\n" + "** where 'comm_1' is the community to which 'node_1' belongs. **\n" + "** **\n" + "** The program prints on STDERR the number of communities and **\n" + "** the value of modularity obtained after the removal of each **\n" + "** edge, in the format: **\n" + "** **\n" + "** **\n" + "** ## nc: NUM_COMM Q_max: Q_MAX **\n" + "** nc_1 Q_1 **\n" + "** nc_2 Q_2 **\n" + "** nc_3 Q_3 **\n" + "** ... **\n" + "** **\n" + "** where 'nc_1', 'nc_2', 'nc_3', etc. is the number of **\n" + "** communities (connected components) remaining after the **\n" + "** 1st, 2nd, 3rd, etc. edge has been removed, and 'Q_1', **\n" + "** 'Q_2', 'Q_3', etc. are the value of the modularity **\n" + "** function of the corresponding node partition. The first **\n" + "** output line reports the number of communities NUM_COMM **\n" + "** and corresponding value of modularity Q_MAX of the best **\n" + "** partition found. **\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 2009-2017 (v.nicosia@qmul.ac.uk)\n" + "********************************************************************\n\n" + ); + printf("Usage: %s \n", argv[0]); + exit(1); +} + + +void add_predecessor(unsigned int **pred, unsigned int k){ + + (*pred)[0] += 1; + *pred = realloc(*pred, ((*pred)[0] + 1) * sizeof(unsigned int)); + (*pred)[ (*pred)[0] ] = k; +} + + + +/* + * + * Compute node and edge betweenness, based on shortest paths + * originating on the "num" nodes specified in "nlist". "edge_bet" + * should be an appropriately allocated (and initialised to zero!!!!) + * vector of length equal to J_slap, and will contain the values of + * edge betweenness. + * + */ +double* compute_bet_dependency_active(unsigned int N, unsigned int *J_slap, unsigned int *r_slap, + double *edge_bet, char *active){ + + static unsigned int *marked, **preds, *dist, *nj; + static double *delta, *cB; + int i, j, k, w, idx, cur_node; + double val; + unsigned int d; + unsigned int n, nd, ndp; + unsigned int edge_pos; + + if (!dist) + dist = malloc(N * sizeof(unsigned int)); + if (!marked) + marked = malloc(N * sizeof(unsigned int)); + if (!preds) + preds = malloc(N * sizeof(unsigned int *)); + if (!nj) + nj = malloc(N * sizeof(unsigned int)); + if (!delta) + delta = malloc(N * sizeof(double)); + if (!cB) + cB = malloc(N * sizeof(double)); + + for (i=0; i 0){ + for(i = n; i< n+nd; i ++){ + cur_node = marked[i]; + for (k=r_slap[cur_node]; k=1; k--){ + w = marked[k]; + for (idx=1; idx <= preds[w][0]; idx ++ ){ + i = preds[w][idx]; + val = 1.0 * nj[i] / nj[w] * (1 + delta[w]); + delta[i] += val; + /* Now we should update the betweenness of the edge (i,w) in + the appropriate position of the vector edge_bet*/ + find_neigh_in_Jslap(J_slap, r_slap, N, i, w, &edge_pos); + edge_bet[edge_pos] += val; + find_neigh_in_Jslap(J_slap, r_slap, N, w, i, &edge_pos); + edge_bet[edge_pos] += val; + } + cB[w] += delta[w]; + } + } + //free(marked); + return cB; +} + + + +/** + * + * Depth-First search on the node i.... + * + */ +int dfs_active(unsigned int i, unsigned int *J_slap, unsigned int *r_slap, + unsigned int N, unsigned int nc, unsigned int *ic, unsigned int *f, + char reset, char *active){ + + static unsigned int time; + unsigned int j, s; + + if(reset){ + time = 0; + } + + ic[i] = nc; + s = 1; + time += 1; + + for(j=r_slap[i]; j= max && active[i % K]){ + max = v[i % K]; + pos_max = i % K; + } + } + return pos_max; +} + + +unsigned int find_pos_max(double *v, unsigned int K, char *active){ + + unsigned int i; + double max; + unsigned int base, pos_max; + + base = 0; + while(! active[base] ) + base = (base + 1) % K; + max = v[base]; + pos_max = base; + + for(i=base; i= max && active[i % K]){ + max = v[i % K]; + pos_max = i % K; + } + } + return pos_max; +} + + +/* This function compute the modularity function of the partition + 'part'...