int
main(int argc, char** argv)
{
/**
* fprintf(stdout) | ./block l d x y
* option:
* -x [gpu, cpu]
* -m [lin, sph, exp, gau]
* -l [1..13]
*/
if(argc<5) {
fprintf(stderr, "Error: not enough arguments.\n");
exit(1);
}
int level = atoi(argv[1]);
int depth = atoi(argv[2]);
int xblock = atoi(argv[3]);
int yblock = atoi(argv[4]);
grid g;
features f;
model m;
spectrum s;
/* Stdin -> features */
readfeatures(&f);
/* Estimate grid based on model */
singleblock(&g, level, depth, xblock, yblock);
readgrid(&g);
/* Predict using model */
int i;
if(f.n>0) {
if(argc<11) {
fprintf(stderr, "argc: %d\n", argc);
for(i=0;i<argc;i++) {
fprintf(stderr, "%s\n", argv[i]);
}
fprintf(stderr, "Error: not enough arguments.\n");
exit(1);
}
m.type = atoi(argv[5]);
m.nugget = atof(argv[6]);
m.range = atof(argv[7]);
m.sill = atof(argv[8]);
m.a = atof(argv[9]);
m.MSE = atof(argv[10]);
predict(&g, &m, &f);
heatspectrum(&s);
}
/* Write image */
printppm(&g, &f, &s, f.n==0 ? 1 : 0);
return 0;
}
int main()
{
int i,j,k,l;
memcount = 0;
readgrid();
printf("Grid reading finished, memcount = %ld\n",memcount);
double tol = 1e-6; //0.1;
double kappa = 0.0, beta = 0.5, omega = 1 - kappa/beta, alpha0 = 1-omega;
double tin = 1000.0, tw = 0.0;
double dh1 = 0.0, dh2 = 100.0;
double sigma = 5.67e-8;
buildcoeffs(alpha0,beta);
printf("Built co-efficients, memcount = %ld\n",memcount);
tb = (double*) malloc(sizeof(double)*nbcfaces);
t = (double*) malloc(sizeof(double)*ncells);
memcount += sizeof(double)*nbcfaces + sizeof(double)*ncells;
//printf("Memcount = %ld\n",memcount);
for( i = 0 ; i < ncells ; i++ )
t[i] = 0.0;
for( i = 0 ; i < nbcfaces ; i++){
if( bcname[i] == BOTTOM ){
int face_num = bf_to_f[i];
if( xf[face_num] >= dh1 && xf[face_num] <= dh2 )
tb[i] = tin;
else
tb[i] = tw;
}
else
tb[i] = tw;
}
/* for( i = 0 ; i < nbcfaces ; i++ ) */
/* printf("%lf\n",tb[i]); */
phic_old = malloc_2d(ncells,4);
phic_new = malloc_2d(ncells,4);
sc = malloc_2d(ncells,4);
memcount += sizeof(double)*4*ncells*3 + sizeof(double*)*3*ncells;
//printf("Memcount = %ld\n",memcount);
for( i = 0 ; i < ncells ; i++ ){
for( j = 0 ; j < 4 ;j++){
phic_old[i][j] = 0.0;
phic_new[i][j] = 0.0;
}
}
sb = malloc_2d(nbcfaces,4);
phib = malloc_2d(nbcfaces,4);
memcount += sizeof(double)*4*nbcfaces*2 + sizeof(double*)*2*nbcfaces;
//printf("Memcount = %ld\n",memcount);
for( i = 0 ; i < nbcfaces ; i++ ){
for( j = 0 ; j < 4 ; j++ )
phib[i][j] = 0.0;
}
phiv = malloc_2d(nnodes,4);
memcount += sizeof(double)*4*nnodes + sizeof(double*)*nnodes;
//printf("Memcount = %ld\n",memcount);
for( i = 0 ; i < nnodes ; i++ )
for( j = 0 ; j < 4 ; j++ )
phiv[i][j] = 0.0;
dphi = malloc_2d(nfaces,4);
memcount += sizeof(double)*4*nfaces + sizeof(double*)*nfaces;
//printf("Memcount = %ld, dphi = %p\n",memcount,dphi);
for( i = 0 ; i < nfaces ; i++ )
for( j = 0 ; j < 4 ; j++ )
dphi[i][j] = 0.0;
double resid0,resid1,resid2,resid3;
resid0 = tol * 2;
resid1 = tol * 2;
resid2 = tol * 2;
resid3 = tol * 2;
for( i = 0 ; i < nbcfaces ; i++ ){
