//------//
// MAIN //
//------//
int main(int argc, const char *argv[])
{
// SET DEFAULT VALUES AND INITIALIZE THE VARIABLES
//------------------------------------------------
Params p;
p.cycle_num = 0; // number of the current cycle of colonization tests
p.time_eq = 0; // time step at which the equilibrium is reached (except when equal Tmax)
p.nrep = 1; // number of replicates
p.num = 1; // Number of the species
p.ax[0] = 0.314; // constantes for the per unit rate of metabolism for invertebrate predators
p.ax[1] = 0.88; // constantes for the per unit rate of metabolism for ectothermes
p.ay[0] = 8.0 * 0.314; // constante for the per unit rate of maximum consumption for invertebrate predators
p.ay[1] = 4.0 * 0.88; // constante for the per unit rate of maximum consumption for ectothermes
p.Smax = 0; // maximal diversity during the assembly sequence
p.stab = EAM_NOTHING; // stability of the integration
// USER INTERFACE
//---------------
int n_threads = 1;
read_opt_i("t", argv, argc, &n_threads);
p.nrep = n_threads;
printf("Début de la simulation...\n");
// CREATE THE THREADS
//-------------------
pthread_t threads[n_threads];
int i = 0;
for (; i < n_threads; ++i)
{
pthread_create(&threads[i], NULL, sim, (void*)&p);
}
// WAIT FOR THE THREADS TO END
//----------------------------
for (i = 0; i < n_threads; ++i)
{
pthread_join(threads[i], NULL);
}
printf("Finished!\n");
return EXIT_SUCCESS;
}
/////////////////////////////////////////////////////////////
// Main //
/////////////////////////////////////////////////////////////
int main(int argc, const char *argv[])
{
// Set default values;
Params p;
p.kernel = gaussian_k;
p.communities = 10;
p.j_per_c = 10000;
p.init_species = 20;
p.k_gen = 100;
p.mu = 1e-4;
p.s = 0.15;
p.var = 0.10;
p.width = sqrt(2);
p.eta = -8.0;
p.ofilename = (char*)malloc(50);
// Number of simulations;
int n_threads = 1;
// Options;
if (argc > 1 && argv[1][0] == '-' && argv[1][1] == '-')
{
// --help
if (argv[1][2] == 'h')
{
printf("Usage: ./origin [options]\n");
printf("Example: ./origin -x=8 -shape=circle -model=1 -s=0.10\n");
printf("General options:\n");
printf(" --help How you got here...\n");
printf(" --version Display version.\n");
printf(" --ref Display reference.\n");
printf("Simulation parameters:\n");
printf(" -x\n");
printf(" description: Number of simulations to run. Each simulation\n");
printf(" will use a distinct POSIX thread. \n");
printf(" values: Any unsigned integer.\n");
printf(" default: 1\n");
printf(" -k\n");
printf(" description: Dispersal kernel.\n");
printf(" values: 0 for Gaussian, 1 for fat-tailed.\n");
printf(" default: 0\n");
printf(" -g\n");
printf(" description: Number of generations in thousands.\n");
printf(" values: Any positive integer.\n");
printf(" default: 100 (i.e.: 100 000 generations)\n");
printf(" -c\n");
printf(" description: Number of local communities.\n");
printf(" values: Any integer greater than 0.\n");
printf(" default: 10\n");
printf(" -jpc\n");
printf(" description: Number of individuals per communities.\n");
printf(" values: Any integer greater than 0.\n");
printf(" default: 10000\n");
printf(" -sp\n");
printf(" description: Initial number of species. Must be a factor\n");
printf(" of the number of individuals/community.\n");
printf(" values: Any positive integer greater than 0.\n");
printf(" default: 20\n");
printf(" -s\n");
printf(" description: Set the selection coefficient (model 1 only).\n");
printf(" values: Any double in the (-1.0, 1.0) interval.\n");
printf(" default: 0.15\n");
printf(" -v\n");
printf(" description: Set variance for gaussian kernel.\n");
printf(" values: Any positive double.\n");
printf(" default: 0.10\n");
printf(" -w\n");
printf(" description: The width of the fat-tailed kernel.\n");
printf(" values: Any positive double.\n");
printf(" default: sqrt(2)\n");
printf(" -e\n");
printf(" description: Parameter eta of the fat-tailed kernel.\n");
printf(" values: Any negative values < -4.0.\n");
printf(" default: -8.0\n");
printf(" -o\n");
printf(" description: Name of the output files.\n");
printf(" values: Any string.\n");
return EXIT_SUCCESS;
}
else if (argv[1][2] == 'v') // --version
