void check(double ****f) //calculate energy of pulsations of all components and know if there's crash
{
int i,j,k,l;
PulsEnergy=0;
TotalEnergy=0;
for(l=0;l<=2;l++)
for(i=0;i<m1;i++)
for(k=0;k<m3;k++)
averf[l][i][k] = 0;
for(i=ghost;i<mm1;i++)
for(j=ghost;j<mm2;j++)
for(k=ghost;k<mm3;k++)
if(isType(node[i][k],NodeFluid) && !isType(node[i][k],NodeClued))
{
PulsEnergy+=deviation(f,i,j,k);
for(l=0;l<=2;l++) averf[l][i][k] += pow(f[l+1][i][j][k],2.);
}
for(l=1;l<=3;l++)
for(i=0;i<m1;i++)
for(k=0;k<m3;k++)
if(isType(node[i][k],NodeFluid) && !isType(node[i][k],NodeClued))
TotalEnergy += fabs(1+coordin(i,0)*rc)*averf[l][i][k];
TotalEnergy += 1.; //if zero average field
razlet = (PulsEnergy/TotalEnergy>UpLimit);
}
void check(double ***f) //calculate energy of pulsations of all components and know if there's crash
{
int i,k,l;
//double meanp = 0;
//long kol=0;
PulsEnergy=0;
TotalEnergy=0;
for(i=0;i<m1;i++)
for(k=0;k<m3;k++)
if(isType(node[i][k],NodeFluid) && !isType(node[i][k],NodeClued))
{
// meanp += f[0][i][k];
// kol++;
PulsEnergy+=deviation(f,i,k);
for(l=1;l<=3;l++) TotalEnergy += fabs(1+coordin(i,0)*rc)*pow(f[l][i][k],2.);
}
/*meanp /= kol;
for(i=0;i<m1;i++)
for(k=0;k<m3;k++)
f[0][i][k] -= meanp;*/
TotalEnergy += 1.; //if zero average field
razlet = (PulsEnergy/TotalEnergy>UpLimit);
}
void printing(double ****f1,double dtdid,double t_cur,long count,double en)
{
double temp, divv, divB, totdivv, totdivB;
int i,j,k,l;
double mf[3], totmf[3], toten; //mf[0]=max(f), mf[1]=max(df), mf[2]=max(df/f)
FILE *fv,*fnu,*fen,*fkv;
//clrscr();
time_now = MPI_Wtime();
Master printf("program is working %0.2f seconds\n",time_now-time_begin);
calculate_curl(&f1[4],B,NodeMagn);
divv = divB = 0;
for(i=0;i<m1;i++)
for(j=ghost;j<mm2;j++)
for(k=0;k<m3;k++)
{
if(isType(node[i][k],NodeFluid) && !isType(node[i][k],NodeClued))
{
temp=dr(f1[1],i,j,k,1,0,dx[0],ghost, approx)
+dr(f1[2],i,j,k,2,0,dx[1],ghost, approx)*r_1[i]
+dr(f1[3],i,j,k,3,0,dx[2],ghost, approx)+f1[1][i][j][k]*r_1[i];
if (fabs(temp)>divv) divv=fabs(temp);
}
if(isType(node[i][k],NodeMagn) && !isType(node[i][k],NodeClued))
{
temp=dr(B[0],i,j,k,1,0,dx[0],ghost, approx)
+dr(B[1],i,j,k,2,0,dx[1],ghost, approx)*r_1[i]
+dr(B[2],i,j,k,3,0,dx[2],ghost, approx)+B[0][i][j][k]*r_1[i];
if (fabs(temp)>divB) divB=fabs(temp);
}
}
MPI_Allreduce(&divv, &totdivv, 1, MPI_DOUBLE , MPI_MAX, MPI_COMM_WORLD);
MPI_Allreduce(&divB, &totdivB, 1, MPI_DOUBLE , MPI_MAX, MPI_COMM_WORLD);
Master printf("t=%g dtdid=%g NIter=%d maxdivv=%g(local=%g) maxdivB=%g(local=%g)\n",
t_cur, dtdid, count, totdivv, divv, totdivB, divB);
MPI_Allreduce(&en, &toten, 1, MPI_DOUBLE , MPI_SUM, MPI_COMM_WORLD);
Master printf("Energy of pulsations=%g (local=%g)\n",toten,en);
Master fen = fileopen(NameEnergyFile,count);
Master fprintf(fen,"%8.8g \t%e",t_cur,toten);
// -------------------Maxima of array components and their changes---------------------------