sb[i][0] = 4.0 * sigma * tb[i] * tb[i] * tb[i] * tb[i];
sb[i][1] = 0.0;
sb[i][2] = 4.0 * sigma * tb[i] * tb[i] * tb[i] * tb[i];
sb[i][3] = 0.0;
}
for( i = 0 ; i < ncells ; i++ ){
sc[i][0] = 0.0;
sc[i][1] = 0.0;
sc[i][2] = 0.0;
sc[i][3] = -20.0 * alpha0 * sigma * t[i]*t[i]*t[i]*t[i] * beta * volcell[i];
}
int count = 0;
double start_t = rtclock();
while ( resid0 > tol || resid1 > tol || resid2 > tol || resid3 > tol ){
/* while(count < 1 ){ */
for(i = 0 ; i < nbcfaces ; i++ ){
double new_phib[4];
double lhs_matrix[4][4];
int currf = bf_to_f[i];
assert( currf >=0 && currf < nfaces);
assert( bf_to_c[i] >=0 && bf_to_c[i] < nfaces);
for( j = 0 ; j < 4 ; j++ )
new_phib[j] = sb[i][j];
for( k = 0 ; k < 4 ; k++ )
for( l = 0 ; l < 4 ; l++ ){
new_phib[k] += bc[i][4*k+l] * dphi[currf][l] + bb[i][4*k+l]*phic_new[bf_to_c[i]][l];
lhs_matrix[k][l] = ba[i][4*k+l];
}
inverse_multiply(new_phib,lhs_matrix);
for( j = 0 ; j < 4 ; j++ )
phib[i][j] = new_phib[j];
}
for( i = 0 ; i < nnodes ; i++ )
for( j = 0 ; j < 4 ; j++ )
phiv[i][j] = 0.0;
for( i = 0 ; i < nbcfaces ; i++ ){
int currf = bf_to_f[i];
int n1 = lfv0[currf];
int n2 = lfv1[currf];
assert(currf >=0 && currf < nfaces );
assert(n1 >=0 && n1 < nnodes );
assert(n2 >=0 && n2 < nnodes );
for( j = 0 ; j < 4 ; j++ ){
phiv[n1][j] += phib[i][j] * wbfv[i][0];
phiv[n2][j] += phib[i][j] * wbfv[i][1];
}
}
for( i= 0 ; i < ncells ; i++ ){
for( j = ia_cv[i] ; j < ia_cv[i+1] ; j++ ){
int currv = lcv[j];
assert(currv >=0 && currv < nnodes);
if( bnode[currv] == 0 )
for( k = 0 ; k < 4 ; k++ )
phiv[currv][k] += phic_new[i][k] * wcv[j];
}
for( j = 0 ; j < 4 ; j++ )
phic_old[i][j] = phic_new[i][j];
}
for( i = 0 ; i < nfaces ; i++ ){
int n1 = lfv0[i];
int n2 = lfv1[i];
assert(n1 >= 0 && n1 < nnodes );
assert(n2 >= 0 && n2 < nnodes );
double xv1 = xv[n1];
double xv2 = xv[n2];
double yv1 = yv[n1];
double yv2 = yv[n2];
/* if( i == 0 ) { */
/* printf("i= %d, phiv[%d]=[%lf,%lf,%lf,%lf], phiv[%d]=[%lf,%lf,%lf,%lf]\n",i,n1,phiv[n1][0],phiv[n1][1],phiv[n1][2],phiv[n1][3],n2,phiv[n2][0],phiv[n2][1],phiv[n2][2],phiv[n2][3]); */
/* } */
for( j = 0 ; j < 4 ; j++ )
dphi[i][j] = ( phiv[n2][j] - phiv[n1][j] ) / sqrt( ( xv2 - xv1 ) * ( xv2 - xv1 ) + ( yv2 - yv1 ) * ( yv2 - yv1 ) );
/* if( i == 0 ) */
/* printf("i=%d,dphi[%d]=[%lf,%lf,%lf,%lf]\n",i,i,dphi[i][0],dphi[i][1],dphi[i][2],dphi[i][3]); */
}
for( i = 0 ; i < ncells ; i++ ){
double diag_matrix[4][4];
double new_phi[4];
for( j = 0 ; j < 4 ; j++ ){
for( k = 0 ; k < 4 ; k++ )
diag_matrix[j][k] = 0.0;
new_phi[j] = sc[i][j];
diag_matrix[j][j] = vol_vec[i][j];
}
for( j = ia_cf[i] ; j < ia_cf[i+1] ; j++ ){
int currf = lcf[j];
if( bface[currf] == 0 ){
int currcell;
double alpha;
if( lfc0[currf] == i ){
currcell = lfc1[currf];
alpha = 1;
}
else{
alpha = -1;
currcell = lfc0[currf];
}
for( k = 0 ; k < 4 ; k++ )
for( l = 0 ; l < 4 ; l++ ){
new_phi[k] -= (fclink[currf][k*4+l] * phic_old[currcell][l] + alpha * ftlink[currf][k*4+l] * dphi[currf][l]) ;
diag_matrix[k][l] -= fclink[currf][k*4+l];
}
}
else{
int currbf = f_to_bf[currf];
