/**********************************************************
* form upper triangular part of P
* single block
**********************************************************/
void smat1(mwSize n, const double ir2,
double *A, mwIndex *irA, mwIndex *jcA, mwSize isspA,
mwSize mA, mwSize colidx,
double *B, mwIndex *irB, mwIndex *jcB, mwSize isspB)
{ mwSize idx, i, j, r, jn, k, kstart, kend, idxj, j2, count;
double tmp;
double hf=0.5;
if (!isspA & !isspB) {
idx = colidx*mA;
for (j=0; j<n; j++) {
jn = j*n;
for (i=0; i<j; i++) {
B[i+jn] = ir2*A[idx];
idx++; }
B[j+jn] = A[idx];
idx++;
}
} else if (isspA & !isspB) {
j2 = 0; idxj = 0;
kstart = jcA[colidx]; kend = jcA[colidx+1];
for (k=kstart; k<kend; k++) {
r = irA[k];
for (j=j2; j<n; j++) {i=r-idxj; if (i>j) {idxj+=j+1;} else {break;}} j2=j;
if (i < j) { B[i+j*n] = ir2*A[k]; }
else { B[i+j*n] = A[k]; }
}
} else if (!isspA & isspB) {
idx = colidx*mA;
count = 0;
for (j=0; j<n; j++) {
for (i=0; i<j; i++) {
tmp = A[idx];
if (tmp != 0) { irB[count] = i; B[count] = ir2*tmp; count++; }
idx++;
}
tmp = A[idx];
if (tmp != 0) { irB[count] = j; B[count] = hf*tmp; count++; }
idx++;
jcB[j+1] = count;
}
} else if (isspA & isspB) {
count = 0;
j2 = 0; idxj = 0;
kstart = jcA[colidx]; kend = jcA[colidx+1];
for (k=kstart; k<kend; k++) {
r = irA[k];
for (j=j2; j<n; j++) {i=r-idxj; if (i>j) {idxj+=j+1;} else {break;}} j2=j;
irB[count] = i;
if (i<j) {B[count] = ir2*A[k];} else {B[count] = hf*A[k];}
++jcB[j+1];
count++;
}
for (j=0; j<n; j++) { jcB[j+1] += jcB[j]; }
}
if (!isspB) { symmetrize(B,n); }
return;
}
int main()
{
const int nreps = 100;
const int n = 5000;
double *x;
x = gen_runif2(n*n);
TIMER(symmetrize_naive(n, x), nreps);
TIMER(symmetrize(n, x), nreps);
return COOP_OK;
}
/**
* \brief Start an exposure on the M26C camera
*
* \param exposure exposure structure for the exposure to perform
*/
void SxCcdM26C::startExposure0(const Exposure& exposure) {
debug(LOG_DEBUG, DEBUG_LOG, 0, "exposure %s requested",
exposure.toString().c_str());
// remember the exposre, we need it for the second field for the
// case where we do two fields one after the other
this->exposure = symmetrize(exposure);
m26c = m26cExposure();
// compute a better request for the M26C camera
exposeField(0);
timer.start();
// we are now in exposing state
state = Exposure::exposing;
}
void SymForceAligner::alignCorpus() {
m_alignments.clear();
m_srcTrgAligner.alignCorpus();
m_trgSrcAligner.alignCorpus();
Alignments::iterator it1 = m_srcTrgAligner.getAlignments().begin();
Alignments::iterator it2 = m_trgSrcAligner.getAlignments().begin();
while(it1 != m_srcTrgAligner.getAlignments().end() && it2 != m_trgSrcAligner.getAlignments().end()) {
Alignment a1 = *it1;
Alignment a2 = *it2;
Alignment a = symmetrize(a1, a2);
m_alignments.push_back(a);
it1++; it2++;
}
}
/** Eigenvalues.
\param m Input matrix (unchanged on return).
\return Vector of eigenvalues.