{
printf("origin v.%d.%d (%s)\n", origin2_version, origin2_revision, origin2_date);
printf("Copyright (c) 2012 Philippe Desjardins-Proulx <*****@*****.**>\n");
printf("GPLv2 license (see LICENSE)\n");
return EXIT_SUCCESS;
}
else if (argv[1][2] == 'r') // --ref
{
printf("P. Desjardins-Proul and D. Gravel. How likely is speciation in\n neutral ecology? The American Naturalist 179(1).\n");
return EXIT_SUCCESS;
}
} // end '--' options
// Read options
read_opt_i("g", argv, argc, &p.k_gen);
read_opt_i("jpc", argv, argc, &p.j_per_c);
read_opt_i("c", argv, argc, &p.communities);
read_opt_i("sp", argv, argc, &p.init_species);
read_opt_i("x", argv, argc, &n_threads);
read_opt_i("k", argv, argc, &p.kernel);
read_opt_d("mu", argv, argc, &p.mu);
read_opt_d("v", argv, argc, &p.var);
read_opt_d("w", argv, argc, &p.width);
read_opt_d("e", argv, argc, &p.eta);
read_opt_d("s", argv, argc, &p.s);
if (read_opt_s("o", argv, argc, p.ofilename) == false)
{
sprintf(p.ofilename, "");
}
printf("<?xml version=\"1.0\"?>\n");
printf("<origin2>\n");
printf(" <version>%d</version>\n", origin2_version);
printf(" <revision>%d</revision>\n", origin2_revision);
if (p.kernel == gaussian_k)
{
printf(" <model>Gaussian</model>\n");
}
else
{
printf(" <model>Fat-tailed</model>\n");
}
printf(" <n>%d</n>\n", n_threads);
printf(" <metacom_size>%d</metacom_size>\n", p.j_per_c * p.communities);
printf(" <k_gen>%d</k_gen>\n", p.k_gen);
printf(" <num_comm>%d</num_comm>\n", p.communities);
printf(" <individuals_per_comm>%d</individuals_per_comm>\n", p.j_per_c);
printf(" <initial_num_species>%d</initial_num_species>\n", p.init_species);
printf(" <mutation_rate>%.2e</mutation_rate>\n", p.mu);
if (p.kernel == gaussian_k)
{
printf(" <variance>%.8e</variance>\n", p.var);
}
else
{
printf(" <width>%.8e</width>\n", p.width);
printf(" <eta>%.8e</eta>\n", p.eta);
}
printf(" <selection>%.2e</selection>\n", p.s);
printf(" <filename>%s</filename>\n", p.ofilename);
// The threads:
pthread_t threads[n_threads];
const time_t start = time(NULL);
// Create the threads:
for (int i = 0; i < n_threads; ++i)
{
pthread_create(&threads[i], NULL, sim, (void*)&p);
}
// Wait for the threads to end:
for (int i = 0; i < n_threads; ++i)
{
pthread_join(threads[i], NULL);
}
const time_t end_t = time(NULL);
printf(" <seconds>%lu</seconds>\n", (unsigned long)(end_t - start));
printf(" <time>%s</time>\n", sec_to_string(end_t - start));
printf("</origin2>\n");
return EXIT_SUCCESS; // yeppie !
}
/////////////////////////////////////////////////////////////
// Main //
/////////////////////////////////////////////////////////////
int main(int argc, const char *argv[])
{
// Set default values;
Params p;
p.m = MODEL_BDM_SELECTION;
p.communities = 10;
p.j_per_c = 10000;
p.init_species = 20;
p.k_gen = 100;
p.mu = 1e-4;
p.omega = 5e-4;
p.s = 0.15;
p.r = 0.25;
p.w = 0.25;
p.ofilename = (char*)malloc(50);
p.shape = (char*)malloc(20);
// Number of simulations;
int n_threads = 1;
// Options;
if (argc > 1 && argv[1][0] == '-' && argv[1][1] == '-')
{
// --help
if (argv[1][2] == 'h')
{
printf("Usage: ./origin [options]\n");
printf("Example: ./origin -x=8 -shape=circle -model=1 -s=0.10\n");
printf("General options:\n");
printf(" --help How you got here...\n");
printf(" --version Display version.\n");
printf(" --ref Display reference.\n");
printf("Simulation parameters:\n");
printf(" -x\n");
printf(" description: Number of simulations to run. Each simulation\n");
printf(" will use a distinct POSIX thread. \n");
printf(" values: Any unsigned integer.\n");
printf(" default: 1\n");
printf(" -model\n");
printf(" description: Set the model used.\n");
printf(" values: 0, 1.\n");
printf(" details: 0 = Neutral BDM speciation.\n");
printf(" 1 = BDM speciation with selection.\n");
printf(" default: 1\n");
printf(" -shape\n");
printf(" description: Set the shape of the metacommunity.\n");
printf(" values: circle, complete, random, rectangle, star.\n");
printf(" default: random\n");
printf(" -r\n");
printf(" description: Threshold radius for random geometric\n");
printf(" graphs.\n");
printf(" values: Any double greater than 0.\n");
printf(" default: 0.25\n");
