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); }
/*ARGSUSED*/ int main(int argc, char *argv[]) { int cmode=NC_CLOBBER, omode, ret; int id; char buf[256]; #ifdef SYNCDEBUG char *str = "one"; #endif int ii; size_t ui; const struct tcdfvar *tvp = testvars; union getret got; const size_t initialsz = 8192; size_t chunksz = 8192; size_t align = 8192/32; MPI_Init(&argc, &argv); /* cmode |= NC_PNETCDF |NC_64BIT_OFFSET; */ cmode != NC_PNETCDF |NC_64BIT_DATA; ret = nc_create_par(fname,cmode, MPI_COMM_WORLD, MPI_INFO_NULL, &id); if(ret != NC_NOERR) { fprintf(stderr,"Error %s in file %s at line %d\n",nc_strerror(ret),__FILE__,__LINE__); exit(ret); } assert( nc_put_att_text(id, NC_GLOBAL, "TITLE", 12, "another name") == NC_NOERR); assert( nc_get_att_text(id, NC_GLOBAL, "TITLE", buf) == NC_NOERR); /* (void) printf("title 1 \"%s\"\n", buf); */ assert( nc_put_att_text(id, NC_GLOBAL, "TITLE", strlen(fname), fname) == NC_NOERR); assert( nc_get_att_text(id, NC_GLOBAL, "TITLE", buf) == NC_NOERR); buf[strlen(fname)] = 0; /* (void) printf("title 2 \"%s\"\n", buf); */ assert( strcmp(fname, buf) == 0); createtestdims(id, NUM_DIMS, sizes, dim_names); testdims(id, NUM_DIMS, sizes, dim_names); createtestvars(id, testvars, NUM_TESTVARS); { int ifill = -1; double dfill = -9999; assert( nc_put_att_int(id, Long_id, _FillValue, NC_INT, 1, &ifill) == NC_NOERR); assert( nc_put_att_double(id, Double_id, _FillValue, NC_DOUBLE, 1, &dfill) == NC_NOERR); } #ifdef REDEF assert( nc__enddef(id, 0, align, 0, 2*align) == NC_NOERR ); assert( nc_put_var1_int(id, Long_id, indices[3], &birthday) == NC_NOERR ); fill_seq(id); assert( nc_redef(id) == NC_NOERR ); /* assert( nc_rename_dim(id,2, "a long dim name") == NC_NOERR); */ #endif assert( nc_rename_dim(id,1, "IXX") == NC_NOERR); assert( nc_inq_dim(id, 1, buf, &ui) == NC_NOERR); /* (void) printf("dimrename: %s\n", buf); */ assert( nc_rename_dim(id,1, dim_names[1]) == NC_NOERR); #ifdef ATTRX assert( nc_rename_att(id, 1, "UNITS", "units") == NC_NOERR); assert( nc_del_att(id, 4, "FIELDNAM")== NC_NOERR); assert( nc_del_att(id, 2, "SCALEMIN")== NC_NOERR); assert( nc_del_att(id, 2, "SCALEMAX")== NC_NOERR); #endif /* ATTRX */ assert( nc__enddef(id, 0, align, 0, 2*align) == NC_NOERR ); #ifndef REDEF fill_seq(id); assert( nc_put_var1_int(id, Long_id, indices[3], &birthday)== NC_NOERR ); #endif assert( nc_put_vara_schar(id, Byte_id, s_start, s_edges, (signed char *)sentence) == NC_NOERR); assert( nc_put_var1_schar(id, Byte_id, indices[6], (signed char *)(chs+1)) == NC_NOERR); assert( nc_put_var1_schar(id, Byte_id, indices[5], (signed char *)chs) == NC_NOERR); assert( nc_put_vara_text(id, Char_id, s_start, s_edges, sentence) == NC_NOERR); assert( nc_put_var1_text(id, Char_id, indices[6], (chs+1)) == NC_NOERR) ; assert( nc_put_var1_text(id, Char_id, indices[5], chs) == NC_NOERR); assert( nc_put_var1_short(id, Short_id, indices[4], shs) == NC_NOERR); assert( nc_put_var1_float(id, Float_id, indices[2], &e) == NC_NOERR); assert( nc_put_var1_double(id, Double_id, indices[1], &zed) == NC_NOERR); assert( nc_put_var1_double(id, Double_id, indices[0], &pinot) == NC_NOERR); #ifdef