for(l=0;l<nvar;l++) {
mf[0]=mf[1]=mf[2]=0;
for(i=0;i<m1;i++)
for(j=ghost;j<m2;j++)
for(k=0;k<mm3;k++)
if((l<=3 && isType(node[i][k],NodeFluid) || l>=4&& isType(node[i][k],NodeMagn))
&& !isType(node[i][k],NodeClued))
{
if (fabs(f1[l][i][j][k])>mf[0]) mf[0]=fabs(f1[l][i][j][k]);
temp=fabs(f[l][i][j][k]-f1[l][i][j][k]);
if (temp>mf[1]) mf[1]=temp;
if(f1[l][i][j][k]!=0) temp/=f1[l][i][j][k];
if (temp>mf[2]) mf[2]=temp;
}
MPI_Allreduce(&mf, &totmf, 3, MPI_DOUBLE , MPI_MAX, MPI_COMM_WORLD);
Master printf("%d maxf=%e(loc=%e) \tmaxdf=%e(loc=%e) \tmax(df/f)=%e(loc=%e)\n",
l, totmf[0],mf[0], totmf[1],mf[1], totmf[2],mf[2]);
Master fprintf(fen,"\t %e \t %e",totmf[0],totmf[1]);
}
for(l=0;l<3;l++) {
mf[0]=mf[1]=mf[2]=0;
for(i=0;i<m1;i++)
for(j=ghost;j<m2;j++)
for(k=0;k<mm3;k++)
if(isType(node[i][k],NodeMagn) && !isType(node[i][k],NodeClued))
{
if (fabs(B[l][i][j][k])>mf[0]) mf[0]=fabs(B[l][i][j][k]);
}
MPI_Allreduce(&mf, &totmf, 1, MPI_DOUBLE , MPI_MAX, MPI_COMM_WORLD);
Master printf("%d maxB=%e(loc=%e)\n",
l, totmf[0],mf[0]);
Master fprintf(fen,"\t %e",totmf[0]);
}
// --------------- quadratic norma of arrays --------------------------------------
for(l=0;l<nvar;l++) {
mf[0]=0;
for(i=0;i<m1;i++)
for(j=ghost;j<m2;j++)
for(k=0;k<mm3;k++)
if((l<=3 && isType(node[i][k],NodeFluid) || l>=4&& isType(node[i][k],NodeMagn))
&& !isType(node[i][k],NodeClued))
mf[0] += coordin(i,0)*pow(f1[l][i][j][k],2);
MPI_Allreduce(&mf, &totmf, 1, MPI_DOUBLE , MPI_SUM, MPI_COMM_WORLD);
Master fprintf(fen,"\t %e",totmf[0]/N1/N2/N3);
}
for(l=0;l<3;l++) {
mf[0]=0;
for(i=0;i<m1;i++)
for(j=ghost;j<m2;j++)
for(k=0;k<mm3;k++)
if(isType(node[i][k],NodeMagn))
mf[0] += coordin(i,0)*pow(B[l][i][j][k],2);
MPI_Allreduce(&mf, &totmf, 1, MPI_DOUBLE , MPI_SUM, MPI_COMM_WORLD);
Master fprintf(fen,"\t %e",totmf[0]/N1/N2/N3);
}
Master fprintf(fen,"\n");
Master fclose(fen);
// Master printf("number of runge-kutt calculations=%d\n",enter);
// -------------------- average profile of velocity ---------------------
for(i=0;i<N3;i++) vfi[i]=0;
for(i=0;i<N3;i++) totvfi[i]=0;
for(i=0;i<m1;i++)
for(j=ghost;j<mm2;j++)
for(k=0;k<m3;k++)
if(isType(node[i][k],NodeFluid) && !isType(node[i][k],NodeClued))
vfi[k-ghost+n[2]] += f[2][i][j][k];
MPI_Allreduce(vfi, totvfi, N2, MPI_DOUBLE , MPI_SUM, MPI_COMM_WORLD);
Master {for(i=0;i<N3;i++) totvfi[i] /= N1*N3;
fv = fileopen(NameVFile,count);
fprintf(fv,"{%8.8f}\t",t_cur);
print_array1d(fv,totvfi,0,N3);
fclose(fv);
}
}
void init_conditions()
{
int i,j,k,l;
double r, rho, r1, z1;
// double k1,k2,k3;
// -------- filling of nodes' types +reflections rel circle + nut ---------------
for(i=0;i<m1;i++)
for(k=0;k<m3;k++)
{
node[i][k] = NodeUnknown;
for(j=0;j<m2;j++) nut[i][j][k]=(
// (0.39+14.8*exp(-2.13*pow(2*coordin(k,2)-l3,2)))*0.1*0
+1.)/Re;
if(pr_neighbour[0]!=-1 && i<ghost ||
pr_neighbour[1]!=-1 && i>=mm1 ||
