nlopt_opt make_opt(const mxArray *opts, unsigned n)
{
nlopt_opt opt = NULL, local_opt = NULL;
nlopt_algorithm algorithm;
double *tmp = NULL;
unsigned i;
algorithm = (nlopt_algorithm)
struct_val_default(opts, "algorithm", NLOPT_NUM_ALGORITHMS);
CHECK1(((int)algorithm) >= 0 && algorithm < NLOPT_NUM_ALGORITHMS,
"invalid opt.algorithm");
tmp = (double *) mxCalloc(n, sizeof(double));
opt = nlopt_create(algorithm, n);
CHECK1(opt, "nlopt: out of memory");
nlopt_set_lower_bounds(opt, struct_arrval(opts, "lower_bounds", n,
fill(tmp, n, -HUGE_VAL)));
nlopt_set_upper_bounds(opt, struct_arrval(opts, "upper_bounds", n,
fill(tmp, n, +HUGE_VAL)));
nlopt_set_stopval(opt, struct_val_default(opts, "stopval", -HUGE_VAL));
nlopt_set_ftol_rel(opt, struct_val_default(opts, "ftol_rel", 0.0));
nlopt_set_ftol_abs(opt, struct_val_default(opts, "ftol_abs", 0.0));
nlopt_set_xtol_rel(opt, struct_val_default(opts, "xtol_rel", 0.0));
nlopt_set_xtol_abs(opt, struct_arrval(opts, "xtol_abs", n,
fill(tmp, n, 0.0)));
nlopt_set_maxeval(opt, struct_val_default(opts, "maxeval", 0.0) < 0 ?
0 : struct_val_default(opts, "maxeval", 0.0));
nlopt_set_maxtime(opt, struct_val_default(opts, "maxtime", 0.0));
nlopt_set_population(opt, struct_val_default(opts, "population", 0));
nlopt_set_vector_storage(opt, struct_val_default(opts, "vector_storage", 0));
if (struct_arrval(opts, "initial_step", n, NULL))
nlopt_set_initial_step(opt,
struct_arrval(opts, "initial_step", n, NULL));
if (mxGetField(opts, 0, "local_optimizer")) {
const mxArray *local_opts = mxGetField(opts, 0, "local_optimizer");
CHECK1(mxIsStruct(local_opts),
"opt.local_optimizer must be a structure");
CHECK1(local_opt = make_opt(local_opts, n),
"error initializing local optimizer");
nlopt_set_local_optimizer(opt, local_opt);
nlopt_destroy(local_opt); local_opt = NULL;
}
mxFree(tmp);
return opt;
}
int main(int argc, char **argv)
{
/* -------Initialize and Get the parameters from command line ------*/
PetscInitialize(&argc, &argv, PETSC_NULL, PETSC_NULL);
PetscPrintf(PETSC_COMM_WORLD,"--------Initializing------ \n");
PetscErrorCode ierr;
PetscBool flg;
int myrank;
MPI_Comm_rank(MPI_COMM_WORLD,&myrank);
if(myrank==0)
mma_verbose=1;
/*-------------------------------------------------*/
int Mx,My,Mz,Mzslab, Npmlx,Npmly,Npmlz,DegFree, anisotropic;
PetscOptionsGetInt(PETSC_NULL,"-Nx",&Nx,&flg); MyCheckAndOutputInt(flg,Nx,"Nx","Nx");
PetscOptionsGetInt(PETSC_NULL,"-Ny",&Ny,&flg); MyCheckAndOutputInt(flg,Ny,"Ny","Nx");
PetscOptionsGetInt(PETSC_NULL,"-Nz",&Nz,&flg); MyCheckAndOutputInt(flg,Nz,"Nz","Nz");
PetscOptionsGetInt(PETSC_NULL,"-Mx",&Mx,&flg); MyCheckAndOutputInt(flg,Mx,"Mx","Mx");
PetscOptionsGetInt(PETSC_NULL,"-My",&My,&flg); MyCheckAndOutputInt(flg,My,"My","My");
PetscOptionsGetInt(PETSC_NULL,"-Mz",&Mz,&flg); MyCheckAndOutputInt(flg,Mz,"Mz","Mz");
PetscOptionsGetInt(PETSC_NULL,"-Mzslab",&Mzslab,&flg); MyCheckAndOutputInt(flg,Mzslab,"Mzslab","Mzslab");
PetscOptionsGetInt(PETSC_NULL,"-Npmlx",&Npmlx,&flg); MyCheckAndOutputInt(flg,Npmlx,"Npmlx","Npmlx");
PetscOptionsGetInt(PETSC_NULL,"-Npmly",&Npmly,&flg); MyCheckAndOutputInt(flg,Npmly,"Npmly","Npmly");
PetscOptionsGetInt(PETSC_NULL,"-Npmlz",&Npmlz,&flg); MyCheckAndOutputInt(flg,Npmlz,"Npmlz","Npmlz");
Nxyz = Nx*Ny*Nz;
// if anisotropic !=0, Degree of Freedom = 3*Mx*My*Mz; else DegFree = Mx*My*Mz;
PetscOptionsGetInt(PETSC_NULL,"-anisotropic",&anisotropic,&flg);
if(!flg) anisotropic = 0; // by default, it is isotropc.