*/
dvector eigenvalues(const dmatrix& m)
{
if (m.rowsize()!=m.colsize())
{
cerr << "error -- non square matrix passed to "
"dvector eigen(const dmatrix& m)\n";
ad_exit(1);
}
dmatrix m1=symmetrize(m);
m1.colshift(1); // set minimum column and row indices to 1
m1.rowshift(1);
int n=m1.rowsize();
dvector diag(1,n);
dvector off_diag(1,n);
tri_dag(m1,diag,off_diag);
get_eigen(diag,off_diag,m1); // eigenvalues are returned in diag
// eigenvalues are returned in columns of z
return diag;
}
/**
* \brief Start an exposure on the M26C camera
*
* \param exposure exposure structure for the exposure to perform
*/
void SxCcdM26C::startExposure0(const Exposure& exposure) {
debug(LOG_DEBUG, DEBUG_LOG, 0, "exposure %s requested",
exposure.toString().c_str());
// remember the exposure, we need it for the second field for the
// case where we do two fields one after the other
this->exposure = symmetrize(exposure);
// compute a better request for the M26C camera
m26c = m26cExposure();
// start the exposure
if (!camera.reserve("exposure M26C", 1000)) {
std::string msg("cannot reserve camera");
debug(LOG_ERR, DEBUG_LOG, 0, "%s", msg.c_str());
throw std::runtime_error(msg);
}
exposeField(0);
timer.start();
// we are now in exposing state
state(CcdState::exposing);
}
int main()
{
int ret;
const int n = 10;
double *x, *sym, *truth;
printf("# Symmetrize: ");
x = gen_boring2(n*n);
truth = cpalloc2(n*n, x);
symmetrize_naive(n, truth);
sym = cpalloc2(n*n, x);
symmetrize(n, sym);
ret = all_equal(true, n, n, sym, truth);
free(x);
free(sym);
free(truth);
return ret;
}
void MainWindow::createMenus()
{
QAction* action;
QString name;
QMenu* menu;
QMenu* subMenu;
// ----- File Menu -----
menu = menuBar()->addMenu("File");
name = "About";
action = menu->addAction(name);
connect(action, SIGNAL(triggered()), this, SLOT(showAbout()));
name = "New Molecule";
action = menu->addAction(name);
connect(action, SIGNAL(triggered()), &m_viewerModel, SLOT(newMoleculeMenu()));
action->setShortcut(QKeySequence::New);
name = "New Viewer";
action = menu->addAction(name);
connect(action, SIGNAL(triggered()), this, SLOT(newViewer()));
name = "Open";
action = menu->addAction(name);
connect(action, SIGNAL(triggered()), this, SLOT(openFile()));
action->setShortcut(QKeySequence::Open);
name = "Open Recent";
m_recentFilesMenu = menu->addMenu(name);
updateRecentFilesMenu();
menu->addSeparator();
/*
name = "Parse Test File";
action = menu->addAction(name);
connect(action, SIGNAL(triggered()), this, SLOT(parseFile()));
menu->addSeparator();
*/
name = "Close Viewer";
action = menu->addAction(name);
connect(action, SIGNAL(triggered()), this, SLOT(close()));
action->setShortcut(QKeySequence::Close);
name = "Save";
action = menu->addAction(name);
connect(action, SIGNAL(triggered()), &m_viewerModel, SLOT(saveAll()));
action->setShortcut(QKeySequence::Save);
name = "Save As";
action = menu->addAction(name);
connect(action, SIGNAL(triggered()), &m_viewerModel, SLOT(saveAs()));
action->setShortcut(Qt::SHIFT + Qt::CTRL + Qt::Key_S);
menu->addSeparator();
name = "Save Picture";
action = menu->addAction(name);
connect(action, SIGNAL(triggered()), &m_viewer, SLOT(saveSnapshot()));
action->setShortcut(Qt::CTRL + Qt::Key_P);
name = "Record Animation";
