//
// operator <<= (CUTS_Virtual_Env &, const CUTS::schemas::EnvConfig &)
//
bool
operator <<= (CUTS_Virtual_Env & env, const CUTS::schemas::EnvConfig & config)
{
ACE_DEBUG ((LM_DEBUG,
ACE_TEXT ("%T (%t) - %M - loading environment's configuration\n")));
if (config.variables_p ())
env.env_table () <<= config.variables ();
if (config.startup_p ())
std::for_each (config.startup ().begin_process (),
config.startup ().end_process (),
install_process (env, true));
if (config.shutdown_p ())
std::for_each (config.shutdown ().begin_process (),
config.shutdown ().end_process (),
install_process (env, false));
return true;
}
void create_assembled_pool(Params *p, double **pool, int divpool, double fert)
{
restart:;
// define and initialize the ecosystem list
//-----------------------------------------
sll ecosys;
sll_init(&ecosys,(void*)free_species);
// create the basal resources
//---------------------------
basal(p,&ecosys,fert);
// assemble until the targetted diversity is reached
//--------------------------------------------------
int a = divpool + EAM_NBNUT + EAM_NBDET;
int counter = EAM_STOP_UNSUCCESS_ASSEMBLY*divpool;
while(ecosys.length != a)
{
ParamSP *sp = (void*)species(p,2);
install_process(p,&ecosys,sp);
sll_rm(&ecosys,extinct_condition);
++(p->num);
--counter;
if(counter == 0)
{
sll_rm_all(&ecosys);
//create_assembled_pool(p, pool, divpool, fert);
goto restart;
}
}
// remove the resources
//---------------------
sll_rm(&ecosys,is_resource);
// create the subpool matrix and fill it with the selected species
//----------------------------------------------------------------
sllnode *node = ecosys.head;
for (int i = 0; node != NULL; i++, node = node->next)
{
ParamSP sp = *(ParamSP*)(node->data);
sp.d = EAM_N0SP;
tr_sp_array(&sp,pool[i]);
}
// free the memory
//----------------
sll_rm_all(&ecosys);
}
void assembly_run(Params *p, double nfert, double **regpool, int poolsize, char *folder, char *replicate_identity)
{
// Define and initialize the history and ecosystem lists
//------------------------------------------------------
sll history;
sll_init(&history,(void*)free_seq);
sll ecosys;
sll_init(&ecosys,(void*)free_species);
// create the basal resources
//---------------------------
basal(p,&ecosys,nfert);
// create and initialize the presence matrix (ne pas oublier de mettre les espèces au minimum pour l'invasion)
//------------------------------------------
unsigned int **presence = (unsigned int**)mat_alloc(2,poolsize,sizeof(unsigned int));
for(int i = 0 ; i < poolsize ; ++i)
{
presence[0][i] = regpool[i][1];
presence[1][i] = 0;
}
// get the initial values of the sequence
//---------------------------------------
seqlevel *seq0 = fill_seq(&ecosys,0,0);
seq0->success = 0;
sll_add_head(&history,seq0);
// assemble until any species can install (or all are already installed)
//----------------------------------------------------------------------
int a = poolsize + EAM_NBNUT + EAM_NBDET; /* expected ecosystem size */
int stop_endcycles = poolsize * EAM_STOP_ENDCYCLE; /* variable to stop the sequence if infinite */
int endcycles = 0; /* 0 if endpoint / 1 if endcycle */
int unsucc = EAM_STOP; /* check the success of the invader */
int invasion = 1; /* invasion number */
while(ecosys.length != a)
{
int b = get_int(p->rng,0,poolsize); /* select randomly the number of the species in the regional pool */
if(presence[1][b] == 0) /* if the species is not already in the ecosystem */
{
ParamSP *sp = (ParamSP*)malloc(sizeof(ParamSP));
tr_sp_struct(regpool[b],sp);
install_process(p,&ecosys,sp); /* install the species */
seqlevel *seq = fill_seq(&ecosys,invasion,presence[0][b]); /* create and initialize a sequence node */
sll_rm(&ecosys,extinct_condition); /* remove the extincted species */
presence_absence(&ecosys,presence,poolsize); /* fill the presence-absence matrix */
unsucc = (presence[1][b] == 0) ? unsucc-1 : EAM_STOP; /* upgrade the counter of unsuccessfull installations */
seq->success = presence[1][b]; /* fill the success of invader installation in the sequence node */
sll_add_head(&history,seq); /* add the sequence node to the assembly history */
++invasion; /* upgrade the invasion number */
--stop_endcycles; /* upgrade the endcycle detector */
}
if(unsucc == 0) break;
if(stop_endcycles == 0) /* break the loop if its an endcycle */
{
endcycles = 1;
break;
}
}
// print the outputs : subpool / final community / sequence / abundances history / identity history
//------------------
print_final_community(&ecosys,folder,replicate_identity);
print_id_history(&history,poolsize,folder,replicate_identity);
print_final_biomasses_history(&history,poolsize,folder,replicate_identity);
print_sequence(&history,folder,replicate_identity);
char *buffer = (char*)malloc(100);
sprintf(buffer, "%s/%s_endcycle.txt",folder,replicate_identity);
FILE *out = fopen(buffer,"w");
fprintf(out,"%d",endcycles);
fclose(out);
// free the memory
//----------------
mat_free((void**)presence,2);
sll_rm_all(&history);
sll_rm_all(&ecosys);
free(buffer);
}