DegFree = (anisotropic ? 3 : 1 )*Mx*My*((Mzslab==0)?Mz:1);
PetscPrintf(PETSC_COMM_WORLD," the Degree of Freedoms is %d \n ", DegFree);
int DegFreeAll=DegFree+1;
PetscPrintf(PETSC_COMM_WORLD," the Degree of Freedoms ALL is %d \n ", DegFreeAll);
int BCPeriod, Jdirection, Jdirectiontwo, LowerPML;
int bx[2], by[2], bz[2];
PetscOptionsGetInt(PETSC_NULL,"-BCPeriod",&BCPeriod,&flg); MyCheckAndOutputInt(flg,BCPeriod,"BCPeriod","BCPeriod given");
PetscOptionsGetInt(PETSC_NULL,"-Jdirection",&Jdirection,&flg); MyCheckAndOutputInt(flg,Jdirection,"Jdirection","Diapole current direction");
PetscOptionsGetInt(PETSC_NULL,"-Jdirectiontwo",&Jdirectiontwo,&flg); MyCheckAndOutputInt(flg,Jdirectiontwo,"Jdirectiontwo","Diapole current direction for source two");
PetscOptionsGetInt(PETSC_NULL,"-LowerPML",&LowerPML,&flg); MyCheckAndOutputInt(flg,LowerPML,"LowerPML","PML in the lower xyz boundary");
PetscOptionsGetInt(PETSC_NULL,"-bxl",bx,&flg); MyCheckAndOutputInt(flg,bx[0],"bxl","BC at x lower");
PetscOptionsGetInt(PETSC_NULL,"-bxu",bx+1,&flg); MyCheckAndOutputInt(flg,bx[1],"bxu","BC at x upper");
PetscOptionsGetInt(PETSC_NULL,"-byl",by,&flg); MyCheckAndOutputInt(flg,by[0],"byl","BC at y lower");
PetscOptionsGetInt(PETSC_NULL,"-byu",by+1,&flg); MyCheckAndOutputInt(flg,by[1],"byu","BC at y upper");
PetscOptionsGetInt(PETSC_NULL,"-bzl",bz,&flg); MyCheckAndOutputInt(flg,bz[0],"bzl","BC at z lower");
PetscOptionsGetInt(PETSC_NULL,"-bzu",bz+1,&flg); MyCheckAndOutputInt(flg,bz[1],"bzu","BC at z upper");
double epssub, RRT, sigmax, sigmay, sigmaz ;
PetscOptionsGetReal(PETSC_NULL,"-hx",&hx,&flg); MyCheckAndOutputDouble(flg,hx,"hx","hx");
hy = hx;
hz = hx;
hxyz = (Nz==1)*hx*hy + (Nz>1)*hx*hy*hz;
double omega, omegaone, omegatwo, wratio;
PetscOptionsGetReal(PETSC_NULL,"-omega",&omega,&flg); MyCheckAndOutputDouble(flg,omega,"omega","omega");
PetscOptionsGetReal(PETSC_NULL,"-wratio",&wratio,&flg); MyCheckAndOutputDouble(flg,wratio,"wratio","wratio");
omegaone=omega;
omegatwo=wratio*omega;
PetscPrintf(PETSC_COMM_WORLD,"---omegaone is %.16e and omegatwo is %.16e ---\n",omegaone, omegatwo);
PetscOptionsGetReal(PETSC_NULL,"-Qabs",&Qabs,&flg);
if (flg && Qabs>1e+15)
Qabs=1.0/0.0;
MyCheckAndOutputDouble(flg,Qabs,"Qabs","Qabs");
PetscOptionsGetReal(PETSC_NULL,"-epsair",&epsair,&flg); MyCheckAndOutputDouble(flg,epsair,"epsair","epsair");
PetscOptionsGetReal(PETSC_NULL,"-epssub",&epssub,&flg); MyCheckAndOutputDouble(flg,epssub,"epssub","epssub");
PetscOptionsGetReal(PETSC_NULL,"-RRT",&RRT,&flg); MyCheckAndOutputDouble(flg,RRT,"RRT","RRT given");
sigmax = pmlsigma(RRT,Npmlx*hx);
sigmay = pmlsigma(RRT,Npmly*hy);
sigmaz = pmlsigma(RRT,Npmlz*hz);
PetscPrintf(PETSC_COMM_WORLD,"----sigmax is %.12e \n",sigmax);
PetscPrintf(PETSC_COMM_WORLD,"----sigmay is %.12e \n",sigmay);
PetscPrintf(PETSC_COMM_WORLD,"----sigmaz is %.12e \n",sigmaz);
char initialdata[PETSC_MAX_PATH_LEN]; //filenameComm[PETSC_MAX_PATH_LEN];
PetscOptionsGetString(PETSC_NULL,"-initialdata",initialdata,PETSC_MAX_PATH_LEN,&flg); MyCheckAndOutputChar(flg,initialdata,"initialdata","Inputdata file");
PetscOptionsGetString(PETSC_NULL,"-filenameComm",filenameComm,PETSC_MAX_PATH_LEN,&flg); MyCheckAndOutputChar(flg,filenameComm,"filenameComm","Output filenameComm");
// add cx, cy, cz to indicate where the diapole current is;
int cx, cy, cz;
PetscOptionsGetInt(PETSC_NULL,"-cx",&cx,&flg);
if (!flg)
{cx=(LowerPML)*floor(Nx/2); PetscPrintf(PETSC_COMM_WORLD,"cx is %d by default \n",cx);}
else
{PetscPrintf(PETSC_COMM_WORLD,"the current poisiont cx is %d \n",cx);}
PetscOptionsGetInt(PETSC_NULL,"-cy",&cy,&flg);
if (!flg)
{cy=(LowerPML)*floor(Ny/2); PetscPrintf(PETSC_COMM_WORLD,"cy is %d by default \n",cy);}
else