assert(currbf >= 0 );
for( k = 0 ; k < 4 ; k++ )
for( l = 0 ; l < 4 ; l++ ){
new_phi[k] -= (fclink[currf][k*4+l] * phib[currbf][l] + ftlink[currf][k*4+l] * dphi[currf][l]) ;
diag_matrix[k][l] -= fclink[currf][k*4+l];
}
}
}
inverse_multiply(new_phi,diag_matrix);
for( j = 0 ; j < 4 ; j++ )
phic_new[i][j] = new_phi[j];
}
resid0 = 0.0;
resid1 = 0.0;
resid2 = 0.0;
resid3 = 0.0;
for( i = 0 ; i < ncells ; i++ ){
double temp = phic_new[i][0] - phic_old[i][0];
resid0 += temp * temp;
temp = phic_new[i][1] - phic_old[i][1];
resid1 += temp * temp;
temp = phic_new[i][2] - phic_old[i][2];
resid2 += temp * temp;
temp = phic_new[i][3] - phic_old[i][3];
resid3 += temp * temp;
}
resid0 = sqrt(resid0) / ncells;
resid1 = sqrt(resid1) / ncells;
resid2 = sqrt(resid2) / ncells;
resid3 = sqrt(resid3) / ncells;
count++;
#ifndef NDEBUG
printf("%d %lf %lf %lf %lf\n",count,resid0,resid1,resid2,resid3);
#endif
}
double stop_t = rtclock();
printf("[IEC]:OriginalTime:%lf\n",stop_t - start_t);
//printf("%d %lf %lf %lf %lf\n",count,resid0,resid1,resid2,resid3);
/* print_output(); */
free(xc);
free(yc);
free(xf);
free(yf);
free(volcell);
free(areaf);
free(vecfx);
free(vecfy);
free(xv);
free(yv);
free(ia_cf);
free(ia_cv);
free(lcf);
free(lcv);
/* free_2d_int(lfc); */
/* free_2d_int(lfv); */
free(lfc0);
free(lfc1);
free(lfv0);
free(lfv1);
free(bface);
free(f_to_bf);
free(bf_to_f);
free(bf_to_c);
free(bnode);
free(bctype);
free(bcname);
free(wcv);
free_2d(wbfv);
free(t);
free(tb);
free_2d(sc);
free_2d(sb);
free_2d(phic_new);
free_2d(phic_old);
free_2d(phib);
free_2d(phiv);
free_2d(dphi);
free_2d(fclink);
free_2d(ftlink);
free_2d(vol_vec);
free_2d(ba);
free_2d(bb);
free_2d(bc);
return 0;
}
int main (int argc, char* argv[]) {
srand(atoi(argv[1])); //Take argument to write special extension to file
double Btotalple, Bnurseple, Bspawnple, Btotalsol, Bnursesol, Bspawnsol ; /* biomass on nursery, total biomass */
//Read in the data
readgrid(&GridFood , X_MAX, Y_MAX, 52, theFood);
cout << "Read Food completed" << endl;
readgrid(&GridTemp , X_MAX, Y_MAX, 52, theTemp);
cout << "Read Temp completed" << endl;
readgrid(&GridLMort , X_MAX, Y_MAX, 52, theLMort);
cout << "Read Larval Mortality completed" << endl;
readgrowthgam(&WeekPropFood,52,theGrowthGam);
cout << "Read growth gam completed" << endl;
/* INITIALISE INDIVIDUALS AT START, FIRST PLAICE, THEN SOLE */
for(int i=0; i < POPMAX; i++) {
ple[i].sex = (i%2)+1;
ple[i].weight = BORNWGHT;
ple[i].id = id ;
ple[i].stage = 1 ; /* everybody should be mature */
ple[i].age = 52 ;
ple[i].u_m = U_M ;
ple[i].u_f = U_F;
if(SPAREA == 1){
ple[i].X = 75 ;
ple[i].Y = 53 ;
} else if(SPAREA == 2){
ple[i].X = 91 ;
ple[i].Y = 67 ;
}
int X = ple[i].X;
int Y = ple[i].Y;
int resX, resY;
for(int dd=0; dd < L_CHR1; dd++){ //check juvenile strategy
do{ple[i].juvXdir[dd] = (char)( (rand()% 11) -5); // Movement of maximum 5 left or right //
ple[i].juvYdir[dd] = (char)( (rand()% 11) -5); // Movement of maximum 5 up or down //
resX = (int) (ple[i].juvXdir[dd] * ple[i].swim()) ;