action = menu->addAction(name);
action->setCheckable(true);
action->setChecked(false);
connect(action, SIGNAL(triggered()), this, SLOT(toggleRecordingActive()));
action->setShortcut(Qt::SHIFT + Qt::CTRL + Qt::Key_P);
m_recordAnimationAction = action;
name = "Show Message Log";
action = menu->addAction(name);
connect(action, SIGNAL(triggered()), this, SLOT(showLogMessages()));
action->setShortcut(Qt::CTRL + Qt::Key_L);
name = "Quit";
action = menu->addAction(name);
connect(action, SIGNAL(triggered()), this, SLOT(quit()));
action->setShortcut(Qt::CTRL + Qt::Key_Q);
// ----- Edit Menu -----
menu = menuBar()->addMenu("Edit");
name = "Undo";
action = menu->addAction(name);
connect(action, SIGNAL(triggered()), &m_undoStack, SLOT(undo()));
action->setShortcut(QKeySequence::Undo);
connect(&m_undoStack, SIGNAL(canUndoChanged(bool)), action, SLOT(setEnabled(bool)));
name = "Redo";
action = menu->addAction(name);
connect(action, SIGNAL(triggered()), &m_undoStack, SLOT(redo()));
action->setShortcut(QKeySequence::Redo);
connect(&m_undoStack, SIGNAL(canRedoChanged(bool)), action, SLOT(setEnabled(bool)));
menu->addSeparator();
name = "Cut";
action = menu->addAction(name);
connect(action, SIGNAL(triggered()), &m_viewerModel, SLOT(cutSelection()));
action->setShortcut(Qt::CTRL + Qt::Key_X);
name = "Copy";
action = menu->addAction(name);
connect(action, SIGNAL(triggered()), &m_viewerModel, SLOT(copySelectionToClipboard()));
action->setShortcut(Qt::CTRL + Qt::Key_C);
name = "Paste";
action = menu->addAction(name);
connect(action, SIGNAL(triggered()), &m_viewerModel, SLOT(pasteSelectionFromClipboard()));
action->setShortcut(Qt::CTRL + Qt::Key_V);
menu->addSeparator();
name = "Select All";
action = menu->addAction(name);
connect(action, SIGNAL(triggered()), &m_viewerModel, SLOT(selectAll()));
action->setShortcut(Qt::CTRL + Qt::Key_A);
name = "Select None";
action = menu->addAction(name);
connect(action, SIGNAL(triggered()), &m_viewerModel, SIGNAL(clearSelection()));
action->setShortcut(Qt::SHIFT + Qt::CTRL + Qt::Key_A);
name = "Invert Selection";
action = menu->addAction(name);
connect(action, SIGNAL(triggered()), &m_viewerModel, SLOT(invertSelection()));
action->setShortcut(Qt::CTRL + Qt::Key_I);
menu->addSeparator();
name = "Reindex Atoms";
action = menu->addAction(name);
connect(action, SIGNAL(triggered()), this, SLOT(reindexAtoms()));
menu->addSeparator();
name = "Preferences";
action = menu->addAction(name);
connect(action, SIGNAL(triggered()), this, SLOT(showPreferences()));
// ----- Display Menu -----
menu = menuBar()->addMenu("Display");
name = "Full Screen";
action = menu->addAction(name);
action->setCheckable(true);
action->setChecked(false);
connect(action, SIGNAL(triggered()), this, SLOT(fullScreen()));
action->setShortcut(Qt::CTRL + Qt::Key_0);
m_fullScreenAction = action;
name = "Reset View";
action = menu->addAction(name);
connect(action, SIGNAL(triggered()), &m_viewer, SLOT(resetView()));
action->setShortcut(Qt::CTRL + Qt::Key_R);
name = "Show Axes";
action = menu->addAction(name);
action->setCheckable(true);
action->setChecked(false);
connect(action, SIGNAL(triggered()), &m_viewerModel, SLOT(toggleAxes()));
connect(&m_viewerModel, SIGNAL(axesOn(bool)), action, SLOT(setChecked(bool)));