{PetscPrintf(PETSC_COMM_WORLD,"the current poisiont cy is %d \n",cy);}
PetscOptionsGetInt(PETSC_NULL,"-cz",&cz,&flg);
if (!flg)
{cz=(LowerPML)*floor(Nz/2); PetscPrintf(PETSC_COMM_WORLD,"cz is %d by default \n",cz);}
else
{PetscPrintf(PETSC_COMM_WORLD,"the current poisiont cz is %d \n",cz);}
posj = (cx*Ny+ cy)*Nz + cz;
PetscPrintf(PETSC_COMM_WORLD,"the posj is %d \n. ", posj);
int fixpteps;
PetscOptionsGetInt(PETSC_NULL,"-fixpteps",&fixpteps,&flg); MyCheckAndOutputInt(flg,fixpteps,"fixpteps","fixpteps");
// Get minapproach;
PetscOptionsGetInt(PETSC_NULL,"-minapproach",&minapproach,&flg); MyCheckAndOutputInt(flg,minapproach,"minapproach","minapproach");
// Get withepsinldos;
PetscOptionsGetInt(PETSC_NULL,"-withepsinldos",&withepsinldos,&flg); MyCheckAndOutputInt(flg,withepsinldos,"withepsinldos","withepsinldos");
// Get outputbase;
PetscOptionsGetInt(PETSC_NULL,"-outputbase",&outputbase,&flg); MyCheckAndOutputInt(flg,outputbase,"outputbase","outputbase");
// Get cavityverbose;
PetscOptionsGetInt(PETSC_NULL,"-cavityverbose",&cavityverbose,&flg);
if(!flg) cavityverbose=0;
PetscPrintf(PETSC_COMM_WORLD,"the cavity verbose is set as %d \n", cavityverbose);
// Get refinedldos;
PetscOptionsGetInt(PETSC_NULL,"-refinedldos",&refinedldos,&flg);
if(!flg) refinedldos=0;
PetscPrintf(PETSC_COMM_WORLD,"the refinedldos is set as %d \n", refinedldos);
// Get cmpwrhs;
int cmpwrhs;
PetscOptionsGetInt(PETSC_NULL,"-cmpwrhs",&cmpwrhs,&flg);
if(!flg) cmpwrhs=0;
PetscPrintf(PETSC_COMM_WORLD,"the cmpwrhs is set as %d \n", cmpwrhs);
// Get lrzsqr;
PetscOptionsGetInt(PETSC_NULL,"-lrzsqr",&lrzsqr,&flg);
if(!flg) lrzsqr=0;
PetscPrintf(PETSC_COMM_WORLD,"the lrzsqr is set as %d \n", lrzsqr);
// Get newQdef;
PetscOptionsGetInt(PETSC_NULL,"-newQdef",&newQdef,&flg);
if(!flg) newQdef=0;
PetscPrintf(PETSC_COMM_WORLD,"the newQdef is set as %d \n", newQdef);
/*--------------------------------------------------------*/
/*--------------------------------------------------------*/
/*---------- Set the current source---------*/
//Mat D; //ImaginaryIMatrix;
ImagIMat(PETSC_COMM_WORLD, &D,6*Nxyz);
Vec J;
ierr = VecCreateMPI(PETSC_COMM_WORLD, PETSC_DECIDE, 6*Nxyz, &J);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) J, "Source");CHKERRQ(ierr);
VecSet(J,0.0); //initialization;
if (Jdirection == 1)
SourceSingleSetX(PETSC_COMM_WORLD, J, Nx, Ny, Nz, cx, cy, cz,1.0/hxyz);
else if (Jdirection ==2)
SourceSingleSetY(PETSC_COMM_WORLD, J, Nx, Ny, Nz, cx, cy, cz,1.0/hxyz);
else if (Jdirection == 3)
SourceSingleSetZ(PETSC_COMM_WORLD, J, Nx, Ny, Nz, cx, cy, cz,1.0/hxyz);
else
PetscPrintf(PETSC_COMM_WORLD," Please specify correct direction of current: x (1) , y (2) or z (3)\n ");
Vec Jtwo;
ierr = VecDuplicate(J, &Jtwo);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) Jtwo, "Sourcetwo");CHKERRQ(ierr);
VecSet(Jtwo,0.0); //initialization;
if (Jdirectiontwo == 1)
SourceSingleSetX(PETSC_COMM_WORLD, Jtwo, Nx, Ny, Nz, cx, cy, cz,1.0/hxyz);
else if (Jdirectiontwo ==2)
SourceSingleSetY(PETSC_COMM_WORLD, Jtwo, Nx, Ny, Nz, cx, cy, cz,1.0/hxyz);
else if (Jdirectiontwo == 3)
SourceSingleSetZ(PETSC_COMM_WORLD, Jtwo, Nx, Ny, Nz, cx, cy, cz,1.0/hxyz);
else
PetscPrintf(PETSC_COMM_WORLD," Please specify correct direction of current two: x (1) , y (2) or z (3)\n ");
//Vec b; // b= i*omega*J;
Vec bone, btwo;
ierr = VecDuplicate(J,&b);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) b, "rhsone");CHKERRQ(ierr);
ierr = VecDuplicate(J,&bone);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) bone, "rhsone");CHKERRQ(ierr);
ierr = VecDuplicate(Jtwo,&btwo);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) btwo, "rhstwo");CHKERRQ(ierr);
if (cmpwrhs==0)
{
ierr = MatMult(D,J,b);CHKERRQ(ierr);
