void SDPSDQPInternal::init() {
// Initialize the base classes
SdqpSolverInternal::init();
cholesky_ = LinearSolver("csparsecholesky", st_[SDQP_STRUCT_H]);
cholesky_.init();
MX g_socp = MX::sym("x", cholesky_.getFactorizationSparsity(true));
MX h_socp = MX::sym("h", n_);
MX f_socp = sqrt(inner_prod(h_socp, h_socp));
MX en_socp = 0.5/f_socp;
MX f_sdqp = MX::sym("f", input(SDQP_SOLVER_F).sparsity());
MX g_sdqp = MX::sym("g", input(SDQP_SOLVER_G).sparsity());
std::vector<MX> fi(n_+1);
MX znp = MX::sparse(n_+1, n_+1);
for (int k=0;k<n_;++k) {
MX gk = vertcat(g_socp(ALL, k), DMatrix::sparse(1, 1));
MX fk = -blockcat(znp, gk, gk.T(), DMatrix::sparse(1, 1));
// TODO(Joel): replace with ALL
fi.push_back(blkdiag(f_sdqp(ALL, Slice(f_sdqp.size1()*k, f_sdqp.size1()*(k+1))), fk));
}
MX fin = en_socp*DMatrix::eye(n_+2);
fin(n_, n_+1) = en_socp;
fin(n_+1, n_) = en_socp;
fi.push_back(blkdiag(DMatrix::sparse(f_sdqp.size1(), f_sdqp.size1()), -fin));
MX h0 = vertcat(h_socp, DMatrix::sparse(1, 1));
MX g = blockcat(f_socp*DMatrix::eye(n_+1), h0, h0.T(), f_socp);
g = blkdiag(g_sdqp, g);
IOScheme mappingIn("g_socp", "h_socp", "f_sdqp", "g_sdqp");
IOScheme mappingOut("f", "g");
mapping_ = MXFunction(mappingIn("g_socp", g_socp, "h_socp", h_socp,
"f_sdqp", f_sdqp, "g_sdqp", g_sdqp),
mappingOut("f", horzcat(fi), "g", g));
mapping_.init();
// Create an sdpsolver instance
std::string sdpsolver_name = getOption("sdp_solver");
sdpsolver_ = SdpSolver(sdpsolver_name,
sdpStruct("g", mapping_.output("g").sparsity(),
"f", mapping_.output("f").sparsity(),
"a", horzcat(input(SDQP_SOLVER_A).sparsity(),
Sparsity::sparse(nc_, 1))));
if (hasSetOption("sdp_solver_options")) {
sdpsolver_.setOption(getOption("sdp_solver_options"));
}
// Initialize the SDP solver
sdpsolver_.init();
sdpsolver_.input(SDP_SOLVER_C).at(n_)=1;
// Output arguments
setNumOutputs(SDQP_SOLVER_NUM_OUT);
output(SDQP_SOLVER_X) = DMatrix::zeros(n_, 1);
std::vector<int> r = range(input(SDQP_SOLVER_G).size1());
output(SDQP_SOLVER_P) = sdpsolver_.output(SDP_SOLVER_P).isEmpty() ? DMatrix() :
sdpsolver_.output(SDP_SOLVER_P)(r, r);
output(SDQP_SOLVER_DUAL) = sdpsolver_.output(SDP_SOLVER_DUAL).isEmpty() ? DMatrix() :
sdpsolver_.output(SDP_SOLVER_DUAL)(r, r);
output(SDQP_SOLVER_COST) = 0.0;
output(SDQP_SOLVER_DUAL_COST) = 0.0;
output(SDQP_SOLVER_LAM_X) = DMatrix::zeros(n_, 1);
output(SDQP_SOLVER_LAM_A) = DMatrix::zeros(nc_, 1);
}
void SdqpToSdp::init() {
// Initialize the base classes
SdqpSolverInternal::init();
cholesky_ = LinearSolver("cholesky", "csparsecholesky", st_[SDQP_STRUCT_H]);
MX g_socp = MX::sym("x", cholesky_.getFactorizationSparsity(true));
MX h_socp = MX::sym("h", n_);
MX f_socp = sqrt(inner_prod(h_socp, h_socp));
MX en_socp = 0.5/f_socp;
MX f_sdqp = MX::sym("f", input(SDQP_SOLVER_F).sparsity());
MX g_sdqp = MX::sym("g", input(SDQP_SOLVER_G).sparsity());
std::vector<MX> fi(n_+1);
MX znp = MX(n_+1, n_+1);
for (int k=0;k<n_;++k) {
MX gk = vertcat(g_socp(ALL, k), MX(1, 1));