pr_neighbour[4]!=-1 && k<ghost ||
pr_neighbour[5]!=-1 && k>=mm3) setType(&node[i][k],NodeClued);
}
for(i=0;i<m1;i++)
for(k=0;k<m3;k++)
{
r1 = coordin(i,0); z1 = coordin(k,2);
rho=sqrt(pow(r1-rc,2) + z1*z1);
//regions
if(rho>Rsh) setType(&node[i][k],NodeVacuum);
else if(rho>Rfl) setType(&node[i][k],NodeShell);
else setType(&node[i][k],NodeFluid);
//for hydrodynamics
if(isType(node[i][k],NodeFluid))
{ if(isType(node[i][k],NodeGhostFluid)) node[i][k] -= NodeGhostFluid;
for(l=-ghost;l<=ghost;l++)
{ if(i+l>=0&&i+l<m1) if(!isType(node[i+l][k],NodeFluid))
setType(&node[i+l][k],NodeGhostFluid);
if(k+l>=0&&k+l<m3) if(!isType(node[i][k+l],NodeFluid))
setType(&node[i][k+l],NodeGhostFluid);
}
}
refr_f[i][k] = rc + (r1-rc)*(2*Rfl/rho-1); //physical coordinates
refz_f[i][k] = z1*(2*Rfl/rho-1);
refr_f[i][k] = (refr_f[i][k]-rc+R)/dx[0]-0.5-n[0]+ghost; // simulation indices
refz_f[i][k] = (refz_f[i][k]+R )/dx[2]-0.5-n[2]+ghost;
if(fabs(refr_f[i][k]-i)<1 && fabs(refz_f[i][k]-k)<1 && !isType(node[i][k],NodeFluid))
{ setType(&node[i][k],NodeFluid);
if(isType(node[i][k],NodeGhostFluid)) node[i][k] -= NodeGhostFluid;
for(l=-ghost;l<=ghost;l++)
{ if(i+l>=0&&i+l<m1) if(!isType(node[i+l][k],NodeFluid))
setType(&node[i+l][k],NodeGhostFluid);
if(k+l>=0&&k+l<m3) if(!isType(node[i][k+l],NodeFluid))
setType(&node[i][k+l],NodeGhostFluid);
}
}
//for magnetism
refr_m[i][k] = i;
refz_m[i][k] = k;
if(i+n[0]<ghost) {setType(&node[i][k],NodeGhostMagn);
refr_m[i][k] = 2*ghost-i-1;}
else if(i+n[0]>=N1+ghost)
{setType(&node[i][k],NodeGhostMagn);
refr_m[i][k] = 2*mm1-i-1;}
if(k+n[2]<ghost) {setType(&node[i][k],NodeGhostMagn);
refz_m[i][k] = 2*ghost-k-1;}
else if(k+n[2]>=N3+ghost)
{setType(&node[i][k],NodeGhostMagn);
refz_m[i][k] = 2*mm3-k-1;}
if(!isType(node[i][k],NodeGhostMagn)) setType(&node[i][k],NodeMagn);
//for divertor's blade
sinth[i][k]=(r1-rc)/rho;
costh[i][k]= z1 /rho;
chi[i][k] = chimax*M_PI/180.*rho/R;
}
for(i=0;i<m1;i++) { r_1[i]=1./coordin(i,0); r_2[i]=r_1[i]*r_1[i]; }
for(i=0;i<m1;i++)
for(j=0;j<m2;j++)
for(k=0;k<m3;k++)
{
if(isType(node[i][k],NodeFluid)) eta[i][j][k]=1./Rm/etavac;
if(isType(node[i][k],NodeShell)) eta[i][j][k]=etash/Rm/etavac;
if(isType(node[i][k],NodeVacuum)) eta[i][j][k]=1./Rm;
for(l=0;l<3;l++) B[l][i][j][k] = 0;
}
// --------------- initial conditions -----------------------------------------
// k1=2*M_PI/lfi; k3=M_PI/l3;
if(!goon) {
for(i=0;i<m1;i++)
for(j=0;j<m2;j++)
for(k=0;k<m3;k++)
{
if(isType(node[i][k],NodeFluid)) {
f[0][i][j][k]=0;
/* f[1][i][j][k]=Noise*((double)rand()-RAND_MAX/2)/RAND_MAX*
(Rfl*Rfl-pow(coordin(i,0)-rc,2) - pow(coordin(k,2),2))*4/Rfl/Rfl;
f[2][i][j][k]=NoiseNorm*cos(2*M_PI*coordin(j,1)/R)*sin(2*M_PI*coordin(k,2)/Rfl)
+ (parabole+Noise*((double)rand()-RAND_MAX/2)/RAND_MAX)*
(Rfl*Rfl-pow(coordin(i,0)-rc,2) - pow(coordin(k,2),2))*4/Rfl/Rfl;