ierr = MatMult(D,Jtwo,btwo);CHKERRQ(ierr);
VecCopy(b,bone);
VecScale(bone,omegaone);
VecScale(btwo,omegatwo);
VecScale(b,omega);
}
else
{
double complex cmpiomega;
cmpiomega = cpow(1+I/Qabs,newQdef+1);
double sqrtiomegaR = -omega*cimag(csqrt(cmpiomega));
double sqrtiomegaI = omega*creal(csqrt(cmpiomega));
PetscPrintf(PETSC_COMM_WORLD,"the real part of sqrt cmpomega is %g and imag sqrt is % g ", sqrtiomegaR, sqrtiomegaI);
Vec tmpi;
ierr = VecDuplicate(J,&tmpi);
VecSet(b,0.0);
VecSet(tmpi,0.0);
CmpVecScale(J,b,sqrtiomegaR,sqrtiomegaI,D,tmpi);
VecDestroy(&tmpi);
}
/*-------Get the weight vector ------------------*/
//Vec weight;
ierr = VecDuplicate(J,&weight); CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) weight, "weight");CHKERRQ(ierr);
if(LowerPML==0)
GetWeightVec(weight, Nx, Ny,Nz); // new code handles both 3D and 2D;
else
VecSet(weight,1.0);
Vec weightedJ;
ierr = VecDuplicate(J,&weightedJ); CHKERRQ(ierr);
ierr = VecPointwiseMult(weightedJ,J,weight);
ierr = PetscObjectSetName((PetscObject) weightedJ, "weightedJ");CHKERRQ(ierr);
Vec weightedJtwo;
ierr = VecDuplicate(Jtwo,&weightedJtwo); CHKERRQ(ierr);
ierr = VecPointwiseMult(weightedJtwo,Jtwo,weight);
ierr = PetscObjectSetName((PetscObject) weightedJtwo, "weightedJtwo");CHKERRQ(ierr);
//Vec vR;
ierr = VecDuplicate(J,&vR); CHKERRQ(ierr);
GetRealPartVec(vR, 6*Nxyz);
// VecFReal;
if (lrzsqr)
{ ierr = VecDuplicate(J,&epsFReal); CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) epsFReal, "epsFReal");CHKERRQ(ierr);
if (newQdef==0)
{
sqrtomegaI = omega*cimag(csqrt(1+I/Qabs));
PetscPrintf(PETSC_COMM_WORLD,"the real part of sqrt cmpomega is %g and imag sqrt is % g ", omega*creal(csqrt(1+I/Qabs)), sqrtomegaI);
betar = 2*sqrtomegaI;
betai = betar/Qabs;
}
else
{
double gamma;
gamma = omega/Qabs;
betar = 2*gamma*(1-1.0/pow(Qabs,2));
betai = 2*gamma*(2.0/Qabs);
}
ierr = VecDuplicate(J,&nb); CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) nb, "nb"); CHKERRQ(ierr);
ierr = VecDuplicate(J,&y); CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) y, "y"); CHKERRQ(ierr);
ierr = VecDuplicate(J,&xsqr); CHKERRQ(ierr); // xsqr = x*x;
ierr = PetscObjectSetName((PetscObject) xsqr, "xsqr"); CHKERRQ(ierr);
CongMat(PETSC_COMM_WORLD, &C, 6*Nxyz);
}
/*----------- Define PML muinv vectors */
Vec muinvpml;
MuinvPMLFull(PETSC_COMM_SELF, &muinvpml,Nx,Ny,Nz,Npmlx,Npmly,Npmlz,sigmax,sigmay,sigmaz,omega, LowerPML);
//double *muinv;
muinv = (double *) malloc(sizeof(double)*6*Nxyz);
int add=0;
AddMuAbsorption(muinv,muinvpml,Qabs,add);
ierr = VecDestroy(&muinvpml); CHKERRQ(ierr);
/*---------- Define PML eps vectors: epspml---------- */
Vec epspml; //epspmlQ, epscoef;
ierr = VecDuplicate(J,&epspml);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) epspml,"EpsPMLFull"); CHKERRQ(ierr);
EpsPMLFull(PETSC_COMM_WORLD, epspml,Nx,Ny,Nz,Npmlx,Npmly,Npmlz,sigmax,sigmay,sigmaz,omega, LowerPML);
ierr = VecDuplicate(J,&epspmlQ);CHKERRQ(ierr);
Vec epscoefone, epscoeftwo;
ierr = VecDuplicate(J,&epscoefone);CHKERRQ(ierr);
ierr = VecDuplicate(J,&epscoeftwo);CHKERRQ(ierr);
// compute epspmlQ,epscoef;
EpsCombine(D, weight, epspml, epspmlQ, epscoefone, Qabs, omegaone);
EpsCombine(D, weight, epspml, epspmlQ, epscoeftwo, Qabs, omegatwo);
/*--------- Setup the interp matrix ----------------------- */
/* for a samll eps block, interp it into yee-lattice. The interp matrix A and PML epspml only need to generated once;*/
//Mat A;
//new routine for myinterp;
myinterp(PETSC_COMM_WORLD, &A, Nx,Ny,Nz, LowerPML*floor((Nx-Mx)/2),LowerPML*floor((Ny-My)/2),LowerPML*floor((Nz-Mz)/2), Mx,My,Mz,Mzslab, anisotropic); // LoweerPML*Npmlx,..,.., specify where the interp starts;
//Vec epsSReal, epsgrad, vgrad; // create compatiable vectors with A.