resY = (int) (ple[i].juvYdir[dd] * ple[i].swim()) ;
} while ((theTemp[1][X + resX][Y + resY ] < -15) ||(( X + resX) <0) || (( X + resX) > X_MAX) ||(( Y + resY) < 0) || ((Y + resY) > Y_MAX));
X += resX;
Y += resY;
ple[i].weight = ple[i].weight + ple[i].growth(theFood[(dd+6)%52][X][Y], theTemp[(dd+6)%52][X][Y],theGrowthGam[(dd+6)%52]);
}
for(int dd=0; dd <L_CHR2; dd++){ //check juvenile strategy
ple[i].adultXdir[dd] = (char)( (rand()% 11) -5); // Movement of maximum 5 left or right //
ple[i].adultYdir[dd] = (char)( (rand()% 11) -5); // Movement of maximum 5 up or down //
}
ple[i].weight = BORNWGHT;
id++;
}
// for(int i=0; i < POPMAX; i++){
// sol[i].sex = (i%2)+1;
// sol[i].weight = BORNWGHT ;
// sol[i].id = id ;
// sol[i].stage = 1 ;
// sol[i].age = 52 ;
// sol[i].u_m = U_M ;
// sol[i].u_f = U_F;
// if(SPAREA == 1){
// sol[i].X = 75 ;
// sol[i].Y = 53 ;
// } else if(SPAREA == 2){
// sol[i].X = 91 ;
// sol[i].Y = 67 ;
// }
// int X = sol[i].X;
// int Y = sol[i].Y;
// int resX, resY;
// for(int dd=0; dd < L_CHR1; dd++){ //check juvenile strategy
// do{sol[i].juvXdir[dd] = (char)( (rand()% 11) -5); // Movement of maximum 5 left or right //
// sol[i].juvYdir[dd] = (char)( (rand()% 11) -5); // Movement of maximum 5 up or down //
// resX = (int) (sol[i].juvXdir[dd] * sol[i].swim()) ;
// resY = (int) (sol[i].juvYdir[dd] * sol[i].swim()) ;
// } while ((theTemp[1][X + resX][Y + resY ] < -15) ||(( X + resX) <0) ||((X + resX) > X_MAX) ||((Y + resY )< 0) ||((Y + resY) > Y_MAX));
// X += resX;
// Y += resY;
// sol[i].weight = sol[i].weight + sol[i].growth(theFood[(dd+6)%52][X][Y], theTemp[(dd+6)%52][X][Y],theGrowthGam[(dd+6)%52]);
// }
// for(int dd=0; dd < L_CHR2 ; dd++){ //check juvenile strategy
// sol[i].adultXdir[dd] = (char)((rand()% 11) -5); // Movement of maximum 5 left or right //
// sol[i].adultYdir[dd] = (char)((rand()% 11) -5); // Movement of maximum 5 up or down //
// }
// sol[i].weight = BORNWGHT;
// id++;
// } // end for loop over individuals /
cout << "Initialisation of Plaice and Sole done" << endl;
int aliveple = POPMAX, alivesol = POPMAX;
string ext(".csv"); //Open file to write output to disk
string SPname("_SPAREA");
char buffer [4];
string SP(itoa(SPAREA,buffer,10));
filename += ( argv[1] + SPname + SP + ext);
cout << filename << endl;
popname += (argv[1] + SPname + SP + ext);
myfile.open (filename.c_str() );
mypopulation.open(popname.c_str());
/* START SIM */
for(int t = 6; t < T_MAX; t++){
/* CALCULATE TOTAL BIOMASS AND BIOMASS ON NURSERY FOR TWO SPECIES */
Bnurseple = Btotalple = Bspawnple = Bnursesol = Btotalsol = Bspawnsol = 0;
for(int n = 0 ; n < aliveple ; n++) {
if (ple[n].stage < 3 ) {
Btotalple += ple[n].weight ;
if (ple[n].stage < 2 ) Bnurseple += ple[n].weight;
}
}
// for(int n = 0 ; n < alivesol ; n++) {
// if (sol[n].stage < 3 ) {
// Btotalsol += sol[n].weight ;
// if (sol[n].stage < 2 ) Bnursesol += sol[n].weight;
// }
// }
Bspawnple = Btotalple - Bnurseple;
// Bspawnsol = Btotalsol - Bnursesol;