f[3][i][j][k]=NoiseNorm*sin(2*M_PI*coordin(j,1)/R)*sin(2*M_PI*coordin(k,2)/Rfl)
+ Noise*((double)rand()-RAND_MAX/2)/RAND_MAX*
(Rfl*Rfl-pow(coordin(i,0)-rc,2) - pow(coordin(k,2),2))*4/Rfl/Rfl;*/
f[1][i][j][k]=f[2][i][j][k]=f[3][i][j][k]=0;
}
if(isType(node[i][k],NodeMagn))
{
f[4][i][j][k]=coordin(i,0)*cos(coordin(j,1))*sin(coordin(j,1));
f[5][i][j][k]=coordin(i,0)*cos(coordin(j,1))*cos(coordin(j,1));
f[6][i][j][k]=0;
/* f[4][i][j][k]=0;
f[5][i][j][k]=0;
f[6][i][j][k]=coordin(i,0);*/
}
}
// struct_func(f,2,2,3);
nmessage("Arrays were filled with initial values - calculation from beginning",0,0);
} else nmessage("Arrays were filled with initial values - calculation is continuing",t_cur,count);
}
int main (int argc, char ** argv)
{
pca::pcafitter fitter;
bool fast = false;
bool verbose = false;
bool selectsubsector = true;
bool selectsubladder = false;
bool useallsubsectors = false;
bool useallsubladders = false;
bool useonlyeven = false;
bool usesegid = false;
bool printallcoords = false;
while (1)
{
int c, option_index;
static struct option long_options[] = {
{"help", 0, NULL, 'h'},
{"verbose", 0, NULL, 'V'},
{"bigger-sub-tower", 0, NULL, 's'},
{"bigger-sub-sub-tower", 0, NULL, 'l'},
{"fast", 0, NULL, 'f'},
{"version", 0, NULL, 'v'},
{"all-sub-tower", 0, NULL, 'a'},
{"all-sub-sub-tower", 0, NULL, 'r'},
{"seg-id", 0, NULL, 'i'},
{"jump-tracks", 0, NULL, 'j'},
{"dump-allcoords", 0, NULL, 'p'},
{0, 0, 0, 0}
};
c = getopt_long (argc, argv, "iravhVslfjp", long_options, &option_index);
if (c == -1)
break;
switch (c)
{
case 'p':
printallcoords = true;
break;
case 'j':
useonlyeven = true;
break;
case 'i':
usesegid = true;
break;
case 'h':
usage (argv[0]);
break;
case 'v':
std::cout << "Version: " << pca::pcafitter::get_version_string() << std::endl;
exit(1);
break;
case 'a':
useallsubsectors = true;
break;
case 'r':
useallsubladders = true;
break;
case 'f':
fast = true;
break;
case 'V':
verbose = true;
break;
case's':
selectsubsector = true;
selectsubladder = false;
break;
case 'l':
selectsubladder = true;
selectsubsector = false;
break;
default:
usage (argv[0]);
break;
}
}
if (usesegid)
fitter.set_coordim (6);
fitter.set_paramdim(5);
if (!fitter.set_paramidx(ONEOVERPTIDX, "oneoverpt"))
{
std::cerr << fitter.get_errmsg() << std::endl;
return EXIT_FAILURE;
}
if (!fitter.set_paramidx(PHIIDX, "phi"))
{
std::cerr << fitter.get_errmsg() << std::endl;
return EXIT_FAILURE;
}
if (!fitter.set_paramidx(COTTETHAIDX, "cot(tetha)"))
{
std::cerr << fitter.get_errmsg() << std::endl;
return EXIT_FAILURE;
}
if (!fitter.set_paramidx(Z0IDX, "z0"))
{
std::cerr << fitter.get_errmsg() << std::endl;
return EXIT_FAILURE;
}
if (!fitter.set_paramidx(D0IDX, "d0"))
{
std::cerr << fitter.get_errmsg() << std::endl;
return EXIT_FAILURE;
}
if (optind >= argc)
usage (argv[0]);
if (selectsubladder && selectsubsector)
usage (argv[0]);
if (useallsubsectors || useallsubladders)