ierr = MatGetVecs(A,&epsSReal, &epsgrad); CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) epsgrad, "epsgrad");CHKERRQ(ierr);
ierr = VecDuplicate(epsSReal, &vgrad); CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) epsSReal, "epsSReal");CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) vgrad, "vgrad");CHKERRQ(ierr);
/*---------Setup the epsmedium vector----------------*/
//Vec epsmedium;
ierr = VecDuplicate(J,&epsmedium); CHKERRQ(ierr);
GetMediumVec(epsmedium,Nz,Mz,epsair,epssub);
/*--------- Setup the finitie difference matrix-------------*/
//Mat M;
MoperatorGeneral(PETSC_COMM_WORLD, &M, Nx,Ny,Nz,hx,hy,hz, bx, by, bz,muinv,BCPeriod);
free(muinv);
/*--------Setup the KSP variables ---------------*/
KSP kspone;
PC pcone;
ierr = KSPCreate(PETSC_COMM_WORLD,&kspone);CHKERRQ(ierr);
//ierr = KSPSetType(ksp, KSPPREONLY);CHKERRQ(ierr);
ierr = KSPSetType(kspone, KSPGMRES);CHKERRQ(ierr);
ierr = KSPGetPC(kspone,&pcone);CHKERRQ(ierr);
ierr = PCSetType(pcone,PCLU);CHKERRQ(ierr);
ierr = PCFactorSetMatSolverPackage(pcone,MATSOLVERPASTIX);CHKERRQ(ierr);
ierr = PCSetFromOptions(pcone);
int maxkspit = 20;
ierr = KSPSetTolerances(kspone,1e-14,PETSC_DEFAULT,PETSC_DEFAULT,maxkspit);CHKERRQ(ierr);
ierr = KSPSetFromOptions(kspone);CHKERRQ(ierr);
KSP ksptwo;
PC pctwo;
ierr = KSPCreate(PETSC_COMM_WORLD,&ksptwo);CHKERRQ(ierr);
//ierr = KSPSetType(ksp, KSPPREONLY);CHKERRQ(ierr);
ierr = KSPSetType(ksptwo, KSPGMRES);CHKERRQ(ierr);
ierr = KSPGetPC(ksptwo,&pctwo);CHKERRQ(ierr);
ierr = PCSetType(pctwo,PCLU);CHKERRQ(ierr);
ierr = PCFactorSetMatSolverPackage(pctwo,MATSOLVERPASTIX);CHKERRQ(ierr);
ierr = PCSetFromOptions(pctwo);
ierr = KSPSetTolerances(ksptwo,1e-14,PETSC_DEFAULT,PETSC_DEFAULT,maxkspit);CHKERRQ(ierr);
ierr = KSPSetFromOptions(ksptwo);CHKERRQ(ierr);
/*--------- Create the space for solution vector -------------*/
//Vec x;
ierr = VecDuplicate(J,&x);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) x, "Solution");CHKERRQ(ierr);
/*----------- Create the space for final eps -------------*/
//Vec epsC, epsCi, epsP;
ierr = VecDuplicate(J,&epsC);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) epsC, "EpsC");CHKERRQ(ierr);
ierr = VecDuplicate(J,&epsCi);CHKERRQ(ierr);
ierr = VecDuplicate(J,&epsP);CHKERRQ(ierr);
ierr = VecSet(epsP,0.0); CHKERRQ(ierr);
ierr = VecAssemblyBegin(epsP); CHKERRQ(ierr);
ierr = VecAssemblyEnd(epsP); CHKERRQ(ierr);
/*------------ Create space used in the solver ------------*/
//Vec vgradlocal,tmp, tmpa,tmpb;
ierr = VecCreateSeq(PETSC_COMM_SELF, DegFree, &vgradlocal); CHKERRQ(ierr);
ierr = VecDuplicate(J,&tmp); CHKERRQ(ierr);
ierr = VecDuplicate(J,&tmpa); CHKERRQ(ierr);
ierr = VecDuplicate(J,&tmpb); CHKERRQ(ierr);
// Vec pickposvec; this vector is zero except that first entry is one;
if (withepsinldos)
{ ierr = VecDuplicate(J,&pickposvec); CHKERRQ(ierr);
ierr = VecSet(pickposvec,0.0); CHKERRQ(ierr);
ierr = VecSetValue(pickposvec,posj+Jdirection*Nxyz,1.0,INSERT_VALUES);
VecAssemblyBegin(pickposvec);
VecAssemblyEnd(pickposvec);
}
/*------------ Create scatter used in the solver -----------*/
//VecScatter scatter;
//IS from, to;
ierr =ISCreateStride(PETSC_COMM_SELF,DegFree,0,1,&from); CHKERRQ(ierr);
ierr =ISCreateStride(PETSC_COMM_SELF,DegFree,0,1,&to); CHKERRQ(ierr);
/*-------------Read the input file -------------------------*/
double *epsoptAll;
epsoptAll = (double *) malloc(DegFreeAll*sizeof(double));
FILE *ptf;
ptf = fopen(initialdata,"r");
PetscPrintf(PETSC_COMM_WORLD,"reading from input files \n");
int i;
// set the dielectric at the center is fixed, and alwyas high
//epsopt[0]=myub; is defined below near lb and ub;
for (i=0;i<DegFree;i++)
{ //PetscPrintf(PETSC_COMM_WORLD,"current eps reading is %lf \n",epsopt[i]);
fscanf(ptf,"%lf",&epsoptAll[i]);
}
epsoptAll[DegFreeAll-1]=0; //initialize auxiliary variable;
fclose(ptf);
/*----declare these data types, althought they may not be used for job 2 -----------------*/
double mylb,myub, *lb=NULL, *ub=NULL;
int maxeval, maxtime, mynloptalg;
double maxf;
nlopt_opt opt;
nlopt_result result;
/*--------------------------------------------------------------*/
/*----Now based on Command Line, Do the corresponding job----*/
/*----------------------------------------------------------------*/
//int Job; set Job to be gloabl variables;
PetscOptionsGetInt(PETSC_NULL,"-Job",&Job,&flg); MyCheckAndOutputInt(flg,Job,"Job","The Job indicator you set");
int numofvar=(Job==1)*DegFreeAll + (Job==3);
/*-------- convert the epsopt array to epsSReal (if job!=optmization) --------*/
if (Job==2 || Job ==3)
{
// copy epsilon from file to epsSReal; (different from FindOpt.c, because epsilon is not degree-of-freedoms in computeQ.