action->setShortcut(Qt::Key_A);
menu->addSeparator();
name = "Atom Labels";
subMenu = menu->addMenu(name);
name = "Element";
action = subMenu->addAction(name);
connect(action, SIGNAL(triggered()), this, SLOT(setLabel()));
action->setData(Layer::Atom::Element);
action->setShortcut(Qt::Key_E);
action->setCheckable(true);
m_labelActions << action;
name = "Index";
action = subMenu->addAction(name);
connect(action, SIGNAL(triggered()), this, SLOT(setLabel()));
action->setData(Layer::Atom::Index);
action->setShortcut(Qt::Key_I);
action->setCheckable(true);
m_labelActions << action;
name = "Mass";
action = subMenu->addAction(name);
connect(action, SIGNAL(triggered()), this, SLOT(setLabel()));
action->setData(Layer::Atom::Mass);
action->setShortcut(Qt::Key_M);
action->setCheckable(true);
m_labelActions << action;
/*
name = "NMR Shifts";
action = subMenu->addAction(name);
connect(action, SIGNAL(triggered()), this, SLOT(setLabel()));
action->setData(Layer::Atom::NmrShifts);
action->setShortcut(Qt::Key_N);
action->setCheckable(true);
m_labelActions << action;
*/
name = "Partial Charge";
action = subMenu->addAction(name);
connect(action, SIGNAL(triggered()), this, SLOT(setLabel()));
action->setData(Layer::Atom::Charge);
action->setShortcut(Qt::Key_Q);
action->setCheckable(true);
m_labelActions << action;
name = "Spin Densities";
action = subMenu->addAction(name);
connect(action, SIGNAL(triggered()), this, SLOT(setLabel()));
action->setData(Layer::Atom::Spin);
action->setShortcut(Qt::Key_S);
action->setCheckable(true);
m_labelActions << action;
menu->addSeparator();
name = "Configure Appearance";
action = menu->addAction(name);
connect(action, SIGNAL(triggered()), this, SLOT(configureAppearance()));
// These are not working correctly at the moment.
/*
name = "Partial Charge Type";
QActionGroup* partialChargeGroup = new QActionGroup(this);
subMenu = menu->addMenu(name);
QString pc("Gasteiger");
action = subMenu->addAction(pc);
action->setCheckable(true);
action->setChecked(true);
action->setData(pc);
partialChargeGroup->addAction(action);
connect(action, SIGNAL(triggered()), this, SLOT(setPartialChargeType()));
pc = "Sanderson";
action = subMenu->addAction(pc);
action->setCheckable(true);
action->setData(pc);
partialChargeGroup->addAction(action);
connect(action, SIGNAL(triggered()), this, SLOT(setPartialChargeType()));
pc = "Mulliken";
action = subMenu->addAction(pc);
action->setCheckable(true);
action->setData(pc);
partialChargeGroup->addAction(action);
connect(action, SIGNAL(triggered()), this, SLOT(setPartialChargeType()));
*/
// ----- Build Menu -----
menu = menuBar()->addMenu("Build");
name = "Fill Valencies With Hydrogens";
action = menu->addAction(name);
connect(action, SIGNAL(triggered()), &m_viewerModel, SLOT(addHydrogens()));
action->setShortcut(Qt::CTRL + Qt::Key_F);
name = "Reperceive Bonds";
action = menu->addAction(name);
connect(action, SIGNAL(triggered()), &m_viewerModel, SLOT(reperceiveBonds()));
menu->addSeparator();
name = "Set Constraint";
action = menu->addAction(name);
connect(action, SIGNAL(triggered()), &m_viewerModel, SLOT(setConstraint()));
action->setShortcut(Qt::CTRL + Qt::Key_K);
name = "Minimize Structure";