{
selectsubladder = false;
selectsubsector = false;
}
if (useallsubladders && useallsubsectors)
usage (argv[0]);
char * filename = (char *) alloca (strlen(argv[optind]) + 1);
strcpy (filename, argv[optind]);
// leggere file coordinate tracce simulate plus parametri
if (!pca::file_exists(filename))
{
std::cerr << "Inout file does not exist" << std::endl;
return EXIT_FAILURE;
}
int num_of_line = pca::numofline(filename);
std::cout << "file has " << num_of_line << " line " << std::endl;
int num_of_ent_read = (num_of_line-1)/ENTDIM;
int num_of_ent = num_of_ent_read;
if (useonlyeven)
{
if (num_of_ent_read % 2)
num_of_ent = (num_of_ent_read-1)/2;
else
num_of_ent = num_of_ent_read/2;
}
std::cout << "file has " << num_of_ent << " entries " << std::endl;
// non perfomante ma easy to go
arma::mat layer, ladder, module, coordin, paramin;
layer.set_size(num_of_ent,fitter.get_coordim());
ladder.set_size(num_of_ent,fitter.get_coordim());
module.set_size(num_of_ent,fitter.get_coordim());
coordin.set_size(num_of_ent,fitter.get_coordim());
paramin.set_size(num_of_ent,fitter.get_paramdim());
std::map<std::string, int> subsectors, subladders;
std::vector<std::string> subladderslist, subsectorslist;
// leggere file coordinate tracce simulate plus parametri
std::cout << "Reading data from " << filename << " file " << std::endl;
pca::reading_from_file (filename, paramin, coordin,
layer, ladder, module, subsectors, subladders,
subsectorslist, subladderslist, num_of_ent_read, usesegid,
useonlyeven, false);
// write date to file
if (printallcoords)
{
std::cout << "Printout coordinates " << std::endl;
std::ofstream myfilect("allcoords.txt");
for (int i=0; i<(int)coordin.n_rows; ++i)
for (int j=0; j<fitter.get_coordim(); j=j+3)
myfilect << coordin(i, j) << " " <<
coordin(i, j+1) << " " <<
coordin(i, j+2) << std::endl;
myfilect.close();
}
std::cout << "Writing parameters to files" << std::endl;
pca::write_to_file("oneoverpt.txt", paramin, ONEOVERPTIDX);
pca::write_to_file("phi.txt", paramin, PHIIDX);
pca::write_to_file("d0.txt", paramin, D0IDX);
pca::write_to_file("cotetha.txt", paramin, COTTETHAIDX);
pca::write_to_file("z0.txt", paramin, Z0IDX);
if (!useallsubsectors && !useallsubladders)
{
// values selection
std::string slctsubsec = "";
int maxnumber = 0;
arma::mat coord, param;
assert(selectsubsector != selectsubladder);
if (selectsubladder || selectsubsector)
{
if (selectsubsector)
{
std::cout << "Looking for bigger subsector" << std::endl;
std::cout << "We found " << subsectors.size() <<
" subsectors " << std::endl;
fitter.select_bigger_sub (subsectors, verbose,
maxnumber, slctsubsec);
std::cout << "Selected subsector " << slctsubsec <<
" numevt: " << maxnumber << std::endl;
fitter.extract_sub (subsectorslist,
slctsubsec, paramin, coordin, param,
coord);
}
if (selectsubladder)
{
std::cout << "Looking for bigger subladder" << std::endl;