// i) create a array to read file (done above in epsopt); ii) convert the array to epsSReal;
int ns, ne;
ierr = VecGetOwnershipRange(epsSReal,&ns,&ne);
for(i=ns;i<ne;i++)
{ ierr=VecSetValue(epsSReal,i,epsoptAll[i],INSERT_VALUES);
CHKERRQ(ierr); }
if(withepsinldos)
{ epsatinterest = epsoptAll[cx*Ny*Nz + cy*Nz + cz] + epsair;
PetscPrintf(PETSC_COMM_WORLD, " the relative permitivity at the point of current is %.16e \n ",epsatinterest);}
ierr = VecAssemblyBegin(epsSReal); CHKERRQ(ierr);
ierr = VecAssemblyEnd(epsSReal); CHKERRQ(ierr);
}
if (Job==1 || Job==3) // optimization bounds setup;
{
PetscOptionsGetInt(PETSC_NULL,"-maxeval",&maxeval,&flg); MyCheckAndOutputInt(flg,maxeval,"maxeval","max number of evaluation");
PetscOptionsGetInt(PETSC_NULL,"-maxtime",&maxtime,&flg); MyCheckAndOutputInt(flg,maxtime,"maxtime","max time of evaluation");
PetscOptionsGetInt(PETSC_NULL,"-mynloptalg",&mynloptalg,&flg); MyCheckAndOutputInt(flg,mynloptalg,"mynloptalg","The algorithm used ");
PetscOptionsGetReal(PETSC_NULL,"-mylb",&mylb,&flg); MyCheckAndOutputDouble(flg,mylb,"mylb","optimization lb");
PetscOptionsGetReal(PETSC_NULL,"-myub",&myub,&flg); MyCheckAndOutputDouble(flg,myub,"myub","optimization ub");
lb = (double *) malloc(numofvar*sizeof(double));
ub = (double *) malloc(numofvar*sizeof(double));
// the dielectric constant at center is fixed!
for(i=0;i<numofvar;i++)
{
lb[i] = mylb;
ub[i] = myub;
} //initial guess, lower bounds, upper bounds;
// set lower and upper bounds for auxiliary variable;
lb[numofvar-1]=0;
ub[numofvar-1]=1.0/0.0;
//fix the dielectric at the center to be high for topology optimization;
if (Job==1 && fixpteps==1)
{
epsoptAll[0]=myub;
lb[0]=myub;
ub[0]=myub;
}
opt = nlopt_create(mynloptalg, numofvar);
myfundatatypeshg data[2] = {{omegaone, bone, weightedJ, epscoefone,kspone},{omegatwo, btwo, weightedJtwo, epscoeftwo,ksptwo}};
nlopt_add_inequality_constraint(opt,ldosconstraint, &data[0], 1e-8);
nlopt_add_inequality_constraint(opt,ldosconstraint, &data[1], 1e-8);
nlopt_set_lower_bounds(opt,lb);
nlopt_set_upper_bounds(opt,ub);
nlopt_set_maxeval(opt,maxeval);
nlopt_set_maxtime(opt,maxtime);
/*add functionality to choose local optimizer; */
int mynloptlocalalg;
nlopt_opt local_opt;
PetscOptionsGetInt(PETSC_NULL,"-mynloptlocalalg",&mynloptlocalalg,&flg); MyCheckAndOutputInt(flg,mynloptlocalalg,"mynloptlocalalg","The local optimization algorithm used ");
if (mynloptlocalalg)
{
local_opt=nlopt_create(mynloptlocalalg,numofvar);
nlopt_set_ftol_rel(local_opt, 1e-14);
nlopt_set_maxeval(local_opt,100000);
nlopt_set_local_optimizer(opt,local_opt);
}
}
switch (Job)
{
case 1:
{
if (minapproach)
nlopt_set_min_objective(opt,maxminobjfun,NULL);// NULL: no data to be passed because of global variables;
else
nlopt_set_max_objective(opt,maxminobjfun,NULL);
result = nlopt_optimize(opt,epsoptAll,&maxf);
}
break;
case 2 : //AnalyzeStructure
{
int Linear, Eig, maxeigit;
PetscOptionsGetInt(PETSC_NULL,"-Linear",&Linear,&flg); MyCheckAndOutputInt(flg,Linear,"Linear","Linear solver indicator");
PetscOptionsGetInt(PETSC_NULL,"-Eig",&Eig,&flg); MyCheckAndOutputInt(flg,Eig,"Eig","Eig solver indicator");
PetscOptionsGetInt(PETSC_NULL,"-maxeigit",&maxeigit,&flg); MyCheckAndOutputInt(flg,maxeigit,"maxeigit","maximum number of Eig solver iterations is");
/*----------------------------------*/
//EigenSolver(Linear, Eig, maxeigit);
/*----------------------------------*/
OutputVec(PETSC_COMM_WORLD, weight,filenameComm, "weight.m");
}
break;
default:
PetscPrintf(PETSC_COMM_WORLD,"--------Interesting! You're doing nothing!--------\n ");
}
if(Job==1 || Job==3)
{
/* print the optimization parameters */
#if 0
double xrel, frel, fabs;
// double *xabs;
frel=nlopt_get_ftol_rel(opt);