action = menu->addAction(name);
connect(action, SIGNAL(triggered()), &m_viewerModel, SLOT(minimizeEnergy()));
action->setShortcut(Qt::CTRL + Qt::Key_M);
name = "Select Force Field";
QActionGroup* forceFieldGroup = new QActionGroup(this);
subMenu = menu->addMenu(name);
QString ff("MMFF94");
action = subMenu->addAction(ff);
action->setCheckable(true);
action->setData(ff);
forceFieldGroup->addAction(action);
connect(action, SIGNAL(triggered()), this, SLOT(setForceField()));
if (Preferences::DefaultForceField() == ff) action->setChecked(true);
ff = "MMFF94s";
action = subMenu->addAction(ff);
action->setCheckable(true);
action->setData(ff);
forceFieldGroup->addAction(action);
connect(action, SIGNAL(triggered()), this, SLOT(setForceField()));
if (Preferences::DefaultForceField() == ff) action->setChecked(true);
ff = "UFF";
action = subMenu->addAction(ff);
action->setCheckable(true);
action->setData(ff);
forceFieldGroup->addAction(action);
connect(action, SIGNAL(triggered()), this, SLOT(setForceField()));
if (Preferences::DefaultForceField() == ff) action->setChecked(true);
ff = "Ghemical";
action = subMenu->addAction(ff);
action->setCheckable(true);
action->setData(ff);
forceFieldGroup->addAction(action);
connect(action, SIGNAL(triggered()), this, SLOT(setForceField()));
if (Preferences::DefaultForceField() == ff) action->setChecked(true);
ff = "Gaff";
action = subMenu->addAction(ff);
action->setCheckable(true);
action->setData(ff);
forceFieldGroup->addAction(action);
connect(action, SIGNAL(triggered()), this, SLOT(setForceField()));
if (Preferences::DefaultForceField() == ff) action->setChecked(true);
menu->addSeparator();
name = "Translate To Center";
action = menu->addAction(name);
connect(action, SIGNAL(triggered()), &m_viewerModel, SLOT(translateToCenter()));
action->setShortcut(Qt::CTRL + Qt::Key_T );
name = "Symmetrize Molecule";
action = menu->addAction(name);
connect(action, SIGNAL(triggered()), &m_viewerModel, SLOT(symmetrize()));
action->setShortcut(Qt::CTRL + Qt::Key_Y );
name = "Set Symmetry Tolerance";
action = menu->addAction(name);
connect(action, SIGNAL(triggered()), &m_viewerModel, SLOT(adjustSymmetryTolerance()));
name = "Auto-detect Symmetry";
action = menu->addAction(name);
action->setCheckable(true);
action->setChecked(false);
connect(action, SIGNAL(triggered()), &m_viewerModel, SLOT(toggleAutoDetectSymmetry()));
// ----- Calculation Menu -----
menu = menuBar()->addMenu("Calculation");
name = "Q-Chem Setup";
action = menu->addAction(name);
connect(action, SIGNAL(triggered()), this, SLOT(openQChemUI()));
action->setShortcut(Qt::CTRL + Qt::Key_U );
m_qchemSetupAction = action;
name = "Job Monitor";
action = menu->addAction(name);
connect(action, SIGNAL(triggered()), this, SLOT(showProcessMonitor()));
action->setShortcut(Qt::CTRL + Qt::Key_J );
menu->addSeparator();
name = "Edit Servers";
action = menu->addAction(name);
connect(action, SIGNAL(triggered()), this, SLOT(editServers()));
name = "Remove All Processes";
action = menu->addAction(name);
connect(action, SIGNAL(triggered()),
&(ProcessMonitor::instance()), SLOT(clearProcessList()));
name = "Reset Password Vault Key";
action = menu->addAction(name);
connect(action, SIGNAL(triggered()), this, SLOT(setVaultPassword()));