*/ +double compute_modularity(unsigned int *J_slap, unsigned int *r_slap, unsigned int N, + unsigned int *part, unsigned int nc){ + static double *e, *a; + + unsigned int i, j, n, K; + unsigned int ci, cj; + double Q; + + if(!e) + e = malloc((N+1) * sizeof(double)); + if(!a) + a = malloc((N+1) * sizeof(double)); + + memset(e, 0, (N+1) * sizeof(double)); + memset(a, 0, (N+1) * sizeof(double)); + + K = r_slap[N]; + + for (i=0; i 0){ + if (Q > Q_max){ + Q_max = Q; + nc_max = nc; + memcpy (best_part, ic, N * sizeof(unsigned int)); + } + } + else{ + Q_max = Q; + memcpy(best_part, ic, N*sizeof(unsigned int)); + } + } + /* Return the best partition */ + fprintf(stdout, "### nc: %d Q_max: %g\n", nc_max, Q_max); + free(f); + free(ic); + free(sizes); + free(edge_bet); + free(active); + return best_part; +} + + + +void dump_partition(unsigned int *p, unsigned int N){ + + unsigned int i; + for(i=0; i&2; \ + exit 1;; \ + esac; \ + has_opt=no; \ + sane_makeflags=$$MAKEFLAGS; \ + if $(am__is_gnu_make); then \ + sane_makeflags=$$MFLAGS; \ + else \ + case $$MAKEFLAGS in \ + *\\[\ \ ]*) \ + bs=\\; \ + sane_makeflags=`printf '%s\n' "$$MAKEFLAGS" \ + | sed "s/$$bs$$bs[$$bs $$bs ]*//g"`;; \ + esac; \ + fi; \ + skip_next=no; \ + strip_trailopt () \ + { \ + flg=`printf '%s\n' "$$flg" | sed "s/$$1.*$$//"`; \ + }; \ + for flg in $$sane_makeflags; do \ + test $$skip_next = yes && { skip_next=no; continue; }; \ + case $$flg in \ + *=*|--*) continue;; \ + -*I) strip_trailopt 'I'; skip_next=yes;; \ + -*I?*) strip_trailopt 'I';; \ + -*O) strip_trailopt 'O'; skip_next=yes;; \ + -*O?*) strip_trailopt 'O';; \ + -*l) strip_trailopt 'l'; skip_next=yes;; \ + -*l?*) strip_trailopt 'l';; \ + -[dEDm]) skip_next=yes;; \ + -[JT]) skip_next=yes;; \ + esac; \ + case $$flg in \ + *$$target_option*) has_opt=yes; break;; \ + esac; \ + done; \ + test $$has_opt = yes +am__make_dryrun = (target_option=n; $(am__make_running_with_option)) +am__make_keepgoing = (target_option=k; $(am__make_running_with_option)) +pkgdatadir = $(datadir)/@PACKAGE@ +pkgincludedir = $(includedir)/@PACKAGE@ +pkglibdir = $(libdir)/@PACKAGE@ +pkglibexecdir = $(libexecdir)/@PACKAGE@ +am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd +install_sh_DATA = $(install_sh) -c -m 644 +install_sh_PROGRAM = $(install_sh) -c +install_sh_SCRIPT = $(install_sh) -c +INSTALL_HEADER = $(INSTALL_DATA) +transform = $(program_transform_name) +NORMAL_INSTALL = : +PRE_INSTALL = : +POST_INSTALL = : +NORMAL_UNINSTALL = : +PRE_UNINSTALL = : +POST_UNINSTALL = : +bin_PROGRAMS = graph_info$(EXEEXT) +subdir = src/graph_info +ACLOCAL_M4 = $(top_srcdir)/aclocal.m4 +am__aclocal_m4_deps = $(top_srcdir)/configure.ac +am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ + $(ACLOCAL_M4) +DIST_COMMON = $(srcdir)/Makefile.am $(am__DIST_COMMON) +mkinstalldirs = $(install_sh) -d +CONFIG_HEADER = $(top_builddir)/config.h +CONFIG_CLEAN_FILES = +CONFIG_CLEAN_VPATH_FILES = +am__installdirs = "$(DESTDIR)$(bindir)" +PROGRAMS = $(bin_PROGRAMS) +am__dirstamp = $(am__leading_dot)dirstamp +am_graph_info_OBJECTS = graph_info.$(OBJEXT) ../utils/utils.$(OBJEXT) +graph_info_OBJECTS = $(am_graph_info_OBJECTS) +graph_info_DEPENDENCIES = +AM_V_P = $(am__v_P_@AM_V@) +am__v_P_ = $(am__v_P_@AM_DEFAULT_V@) +am__v_P_0 = false +am__v_P_1 = : +AM_V_GEN = $(am__v_GEN_@AM_V@) +am__v_GEN_ = $(am__v_GEN_@AM_DEFAULT_V@) +am__v_GEN_0 = @echo " GEN " $@; +am__v_GEN_1 = +AM_V_at = $(am__v_at_@AM_V@) +am__v_at_ = $(am__v_at_@AM_DEFAULT_V@) +am__v_at_0 = @ +am__v_at_1 = +DEFAULT_INCLUDES = -I.