printf(" -w\n");
printf(" description: The width of a rectangle random geometric\n");
printf(" graph.\n");
printf(" values: 0 < w < 1\n");
printf(" default: 0.25\n");
printf(" -g\n");
printf(" description: Number of generations in thousands.\n");
printf(" values: Any positive integer.\n");
printf(" default: 100 (i.e.: 100 000 generations)\n");
printf(" -c\n");
printf(" description: Number of local communities.\n");
printf(" values: Any integer greater than 0.\n");
printf(" default: 10\n");
printf(" -jpc\n");
printf(" description: Number of individuals per communities.\n");
printf(" values: Any integer greater than 0.\n");
printf(" default: 10000\n");
printf(" -sp\n");
printf(" description: Initial number of species. Must be a factor\n");
printf(" of the number of individuals/community.\n");
printf(" values: Any positive integer greater than 0.\n");
printf(" default: 20\n");
printf(" -s\n");
printf(" description: Set the selection coefficient (model 1 only).\n");
printf(" values: Any double in the (-1.0, 1.0) interval.\n");
printf(" default: 0.15\n");
printf(" -mu\n");
printf(" description: Set the mutation rate.\n");
printf(" values: Any positive double.\n");
printf(" default: 1e-4\n");
printf(" -omega\n");
printf(" description: The weight of the proper edges.\n");
printf(" values: Any nonnegative double.\n");
printf(" default: 5e-4\n");
printf(" -o\n");
printf(" description: Name of the output files.\n");
printf(" values: Any string.\n");
return EXIT_SUCCESS;
}
else if (argv[1][2] == 'v') // --version
{
printf("origin v.%s (%s)\n", ORIGIN_VERSION, ORIGIN_DATE);
printf("Copyright (c) 2010-2011 Philippe Desjardins-Proulx <*****@*****.**>\n");
printf("GPLv2 license (see LICENSE)\n");
return EXIT_SUCCESS;
}
else if (argv[1][2] == 'r') // --ref
{
printf("P. Desjardins-Proul and D. Gravel. How likely is speciation in\n neutral ecology? The American Naturalist 179(1).\n");
return EXIT_SUCCESS;
}
} // end '--' options
// Read options
read_opt_i("g", argv, argc, &p.k_gen);
read_opt_i("jpc", argv, argc, &p.j_per_c);
read_opt_i("model", argv, argc, &p.m);
read_opt_i("c", argv, argc, &p.communities);
read_opt_i("sp", argv, argc, &p.init_species);
read_opt_i("x", argv, argc, &n_threads);
read_opt_d("mu", argv, argc, &p.mu);
read_opt_d("omega", argv, argc, &p.omega);
read_opt_d("r", argv, argc, &p.r);
read_opt_d("w", argv, argc, &p.w);
read_opt_d("s", argv, argc, &p.s);
if (read_opt_s("o", argv, argc, p.ofilename) == false)
{
sprintf(p.ofilename, "");
}
if (read_opt_s("shape", argv, argc, p.shape) == false)
{
sprintf(p.shape, "random");
}
printf("<?xml version=\"1.0\"?>\n");
printf("<origin_ssne>\n");
printf(" <model>");
if (p.m == MODEL_BDM_NEUTRAL)
{
printf("Neutral BDM speciation</model>\n");
}
else if (p.m == MODEL_BDM_SELECTION)
{
printf("BDM speciation with selection</model>\n");
}
printf(" <n>%d</n>\n", n_threads);
printf(" <shape_metacom>%s</shape_metacom>\n", p.shape);
printf(" <metacom_size>%d</metacom_size>\n", p.j_per_c * p.communities);
printf(" <k_gen>%d</k_gen>\n", p.k_gen);
printf(" <num_comm>%d</num_comm>\n", p.communities);
printf(" <individuals_per_comm>%d</individuals_per_comm>\n", p.j_per_c);
printf(" <initial_num_species>%d</initial_num_species>\n", p.init_species);
printf(" <mutation_rate>%.2e</mutation_rate>\n", p.mu);
printf(" <omega>%.2e</omega>\n", p.omega);
if (p.m == MODEL_BDM_SELECTION)
{
printf(" <selection>%.2e</selection>\n", p.s);
}
if (p.shape[0] == 'r')
{
printf(" <radius>%.4f</radius>\n", p.r);
}
if (p.shape[0] == 'r' && p.shape[1] == 'e')
{
printf(" <width>%.4f</width>\n", p.w);
}
printf(" <filename>%s</filename>\n", p.ofilename);
// The threads:
pthread_t threads[n_threads];
const time_t start = time(NULL);
// Create the threads:
for (int i = 0; i < n_threads; ++i)
{
pthread_create(&threads[i], NULL, sim, (void*)&p);
}
// Wait for the threads to end:
for (int i = 0; i < n_threads; ++i)
{
pthread_join(threads[i], NULL);
}
const time_t end_t = time(NULL);
printf(" <seconds>%lu</seconds>\n", (unsigned long)(end_t - start));
printf(" <time>%s</time>\n", sec_to_string(end_t - start));
printf("</origin_ssne>\n");
return EXIT_SUCCESS; // yeppie !
}