// ----- Help Menu -----
menu = menuBar()->addMenu("Help");
name = "Show Help";
action = menu->addAction(name);
connect(action, SIGNAL(triggered()), this, SLOT(showHelp()));
}
int
main(int argc, char *argv[])
{
int prompt;
complex **qin;
Real *q;
double starttime, endtime;
int jflav, k;
int key[4] = {1,1,1,1}; /* 4D Fourier transform */
initialize_machine(&argc,&argv);
/* Remap standard I/O */
if(remap_stdio_from_args(argc, argv) == 1)terminate(1);
g_sync();
starttime=dclock();
/* set up */
prompt = setup();
/* Set up for Fourier transform in all directions */
if(prompt != 2)setup_restrict_fourier(key, NULL);
/* loop over input sets */
while( readin(prompt) == 0){
if(prompt == 2)continue; /* For testing */
/* Create qin array */
qin = (complex **)malloc(sizeof(complex *)*param.nrand);
if(qin == NULL){
node0_printf("main: No room for qin\n");
terminate(1);
}
for(k = 0; k < param.nrand; k++){
qin[k] = create_c_array_field(NMU);
if(qin[k] == NULL){
node0_printf("main: No room for qin[%d]\n",k);
terminate(1);
}
}
for(jflav = 0; jflav < param.nflav; jflav++){
/* Allocate space and read all the data for flavor "jflav" */
/* Accumulate the result in qin, weighted by the charge */
accumulate_current_density(param.fname[jflav], qin, param.charges[jflav],
¶m.mass[jflav], param.nrand);
}
/* Calculate the density-density correlator q */
q = rcorr(qin, param.nrand);
/* Destroy qin array */
for(k = 0; k < param.nrand; k++)
destroy_c_array_field(qin[k], NMU);
free(qin);
/* Symmetrize over hypercubic group transformations */
symmetrize(q);
/* Write the results to the specified file */
print_result(q, param.nrand);
destroy_r_field(q);
} /* readin(prompt) */
node0_printf("RUNNING COMPLETED\n");
endtime=dclock();
node0_printf("Time = %e seconds\n",(double)(endtime-starttime));
normal_exit(0);
return 0;
}
double coordDescent(double *adSigmat, double *adUmat, double dRho,double dscalart, double dTol, int *adIndexList, int iIndexLength, int n, double *adXmat, double dOrigGap, int ibcdOuterIter)
{
int i,j, k,row1, col1, row2, col2, iTemp, row, iCol, iVal, incx = 1, iCounter;
double one = 1, zero = 0, *buffmat, *adevec, *adhvec, sNegOne = -1, dTemp, dTemp2, *adbvec, dscalarc, *aduo, *adwo, *aduvec, *adw, *adVinmat, *buffveca, *adfvec, *buffvecb, *adTempVec,dCurrGap, dRelGap;
adTempVec = calloc(n, sizeof(double));
adevec = calloc(n, sizeof(double));
adhvec = calloc(n, sizeof(double));
adfvec = calloc(n, sizeof(double));
adVinmat = calloc( (n-1)*(n-1) , sizeof(double));
aduo = calloc((n-1), sizeof(double));
adwo = calloc(1, sizeof(double));
aduvec = calloc((n-1), sizeof(double));
adw = calloc(1, sizeof(double));
adbvec = calloc((n-1), sizeof(double));
buffveca = calloc(n, sizeof(double));
buffvecb = calloc(n, sizeof(double));
buffmat = calloc (n*n, sizeof(double));
k =0;
/* DualityGap = -n + trace(Sigma*Xk) + rho*(sum(sum(abs(Xk))));*/
dCurrGap = - n + cblasR_ddot((n*n), adSigmat,incx, adXmat, incx) + dRho*(cblasR_dasum((n*n), adXmat,incx));
dRelGap = dCurrGap/dOrigGap;
/* Main loop: Iterate until converge or till a maximum bcdOuterIter iterations */
iCounter = 0;
while ( (dRelGap > dTol) && (iCounter < ibcdOuterIter )){
iCounter++;
/*
Choose Important Columns to Update.