std::cout << "We found " << subladders.size() <<
" subladders " << std::endl;
fitter.select_bigger_sub (subladders, verbose,
maxnumber, slctsubsec);
std::cout << "Selected subladder " << slctsubsec << " numevt: " << maxnumber << std::endl;
fitter.extract_sub (subladderslist,
slctsubsec, paramin, coordin, param,
coord);
}
}
else
{
param = paramin;
coord = coordin;
}
std::cout << "Printout selected coordinates " << std::endl;
std::ofstream myfileslct("selectedcoords.txt");
for (int i=0; i<(int)coord.n_rows; ++i)
for (int j=0; j<fitter.get_coordim(); j=j+3)
myfileslct << coord(i, j) << " " <<
coord(i, j+1) << " " <<
coord(i, j+2) << std::endl;
myfileslct.close();
// write date to file
std::cout << "Writing extracted parameters to files" << std::endl;
pca::write_to_file("oneoverpt_selected.txt", param, ONEOVERPTIDX);
pca::write_to_file("phi_selected.txt", param, PHIIDX);
pca::write_to_file("d0_selected.txt", param, D0IDX);
pca::write_to_file("cotetha_selected.txt", param, COTTETHAIDX);
pca::write_to_file("z0_selected.txt", param, Z0IDX);
std::ostringstream cfname, qfname;
cfname << "c." << slctsubsec << ".bin";
qfname << "q." << slctsubsec << ".bin";
perform_main_computation (fast, verbose, coord, param,
cfname.str(), qfname.str(), fitter);
}
else
{
assert(useallsubladders != useallsubsectors);
arma::mat coord, param;
unsigned int totalamnt = 0, usedamnt = 0;
std::vector<std::string> * listtouse = NULL;
std::set<std::string> sectrorset;
if (useallsubsectors)
{
std::vector<std::string>::const_iterator selecteds =
subsectorslist.begin();
for (; selecteds != subsectorslist.end(); ++selecteds)
sectrorset.insert(*selecteds);
listtouse = &subsectorslist;
}
else if (useallsubladders)
{
std::vector<std::string>::const_iterator selecteds =
subladderslist.begin();
for (; selecteds != subladderslist.end(); ++selecteds)
sectrorset.insert(*selecteds);
listtouse = &subladderslist;
}
else
usage(argv[0]);
std::set<std::string>::const_iterator selected =
sectrorset.begin();
for (; selected != sectrorset.end(); ++selected)
{
fitter.extract_sub (*listtouse,
*selected, paramin, coordin, param,
coord);
std::cout << "Selected " << *selected << " size " <<
coord.n_rows << std::endl;
totalamnt += coord.n_rows;
if (coord.n_rows > MINDIMLINIT)
{
std::ostringstream cfname, qfname;
cfname << "c." << *selected << ".bin";
qfname << "q." << *selected << ".bin";
perform_main_computation (fast, verbose, coord, param,
cfname.str(), qfname.str(), fitter);
usedamnt += coord.n_rows;
}
}
std::cout << "Total tracks: " << totalamnt << std::endl;
std::cout << "Used tracks: " << usedamnt << std::endl;
}
return EXIT_SUCCESS;
}
void init_conditions(double ****f,double Re)
{
int i,j,k,l;
double Noise=0.3, Noise1=0;
// double k1,k2,k3;
// k1=2*M_PI/l1; k3=M_PI/l3;
for(i=0;i<m1;i++)
for(j=0;j<m2;j++)
for(k=0;k<m3;k++) {