move(ple, aliveple, t%52, theTemp); // Move individuals every tenth timestep //
// move(sol, alivesol, t%52, theTemp); // Move individuals every tenth timestep //
age (ple, aliveple) ; // Function of ageing //
// age (sol, alivesol) ; // Function of ageing //
mortality(ple, LAMBDAple, aliveple ,Bnurseple ) ; // Function mortality //
// mortality(sol, LAMBDAsol, alivesol ,Bnursesol ) ; // Function mortality */
growth (ple, aliveple, Bnurseple, t % 52, theFood, theTemp, theGrowthGam) ; // Function of growth //
// growth (sol, alivesol, Bnursesol, t % 52, theFood, theTemp, theGrowthGam) ; // Function of growth //
if(t%52 == 10 ) maturation (ple, aliveple) ; //Checked with Cindy, gonads start to develop in March // Function of maturation //
// if(t%52 == 10 ) maturation (sol, alivesol) ; // Function of maturation //
if(t%52 == 5) cout<<"i " << argv[1] <<" t " << t << " ssb ple " << Bspawnple<<" num ple "<<aliveple<< endl; //output(ple,t, 3); // Write biomass and number to screen, followed by data for 10$
// if(t%52 == 5) cout<<"i " << argv[1] << " t " << t << " ssb sol " << Bspawnsol<<" num sol "<<alivesol<< endl; //output(sol,t, 3); // Write biomass and number to screen, followed by data fo$
aliveple = alive2front (ple) ; // shuffle so that alives are in front*/
// alivesol = alive2front (sol) ; // shuffle so that alives are in front*/
if(t%52 == 5) aliveple = reproduction(ple, R1ple, R2ple, aliveple, Bspawnple, theTemp); // Function of reproduction in week 5*/
// if(t%52 == 5) alivesol = reproduction(sol, R1sol, R2sol, alivesol, Bspawnsol, theTemp); // Function of reproduction in week 5*/
if(t%52 == 5){ larvalmortality (ple, aliveple, theLMort); aliveple = alive2front (ple);} // larvalmortality depends on field, now uniform field where everybody survives //
// if(t%52 == 5){ larvalmortality (sol, alivesol, theLMort); alivesol = alive2front (sol);} // larvalmortality depends on field, now uniform field where everybody survives //
//Write output
if ((t==6) ||( (t+A_MAX) % (int)(T_MAX/(T_STEP-1)) < 52 && t % 52 == 6)){
int nn = aliveple;
int age = ple[nn].age;
do{ age = ple[nn].age;
nn--;
} while ((nn > (aliveple - P_WRITE)) && (age <= 53));
minid = ple[nn + 1].id;
maxid = ple[aliveple - 1].id;
} else if ((t < 6 + A_MAX) ||( (t + A_MAX)% (int)(T_MAX/(T_STEP-1)) < A_MAX +52)){
for(int nn = 0; nn < aliveple; nn++){
if(ple[nn].stage < 3 && (ple[nn].id > minid & ple[nn].id < maxid)){
myfile <<t << "," << ple[nn].id << "," << (int) ple[nn].sex << "," << ple[nn].age << "," << (int) ple[nn].stage
<< "," << ple[nn].X << "," << ple[nn].Y << "," << ple[nn].weight
<< "," << (int) ple[nn].juvXdir[(int) (ple[nn].age)] << "," << (int) ple[nn].juvYdir[(int) (ple[nn].age)]
<< "," << (int) ple[nn].adultXdir[(t+1)%52] << "," << (int) ple[nn].adultYdir[(t+1)%52] << endl;
}
}
}
//Write output every 15 years (cycle of complete new population)
if(t % (A_MAX) == 5){ writePopStruct(mypopulation, ple,aliveple,t);}
} //end of timeloop
myfile.close() ; mypopulation.close();
return 0 ;
}