ind = indfind(Uk,Xk,Sigma, rhonew,colFraction );
*/
for (i=0;i<n;i++){
adTempVec[i]= (dRho + adSigmat[i + (n*i)] - adUmat[i + (n*i)])*adXmat[i+(n*i)];
adIndexList[i]=i;
}
modsort(adTempVec,adIndexList,n);
/* Update choosen columns */
i = 0;
while (i < iIndexLength){
iCol = adIndexList[i];
/*
1. Form Vin
First Rank 1 update ;
e(i) = 1 ; e(j) = 0 (j != i)
f = -U(:,i); f(i) = 1 - U(i,i)
Vin=Xk-((Xk*f*e'*Xk)/(1+e'*Xk*'f);
*/
adevec[iCol] = 1;
cblasR_daxpy( n , sNegOne, (adUmat + (n*iCol)) ,incx,adfvec,incx);
cblasR_daxpy( n , sNegOne, (adUmat + (n*iCol)) ,incx,adhvec,incx);
adfvec[iCol] = 1 - adUmat[iCol + n*iCol];
adhvec[iCol] = 0.0;
for(iVal = 0 ; iVal < n; iVal++)
{
buffveca[iVal] = adXmat[iCol + n*iVal];
}
dTemp = 1 + cblasR_ddot(n, adfvec,incx, buffveca, incx);
cblasR_dscal(n,(1/dTemp),adfvec,incx);
row1 = n; col1 = n; row2= n; col2=1;
cblasR_dgemv( CblasColMajor,CblasNoTrans, n, n, one, adXmat, n, adfvec ,incx, zero, buffveca, incx); // buffveca contains Xk*f
for(j = 0 ; j < n ; j++){
if ( j != iCol){
if ( j < iCol)
k = j;
else if ( j > iCol)
k = j-1;
cblasR_dcopy( iCol , (adXmat + (n*j)) ,incx,(adVinmat + ((n-1)*(k))),incx);
cblasR_dcopy( n-iCol-1 , (adXmat + (n*j + iCol+1)) ,incx,(adVinmat + (n-1)*k + iCol),incx);
dTemp = (adXmat[iCol + n*j]);
cblasR_daxpy( iCol , -dTemp, buffveca ,incx,(adVinmat + ((n-1)*(k))),incx);
cblasR_daxpy( n-iCol-1 , -dTemp, (buffveca + (iCol+1)) ,incx,(adVinmat + (n-1)*k + iCol),incx);
}
buffvecb[j] = adXmat[iCol + n*j] *(1 - buffveca[iCol]);
}
/*
Second Rank1 update
;h = -U(:,i); h(i) = 0;
Vin=Vin-((Vin*e*h'*Vin)/(1+e'*Vin*'h));Vin(i,:)=[];Vin(:,i)=[];
*/
dTemp2 = 1 + cblasR_ddot(n, adhvec,incx, buffvecb, incx);
cblasR_dscal(n,(1/dTemp2),adhvec,incx);
cblasR_dscal( n ,-adXmat[iCol + n*iCol] ,buffveca,incx);
cblasR_daxpy( n , one, (adXmat + (n*iCol)) ,incx,buffveca,incx);
for ( j = 0 ; j < n ; j++){
if ( j != iCol){
if ( j < iCol)
k = j;
else if ( j > iCol)
k = j-1;
dTemp = cblasR_ddot(iCol, adhvec,incx,(adVinmat + ((n-1)*(k))),incx);
dTemp = dTemp + cblasR_ddot(n-iCol-1, (adhvec + iCol +1),incx,(adVinmat + (n-1)*k + iCol),incx);
cblasR_daxpy( iCol , -dTemp, buffveca ,incx,(adVinmat + ((n-1)*(k))),incx);
cblasR_daxpy( n-iCol-1 , -dTemp, (buffveca + (iCol+1)) ,incx,(adVinmat + (n-1)*k + iCol),incx);
}
}
/*
2. Form b, c, uo, wo - inputs to problem of updating choosen column,
then call cdIndexUpdate
b = Sigma(:,i); c = b(i); b(i) = [];
uo = Uk(indi,i);wo = Uk(i,i);
[u,w] = indexCD_mex(Vin,b,c,t,rho,uo,wo,tolForInitGap);
FOR LATER IF SPEED IS AN ISSUE- Code heuristic to choose rows within the chosen col -. Also change 4 accordingly
*/
//AA: can elimate dcopy calls by using pointer arthmetic
// KV - I definitely need copies.