fabs=nlopt_get_ftol_abs(opt);
xrel=nlopt_get_xtol_rel(opt);
PetscPrintf(PETSC_COMM_WORLD,"nlopt frel is %g \n",frel);
PetscPrintf(PETSC_COMM_WORLD,"nlopt fabs is %g \n",fabs);
PetscPrintf(PETSC_COMM_WORLD,"nlopt xrel is %g \n",xrel);
//nlopt_result nlopt_get_xtol_abs(const nlopt_opt opt, double *tol);
#endif
/*--------------*/
if (result < 0) {
PetscPrintf(PETSC_COMM_WORLD,"nlopt failed! \n", result);
}
else {
PetscPrintf(PETSC_COMM_WORLD,"found extremum %0.16e\n", minapproach?1.0/maxf:maxf);
}
PetscPrintf(PETSC_COMM_WORLD,"nlopt returned value is %d \n", result);
if(Job==1)
{ //OutputVec(PETSC_COMM_WORLD, epsopt,filenameComm, "epsopt.m");
//OutputVec(PETSC_COMM_WORLD, epsgrad,filenameComm, "epsgrad.m");
//OutputVec(PETSC_COMM_WORLD, vgrad,filenameComm, "vgrad.m");
//OutputVec(PETSC_COMM_WORLD, x,filenameComm, "x.m");
int rankA;
MPI_Comm_rank(PETSC_COMM_WORLD, &rankA);
if(rankA==0)
{
ptf = fopen(strcat(filenameComm,"epsopt.txt"),"w");
for (i=0;i<DegFree;i++)
fprintf(ptf,"%0.16e \n",epsoptAll[i]);
fclose(ptf);
PetscPrintf(PETSC_COMM_WORLD,"the t parameter is %.8e \n",epsoptAll[DegFreeAll-1]);
}
}
nlopt_destroy(opt);
}
ierr = PetscPrintf(PETSC_COMM_WORLD,"--------Done!--------\n ");CHKERRQ(ierr);
/*------------------------------------*/
/* ----------------------Destroy Vecs and Mats----------------------------*/
free(epsoptAll);
free(lb);
free(ub);
ierr = VecDestroy(&J); CHKERRQ(ierr);
ierr = VecDestroy(&b); CHKERRQ(ierr);
ierr = VecDestroy(&weight); CHKERRQ(ierr);
ierr = VecDestroy(&weightedJ); CHKERRQ(ierr);
ierr = VecDestroy(&vR); CHKERRQ(ierr);
ierr = VecDestroy(&epspml); CHKERRQ(ierr);
ierr = VecDestroy(&epspmlQ); CHKERRQ(ierr);
ierr = VecDestroy(&epsSReal); CHKERRQ(ierr);
ierr = VecDestroy(&epsgrad); CHKERRQ(ierr);
ierr = VecDestroy(&vgrad); CHKERRQ(ierr);
ierr = VecDestroy(&epsmedium); CHKERRQ(ierr);
ierr = VecDestroy(&epsC); CHKERRQ(ierr);
ierr = VecDestroy(&epsCi); CHKERRQ(ierr);
ierr = VecDestroy(&epsP); CHKERRQ(ierr);
ierr = VecDestroy(&x); CHKERRQ(ierr);
ierr = VecDestroy(&vgradlocal);CHKERRQ(ierr);
ierr = VecDestroy(&tmp); CHKERRQ(ierr);
ierr = VecDestroy(&tmpa); CHKERRQ(ierr);
ierr = VecDestroy(&tmpb); CHKERRQ(ierr);
ierr = MatDestroy(&A); CHKERRQ(ierr);
ierr = MatDestroy(&D); CHKERRQ(ierr);
ierr = MatDestroy(&M); CHKERRQ(ierr);
ierr = VecDestroy(&epscoefone); CHKERRQ(ierr);
ierr = VecDestroy(&epscoeftwo); CHKERRQ(ierr);
ierr = KSPDestroy(&kspone);CHKERRQ(ierr);
ierr = KSPDestroy(&ksptwo);CHKERRQ(ierr);
ISDestroy(&from);
ISDestroy(&to);
if (withepsinldos)
{ierr=VecDestroy(&pickposvec); CHKERRQ(ierr);}
if (lrzsqr)
{
ierr=VecDestroy(&epsFReal); CHKERRQ(ierr);
ierr=VecDestroy(&xsqr); CHKERRQ(ierr);
ierr=VecDestroy(&y); CHKERRQ(ierr);
ierr=VecDestroy(&nb); CHKERRQ(ierr);
ierr=MatDestroy(&C); CHKERRQ(ierr);
}
ierr = VecDestroy(&bone); CHKERRQ(ierr);
ierr = VecDestroy(&btwo); CHKERRQ(ierr);
ierr = VecDestroy(&Jtwo); CHKERRQ(ierr);
/*------------ finalize the program -------------*/
{
int rank;
MPI_Comm_rank(PETSC_COMM_WORLD, &rank);
//if (rank == 0) fgetc(stdin);
MPI_Barrier(PETSC_COMM_WORLD);
}
ierr = PetscFinalize(); CHKERRQ(ierr);
return 0;
}
int CNLopt::run(double (*error_func)(unsigned int nParams, const double* params, double* grad, void* misc))
{
// Create a member function pointer
unsigned int n_data = mWorkerThread->GetDataSize();
mOpt = nlopt_create(mAlgorithm, mNParams);
// xopt = new double [mNParams];
lb = new double [mNParams];
ub = new double [mNParams];
// Copy out the initial values for the parameters:
CModelListPtr model_list = mWorkerThread->GetModelList();
model_list->GetFreeParameters(mParams, mNParams, false);
vector<string> names = model_list->GetFreeParamNames();
vector< pair<double, double> > min_max = model_list->GetFreeParamMinMaxes();