MX fk = -blockcat(znp, gk, gk.T(), MX(1, 1));
// TODO(Joel): replace with ALL
fi.push_back(diagcat(f_sdqp(ALL, Slice(f_sdqp.size1()*k, f_sdqp.size1()*(k+1))), fk));
}
MX fin = en_socp*DMatrix::eye(n_+2);
fin(n_, n_+1) = en_socp;
fin(n_+1, n_) = en_socp;
fi.push_back(diagcat(DMatrix(f_sdqp.size1(), f_sdqp.size1()), -fin));
MX h0 = vertcat(h_socp, DMatrix(1, 1));
MX g = blockcat(f_socp*DMatrix::eye(n_+1), h0, h0.T(), f_socp);
g = diagcat(g_sdqp, g);
Dict opts;
opts["input_scheme"] = IOScheme("g_socp", "h_socp", "f_sdqp", "g_sdqp");
opts["output_scheme"] = IOScheme("f", "g");
mapping_ = MXFunction("mapping", make_vector(g_socp, h_socp, f_sdqp, g_sdqp),
make_vector(horzcat(fi), g), opts);
Dict options;
if (hasSetOption(optionsname())) options = getOption(optionsname());
// Create an SdpSolver instance
solver_ = SdpSolver("sdpsolver", getOption(solvername()),
make_map("g", mapping_.output("g").sparsity(),
"f", mapping_.output("f").sparsity(),
"a", horzcat(input(SDQP_SOLVER_A).sparsity(),
Sparsity(nc_, 1))),
options);
solver_.input(SDP_SOLVER_C).at(n_)=1;
// Output arguments
obuf_.resize(SDQP_SOLVER_NUM_OUT);
output(SDQP_SOLVER_X) = DMatrix::zeros(n_, 1);
std::vector<int> r = range(input(SDQP_SOLVER_G).size1());
output(SDQP_SOLVER_P) = solver_.output(SDP_SOLVER_P).isempty() ? DMatrix() :
solver_.output(SDP_SOLVER_P)(r, r);
output(SDQP_SOLVER_DUAL) = solver_.output(SDP_SOLVER_DUAL).isempty() ? DMatrix() :
solver_.output(SDP_SOLVER_DUAL)(r, r);
output(SDQP_SOLVER_COST) = 0.0;
output(SDQP_SOLVER_DUAL_COST) = 0.0;
output(SDQP_SOLVER_LAM_X) = DMatrix::zeros(n_, 1);
output(SDQP_SOLVER_LAM_A) = DMatrix::zeros(nc_, 1);
}
static void gen_local_top(const gmx_mtop_t *mtop,const t_inputrec *ir,
gmx_bool bMergeConstr,
gmx_localtop_t *top)
{
int mb,srcnr,destnr,ftype,ftype_dest,mt,natoms,mol,nposre_old;
gmx_molblock_t *molb;
gmx_moltype_t *molt;
const gmx_ffparams_t *ffp;
t_idef *idef;
real *qA,*qB;
gmx_mtop_atomloop_all_t aloop;
int ag;
t_atom *atom;
top->atomtypes = mtop->atomtypes;
ffp = &mtop->ffparams;
idef = &top->idef;
idef->ntypes = ffp->ntypes;
idef->atnr = ffp->atnr;
idef->functype = ffp->functype;
idef->iparams = ffp->iparams;
idef->iparams_posres = NULL;
idef->iparams_posres_nalloc = 0;
idef->fudgeQQ = ffp->fudgeQQ;
idef->cmap_grid = ffp->cmap_grid;
idef->ilsort = ilsortUNKNOWN;
init_block(&top->cgs);
init_blocka(&top->excls);
for(ftype=0; ftype<F_NRE; ftype++)
{
idef->il[ftype].nr = 0;
idef->il[ftype].nalloc = 0;
idef->il[ftype].iatoms = NULL;
}
natoms = 0;
for(mb=0; mb<mtop->nmolblock; mb++)
{
molb = &mtop->molblock[mb];
molt = &mtop->moltype[molb->type];
srcnr = molt->atoms.nr;
destnr = natoms;
blockcat(&top->cgs,&molt->cgs,molb->nmol,destnr,srcnr);
blockacat(&top->excls,&molt->excls,molb->nmol,destnr,srcnr);
nposre_old = idef->il[F_POSRES].nr;
for(ftype=0; ftype<F_NRE; ftype++)
{
if (bMergeConstr &&
ftype == F_CONSTR && molt->ilist[F_CONSTRNC].nr > 0)
{
/* Merge all constrains into one ilist.