@am__isrc@ -I$(top_builddir) +depcomp = $(SHELL) $(top_srcdir)/depcomp +am__depfiles_maybe = depfiles +am__mv = mv -f +COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \ + $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS) +AM_V_CC = $(am__v_CC_@AM_V@) +am__v_CC_ = $(am__v_CC_@AM_DEFAULT_V@) +am__v_CC_0 = @echo " CC " $@; +am__v_CC_1 = +CCLD = $(CC) +LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@ +AM_V_CCLD = $(am__v_CCLD_@AM_V@) +am__v_CCLD_ = $(am__v_CCLD_@AM_DEFAULT_V@) +am__v_CCLD_0 = @echo " CCLD " $@; +am__v_CCLD_1 = +SOURCES = $(graph_info_SOURCES) +DIST_SOURCES = $(graph_info_SOURCES) +am__can_run_installinfo = \ + case $$AM_UPDATE_INFO_DIR in \ + n|no|NO) false;; \ + *) (install-info --version) >/dev/null 2>&1;; \ + esac +am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) $(LISP) +# Read a list of newline-separated strings from the standard input, +# and print each of them once, without duplicates. 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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 + * . + * + * (c) Vincenzo Nicosia 2009-2017 -- + * + * 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 + * + *********************************************************************** + * + * Compute and print the basic properties of the undirected graph on + * input, i.e., the number of nodes, the number of edges, and the + * first two uncentered moments of the degree sequence ( and + * ). + * + */ + + +#include +#include +#include +#include "utils.h" + + +void usage(char *argv[]){ + + printf("********************************************************************\n" + "** **\n" + "** -*- graph_info -*- **\n" + "** **\n" + "** Compute basic information about the 'graph_in', namely the **\n" + "** number of nodes, number of edges, average degree, and the **\n" + "** average squared degree. **\n" + "** **\n" + "** The input file 'graph_in' is an edge-list: **\n" + "** **\n" + "** I_1 J_1 **\n" + "** I_2 J_2 **\n" + "** I_3 J_3 **\n" + "** ... ... **\n" + "** I_K J_K **\n" + "** **\n" + "** If 'graph_in' is equal to '-' (dash), read the file from **\n" + "** the standard input (STDIN). **\n" + "** **\n" + "** The output is a single line containing in the format: **\n" + "** **\n" + "** N K avg_k avg_k2 **\n" + "** **\n" + "** where 'N' is the number of nodes, 'K' is the number of **\n" + "** edges, 'avg_k' is the average degree, and 'avg_k2' is the **\n" + "** average of the squared degree. **\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 2009-2017 (v.nicosia@qmul.ac.uk)\n" + "********************************************************************\n\n" + ); + printf("Usage: %s \n", argv[0]); +} + + + +double ksquare_mean(unsigned int N, unsigned int *r_slap){ + + double sum = 0; + unsigned int i; + unsigned int k; + for(i=0; i

[SHOW]\n\n" , argv[0]); +} + + + +/** + * + * This function checks if j is a neighbour of i, looking into the + * m positions of J starting at i*m + * + * In practice, the assumption is that J contains the m neighbours of + * node 0 in the first m positions, then the m neighbours of node 1, + * and to forth + * + */ + +int __ws_is_neigh(unsigned int i, unsigned int j, unsigned int *J, unsigned int m){ + + int k; + + for(k = i*m; k< (i+1)*m; k++){ + if (J[k] == j) + return 1; + } + return 0; +} + + +int create_circle(unsigned int N, unsigned int m, unsigned int **J){ + + int K; + int i, j, l; + + K = N *m; + + *J = malloc(K * sizeof(unsigned int)); + + K = 0; + + for(i=0; i 4 && !my_strcasecmp("SHOW", argv[4])){ + fprintf(stderr, "Rewired edges: %d\n", num_rewire); + } + dump_edges(J, N, m); + free(J); +} -- cgit v1.2.3