// Init parameter values
for(int i = 0; i < mNParams; i++)
{
lb[i] = min_max[i].first;
ub[i] = min_max[i].second;
// xopt = mParams[i];
}
nlopt_set_lower_bounds(mOpt,lb);
nlopt_set_upper_bounds(mOpt,ub);
nlopt_set_ftol_rel(mOpt, 1e-4); // stopping criterion = when chi2 changes by less than 0.1%
nlopt_set_min_objective(mOpt, error_func, (void*)this);
int major=0, minor=0, bugfix=0;
nlopt_version(&major, &minor, &bugfix);
printf("Starting NLopt version %d.%d.%d\n", major, minor, bugfix);
printf("Algorithm = %s \n", nlopt_algorithm_name(mAlgorithm));
if(mAlgorithm == NLOPT_G_MLSL_LDS) // set local optimizer to be used with a global search
{
printf("Secondary Algorithm = %s \n", nlopt_algorithm_name(mAlgorithmSecondary));
mOptSecondary = nlopt_create(mAlgorithmSecondary, mNParams);
nlopt_set_lower_bounds(mOptSecondary,lb);
nlopt_set_upper_bounds(mOptSecondary,ub);
nlopt_set_ftol_rel(mOptSecondary, 1e-4); // stopping criterion = when chi2 changes by less than 0.1%
nlopt_set_min_objective(mOptSecondary, error_func, (void*)this);
nlopt_set_local_optimizer(mOpt, mOptSecondary);
}
mIsRunning = true;
mEvals = 0;
double minf;
// Call NLopt. Note, the results are saved in mParams upon completion.
nlopt_result result = nlopt_optimize(mOpt, mParams, &minf);
mIsRunning = false;
printresult(mParams, mNParams, n_data, names, minf, result);
delete(lb);
delete(ub);
nlopt_destroy(mOpt);
if(mAlgorithm == NLOPT_G_MLSL_LDS) // also destroy local optimizer
{
nlopt_destroy(mOptSecondary);
}
return mEvals;
}
double Geoometry_Optimization_With_Constraint(CMol *pMol)
{
nlopt_opt opt, opt_AugLag;
int Return_Opt, nAtom, nDim, i, iPos;
double E_min, x[MAX_NUM_ATOM*3];
Mol_ESP.Restrain_All_Torsions(1); // apply soft restraints on all soft dihedrals
nAtom = pMol->nAtom;
nDim = 3 * nAtom;
printf("\nPhi before MM optimization:\n");
for(i=0; i<n_Phi; i++) {
printf("%3d %3d %3d %3d %8.4lf\n", DihList[i][0], DihList[i][1], DihList[i][2], DihList[i][3],
Mol_ESP.Query_Dihedral(DihList[i][0], DihList[i][1], DihList[i][2], DihList[i][3], 0, NULL));
}
double AUG_LAG_ICM_TOL = 1.0E-17;
opt_AugLag = nlopt_create(NLOPT_AUGLAG_EQ, nDim);
nlopt_set_min_objective(opt_AugLag, func_Geo_Opt_Constraint, pMol);
// pMol->SavePdb("opt-free.pdb");
for(i=0; i<pMol->nBond_Fixed; i++) {
pMol->Geo_Fix_r0[i].pMol = pMol;
nlopt_add_equality_constraint(opt_AugLag, Geo_Constraint_Bond, &(pMol->Geo_Fix_r0[i]), 2.0E-6);
}
for(i=0; i<pMol->nAngle_Fixed; i++) {
pMol->Geo_Fix_theta0[i].pMol = pMol;
nlopt_add_equality_constraint(opt_AugLag, Geo_Constraint_Angle, &(pMol->Geo_Fix_theta0[i]), 2.0E-6);
}
for(i=0; i<pMol->nPhi_Fixed; i++) {
pMol->Geo_Fix_phi0[i].pMol = pMol;
nlopt_add_equality_constraint(opt_AugLag, Geo_Constraint_Dihedral, &(pMol->Geo_Fix_phi0[i]), 2.0E-6);
}
nlopt_set_xtol_rel(opt_AugLag, 2E-7);
opt = nlopt_create(NLOPT_LD_LBFGS_GEO, nDim);
nlopt_set_min_objective(opt, func_Geo_Opt_Constraint, pMol);
nlopt_set_xtol_rel(opt, 1E-7);
nlopt_set_local_optimizer(opt_AugLag, opt);
nlopt_destroy(opt);
for(i=0; i<nAtom; i++) {
iPos = 3*i;
x[iPos ] = pMol->x[i];
x[iPos+1] = pMol->y[i];
x[iPos+2] = pMol->z[i];
}
Iter_Opt_Constrained = 0;
Return_Opt = nlopt_optimize(opt_AugLag, x, &E_min);
if (Return_Opt < 0) {
printf("nlopt failed! -------- \n");
}
else {
printf("After constrained optimization, E = %12.6lf\n", E_min);
}
nlopt_destroy(opt_AugLag);
printf("Phi after MM optimization:\n");
for(i=0; i<n_Phi; i++) {
printf("%3d %3d %3d %3d %8.4lf\n", DihList[i][0], DihList[i][1], DihList[i][2], DihList[i][3],
Mol_ESP.Query_Dihedral(DihList[i][0], DihList[i][1], DihList[i][2], DihList[i][3], 0, NULL));
}
Mol_ESP.Restrain_All_Torsions(0); // lift soft restraints on all soft dihedrals
return (pMol->Cal_E(0));
}