* This simplifies the constraint code.
*/
for(mol=0; mol<molb->nmol; mol++) {
ilistcat(ftype,&idef->il[F_CONSTR],&molt->ilist[F_CONSTR],
1,destnr+mol*srcnr,srcnr);
ilistcat(ftype,&idef->il[F_CONSTR],&molt->ilist[F_CONSTRNC],
1,destnr+mol*srcnr,srcnr);
}
}
else if (!(bMergeConstr && ftype == F_CONSTRNC))
{
ilistcat(ftype,&idef->il[ftype],&molt->ilist[ftype],
molb->nmol,destnr,srcnr);
}
}
if (idef->il[F_POSRES].nr > nposre_old)
{
set_posres_params(idef,molb,nposre_old/2,natoms);
}
natoms += molb->nmol*srcnr;
}
if (ir == NULL)
{
top->idef.ilsort = ilsortUNKNOWN;
}
else
{
if (ir->efep != efepNO && gmx_mtop_bondeds_free_energy(mtop))
{
snew(qA,mtop->natoms);
snew(qB,mtop->natoms);
aloop = gmx_mtop_atomloop_all_init(mtop);
while (gmx_mtop_atomloop_all_next(aloop,&ag,&atom))
{
qA[ag] = atom->q;
qB[ag] = atom->qB;
}
gmx_sort_ilist_fe(&top->idef,qA,qB);
sfree(qA);
sfree(qB);
}
else
{
top->idef.ilsort = ilsortNO_FE;
}
}
}
static void gen_local_top(gmx_mtop_t *mtop,t_inputrec *ir,
gmx_localtop_t *top)
{
int mb,srcnr,destnr,ftype,mt,natoms,nposre_old;
gmx_molblock_t *molb;
gmx_moltype_t *molt;
gmx_ffparams_t *ffp;
t_idef *idef;
top->atomtypes = mtop->atomtypes;
ffp = &mtop->ffparams;
idef = &top->idef;
idef->ntypes = ffp->ntypes;
idef->atnr = ffp->atnr;
idef->functype = ffp->functype;
idef->iparams = ffp->iparams;
idef->iparams_posres = NULL;
idef->iparams_posres_nalloc = 0;
idef->fudgeQQ = ffp->fudgeQQ;
idef->ilsort = ilsortUNKNOWN;
init_block(&top->cgs);
init_blocka(&top->excls);
for(ftype=0; ftype<F_NRE; ftype++)
{
idef->il[ftype].nr = 0;
idef->il[ftype].nalloc = 0;
idef->il[ftype].iatoms = NULL;
}
natoms = 0;
for(mb=0; mb<mtop->nmolblock; mb++)
{
molb = &mtop->molblock[mb];
molt = &mtop->moltype[molb->type];
srcnr = molt->atoms.nr;
destnr = natoms;
blockcat(&top->cgs,&molt->cgs,molb->nmol,destnr,srcnr);
blockacat(&top->excls,&molt->excls,molb->nmol,destnr,srcnr);
nposre_old = idef->il[F_POSRES].nr;
for(ftype=0; ftype<F_NRE; ftype++)
{
ilistcat(ftype,&idef->il[ftype],&molt->ilist[ftype],molb->nmol,
destnr,srcnr);
}
if (idef->il[F_POSRES].nr > nposre_old)
{
set_posres_params(idef,molb,nposre_old/2,natoms);
}
natoms += molb->nmol*srcnr;
}
if (ir == NULL)
{
top->idef.ilsort = ilsortUNKNOWN;
}
else
{
if (ir->efep != efepNO && gmx_mtop_bondeds_free_energy(mtop))
{
gmx_sort_ilist_fe(&top->idef);
}
else
{
top->idef.ilsort = ilsortNO_FE;
}
}
}