SYNCDEBUG (void) printf("Hit Return to sync\n"); gets(str); nc_sync(id,0); (void) printf("Sync done. Hit Return to continue\n"); gets(str); #endif /* SYNCDEBUG */ ret = nc_close(id); /* (void) printf("nc_close ret = %d\n\n", ret); */ /* * read it */ omode = NC_NOWRITE; omode = NC_NOWRITE | NC_PNETCDF; if(ret != NC_NOERR) { (void) printf("Could not open %s: %s\n", fname, nc_strerror(ret)); exit(1); } /* (void) printf("reopen id = %d for filename %s\n", */ /* id, fname); */ /* NC */ /* (void) printf("NC "); */ assert( nc_inq(id, &(cdesc->num_dims), &(cdesc->num_vars), &(cdesc->num_attrs), &(cdesc->xtendim) ) == NC_NOERR); assert((size_t) cdesc->num_dims == num_dims); assert(cdesc->num_attrs == 1); assert(cdesc->num_vars == NUM_TESTVARS); /* (void) printf("done\n"); */ /* GATTR */ /* (void) printf("GATTR "); */ assert( nc_inq_attname(id, NC_GLOBAL, 0, adesc->mnem) == 0); assert(strcmp("TITLE",adesc->mnem) == 0); assert( nc_inq_att(id, NC_GLOBAL, adesc->mnem, &(adesc->type), &(adesc->len))== NC_NOERR); assert( adesc->type == NC_CHAR ); assert( adesc->len == strlen(fname) ); assert( nc_get_att_text(id, NC_GLOBAL, "TITLE", buf)== NC_NOERR); buf[adesc->len] = 0; assert( strcmp(fname, buf) == 0); /* VAR */ /* (void) printf("VAR "); */ assert( cdesc->num_vars == NUM_TESTVARS ); for(ii = 0; ii < cdesc->num_vars; ii++, tvp++ ) { int jj; assert( nc_inq_var(id, ii, vdesc->mnem, &(vdesc->type), &(vdesc->ndims), vdesc->dims, &(vdesc->num_attrs)) == NC_NOERR); if(strcmp(tvp->mnem , vdesc->mnem) != 0) { (void) printf("attr %d mnem mismatch %s, %s\n", ii, tvp->mnem, vdesc->mnem); continue; } if(tvp->type != vdesc->type) { (void) printf("attr %d type mismatch %d, %d\n", ii, (int)tvp->type, (int)vdesc->type); continue; } for(jj = 0; jj < vdesc->ndims; jj++ ) { if(tvp->dims[jj] != vdesc->dims[jj] ) { (void) printf( "inconsistent dim[%d] for variable %d: %d != %d\n", jj, ii, tvp->dims[jj], vdesc->dims[jj] ); continue; } } /* VATTR */ /* (void) printf("VATTR\n"); */ for(jj=0; jj<vdesc->num_attrs; jj++ ) { assert( nc_inq_attname(id, ii, jj, adesc->mnem) == NC_NOERR); if( strcmp(adesc->mnem, reqattr[jj]) != 0 ) { (void) printf("var %d attr %d mismatch %s != %s\n", ii, jj, adesc->mnem, reqattr[jj] ); break; } } if( nc_inq_att(id, ii, reqattr[0], &(adesc->type), &(adesc->len)) != -1) { assert( adesc->type == NC_CHAR ); assert( adesc->len == strlen(tvp->units) ); assert( nc_get_att_text(id,ii,reqattr[0],buf)== NC_NOERR); buf[adesc->len] = 0; assert( strcmp(tvp->units, buf) == 0); } if( nc_inq_att(id, ii, reqattr[1], &(adesc->type), &(adesc->len)) != -1) { assert( adesc->type == NC_DOUBLE ); assert( adesc->len == 1 ); assert( nc_get_att_double(id, ii, reqattr[1], &got.dbl)== NC_NOERR); chkgot(adesc->type, got, tvp->validmin); } if( nc_inq_att(id, ii, reqattr[2], &(adesc->type), &(adesc->len)) != -1) { assert( adesc->type == NC_DOUBLE ); assert( adesc->len == 1 ); assert( nc_get_att_double(id, ii, reqattr[2], &got.dbl)== NC_NOERR); chkgot(adesc->type, got, tvp->validmax); } if( nc_inq_att(id, ii, reqattr[3], &(adesc->type), &(adesc->len)) != -1) { assert( adesc->type == NC_DOUBLE ); assert( adesc->len ==1 ); assert( nc_get_att_double(id, ii, reqattr[3], &got.dbl)== NC_NOERR); chkgot(adesc->type, got, tvp->scalemin); } if( nc_inq_att(id, ii, reqattr[4], &(adesc->type), &(adesc->len)) != -1) { assert( adesc->type == NC_DOUBLE ); assert( adesc->len == 1 ); assert( nc_get_att_double(id, ii, reqattr[4], &got.dbl)== NC_NOERR); chkgot(adesc->type, got, tvp->scalemax); } if( nc_inq_att(id, ii, reqattr[5], &(adesc->type), &(adesc->len))== NC_NOERR) { assert( adesc->type == NC_CHAR ); assert( adesc->len == strlen(tvp->fieldnam) ); assert( nc_get_att_text(id,ii,reqattr[5],buf)== NC_NOERR); buf[adesc->len] = 0; assert( strcmp(tvp->fieldnam, buf) == 0); } } /* (void) printf("fill_seq "); */ check_fill_seq(id); /* (void) printf("Done\n"); */ assert( nc_get_var1_double(id, Double_id, indices[0], &got.dbl)== NC_NOERR); /* (void) printf("got val = %f\n", got.dbl ); */ assert( nc_get_var1_double(id, Double_id, indices[1], &got.dbl)== NC_NOERR); /* (void) printf("got val = %f\n", got.dbl ); */ assert( nc_get_var1_float(id, Float_id, indices[2], &got.fl[0])== NC_NOERR); /* (void) printf("got val = %f\n", got.fl[0] ); */ assert( nc_get_var1_int(id, Long_id, indices[3], &got.in[0])== NC_NOERR); /* (void) printf("got val = %d\n", got.in[0] ); */ assert( nc_get_var1_short(id, Short_id, indices[4], &got.sh[0])== NC_NOERR); /* (void) printf("got val = %d\n", got.sh[0] ); */ assert( nc_get_var1_text(id, Char_id, indices[5], &got.by[0]) == NC_NOERR); /* (void) printf("got NC_CHAR val = %c (0x%02x) \n", */ /* got.by[0] , got.by[0]); */ assert( nc_get_var1_text(id, Char_id, indices[6], &got.by[0]) == NC_NOERR); /* (void) printf("got NC_CHAR val = %c (0x%02x) \n", */ /* got.by[0], got.by[0] ); */ (void) memset(buf,0,sizeof(buf)); assert( nc_get_vara_text(id, Char_id, s_start, s_edges, buf) == NC_NOERR); /* (void) printf("got NC_CHAR val = \"%s\"\n", buf); */ assert( nc_get_var1_schar(id, Byte_id, indices[5], (signed char *)&got.by[0])== NC_NOERR); /* (void) printf("got val = %c (0x%02x) \n", got.by[0] , got.by[0]); */ assert( nc_get_var1_schar(id, Byte_id, indices[6], (signed char *)&got.by[0])== NC_NOERR); /* (void) printf("got val = %c (0x%02x) \n", got.by[0], got.by[0] ); */ (void) memset(buf,0,sizeof(buf)); assert( nc_get_vara_schar(id, Byte_id, s_start, s_edges, (signed char *)buf)== NC_NOERR ); /* (void) printf("got val = \"%s\"\n", buf); */ { double dbuf[NUM_RECS * SIZE_1 * SIZE_2]; assert(nc_get_var_double(id, Float_id, dbuf) == NC_NOERR); /* (void) printf("got vals = %f ... %f\n", dbuf[0], */ /* dbuf[NUM_RECS * SIZE_1 * SIZE_2 -1] ); */ } ret = nc_close(id); /* (void) printf("re nc_close ret = %d\n", ret); */ MPI_Finalize(); return 0; }