f[0][i][j][k]=(1+Noise*((double)rand()-RAND_MAX/2)/RAND_MAX)*
coordin(k,2)*(l3-coordin(k,2))*4/l3/l3;
f[1][i][j][k]=Noise1*cos(2*M_PI*coordin(j,1)/l2)*cos(2*M_PI*coordin(k,2)/l3)
+ Noise*((double)rand()-RAND_MAX/2)/RAND_MAX*
coordin(k,2)*(l3-coordin(k,2))*4/l3/l3;
f[2][i][j][k]=Noise1*sin(2*M_PI*coordin(j,1)/l2)*sin(2*M_PI*coordin(k,2)/l3)
+ Noise*((double)rand()-RAND_MAX/2)/RAND_MAX*
coordin(k,2)*(l3-coordin(k,2))*4/l3/l3;
f[3][i][j][k]=p1+(i-0.5)*(p2-p1)/n1;
nut[i][j][k]=(
(0.39+14.8*exp(-2.13*pow(2*coordin(k,2)-l3,2)))*0.1
+1)/Re;
}
// struct_func(f,2,2,3);
}
int Engine::initialize()
{
// For Tracing
std::vector < std::string > keys;
keys.push_back("currentEnergy");
keys.push_back("minEnergy");
keys.push_back("nSteps");
keys.push_back("temperature");
tracer_.clear();
tracer_.setKeyList(keys);
if (isVerbose())
{
Rprintf("Initialization...\n");
}
// Init x related vectors
try {
xRange_.resize(x_.size());
xBackup_.resize(x_.size());
xMini_.resize(x_.size());
xBuffer_.resize(x_.size());
g_.resize(x_.size());
}
catch (std::length_error& le) {
Rprintf("Engine: Length error: %s\n",le.what());
}
itSoftMax_ = x_.size() * 6;
factr_ = 1000;
pgTol_ = 1.e-6;
reps_ = 1.e-6;
nbFctCall_ = 0;
idum_ = -100377;
indTrace_ = 0;
// Check markov chain length
if (0 != markovLength_ % x_.size())
{
Rprintf(
"LMarkov should be size of 'x' (recommended) or 2*n or 3*n ... since component.change is 1\n");
return -1;
}
// if (lsEnd_)
// {
// markovLength_ = 200 * x_.size();
// if (markovLength_ < 1000)
// {
// markovLength_ = 1000;
// }
// else if (markovLength_ > 10000)
// {
// markovLength_ = 10000;
// }
// }
if (isVerbose())
{
Rprintf("LMarkov= %i\n", markovLength_);
}
for (unsigned int i = 0; i < x_.size(); ++i)
{
xRange_[i] = upper_[i] - lower_[i];
}
if (isVerbose())
{
Rprintf("xrange: ");
printVect(xRange_);
}
// Check if starting point is in constraint
bool inConstraint = true;
bool initError = true;
unsigned int reinitCount = 0;
while (initError)
{
if (inConstraint)
{
if (hasConstraint_)
{
inConstraint = judgeConstraint();
while (!inConstraint)
{
coordin(idum_, x_);
inConstraint = judgeConstraint();
}
}
}
if (isVerbose())
{
Rprintf("The random intial x coordinates:\n");
printVect(x_);
}
energy(x_);
if (isVerbose())
{
Rprintf("The energy of initial x = %.10g\n", etot_);
}
if (etot_ >= BIG_VALUE)
{
if (isVerbose())
{
Rprintf("x: ");
printVect(x_);
Rprintf(
" give NaN, NA, or inf, generating new starting point\n");
}
if (reinitCount >= MAX_REINIT_COUNT)
{
Rprintf("Stopping algorithm because function to optimize create NaN or (+/-) infinity values even with trying new random parameters");
return -1;
}
double rd = 0;
for (unsigned int i=0; i < x_.size(); ++i)
{
// lower + runif(length(lower))*(upper-lower)
rd = Utils::ran2(&idum_);
x_[i] = lower_[i] + rd * (upper_[i] - lower_[i]);
}
reinitCount++;
}
else
{
initError = false;
}
}
return 0;
}