cblasR_dcopy( iCol , (adUmat + (n*iCol)) ,incx, aduo,incx);
cblasR_dcopy( n-iCol-1 , (adUmat + (n*iCol) + (iCol+1)) ,incx,(aduo + iCol),incx);
cblasR_dcopy( iCol , (adSigmat + (n*iCol)) ,incx, adbvec,incx);
cblasR_dcopy( n-iCol-1 , (adSigmat + (n*iCol) + (iCol+1)) ,incx,(adbvec + iCol),incx);
dscalarc = *((adSigmat + (n*iCol) + iCol));
*adwo = *((adUmat + (n*iCol) + iCol));
cdIndexUpdate(adVinmat, adbvec,dscalarc, dscalart, dRho, aduo, (*adwo), aduvec, adw,(n-1),dTol);
/*
3. Update X = inv(U) by application of SMW - Doing it before update U
First Rank one update
indi = 1:n;indi(indi==i)=[];
f= zeros(n,1); h = zeros(n,1);f(indi)=u-U(indi,i);f(i)= (w - U(i,i); h(indi)=u-U(indi,i);h(i)= 0;
Xk = Xk - ((Xk*f*e'*Xk)/(e'*X*f));
*/
for ( j = 0 ; j <iCol ; j++){
adhvec[j] = aduvec[j] - adUmat[(n*iCol) + j];
adfvec[j] = aduvec[j] - adUmat[(n*iCol) + j];
}
for(j = iCol+1 ; j < n ; j++){
adhvec[j] = aduvec[(j-1)] - adUmat[(n*iCol) + j];
adfvec[j] = aduvec[(j-1)] - adUmat[(n*iCol) + j];
}
adfvec[iCol] = *adw - adUmat[(n*iCol) + iCol];
adhvec[iCol] = 0.0;
for(iVal = 0 ; iVal < n; iVal++){
buffveca[iVal] = adXmat[iCol + n*iVal];
}
dTemp = 1 + cblasR_ddot(n, adfvec,incx, buffveca, incx);
cblasR_dscal(n,(1/dTemp),adfvec,incx);
row1 = n; col1 = n; row2= n; col2=1;
cblasR_dgemv( CblasColMajor,CblasNoTrans, n, n, one, adXmat, n, adfvec ,incx, zero, buffveca, incx); // buffveca contains Xk*f
for(j = 0 ; j < n ; j++){
dTemp = adXmat[iCol + n*j];
cblasR_daxpy( n , -dTemp, buffveca ,incx,(adXmat + n*j) ,incx);
}
/*
Second Rank 1 Update
Xk=Xk-((Xk*e*h'*Xk)/(1+h'*Xk*e);
*/
cblasR_dcopy( n , (adXmat + (n*iCol)) ,incx,buffveca,incx);
dTemp = 1 + cblasR_ddot(n, adhvec,incx, buffveca, incx);
cblasR_dscal(n,(1/dTemp),adhvec,incx);
cblasR_dcopy( n , (adXmat + n*iCol),incx,buffveca,incx);
for(j = 0 ; j <n ; j++){
dTemp = cblasR_ddot(n, adhvec,incx, (adXmat + (n*j)), incx);
cblasR_daxpy( n , -dTemp, buffveca ,incx,(adXmat + n*j) ,incx);
}
symmetrize(adXmat,buffmat, n);
cblasR_dcopy( n*n , buffmat,incx,adXmat,incx);
/*
3. Update U
Uk(i,i) = w;Uk(indi,i) = u;Uk(i,indi) = u';
*/
iTemp = 0;
for(row = 0;row < n;row++){
if ( row != iCol )
{
adUmat[row + n*iCol ] = aduvec[iTemp];
adUmat[iCol + n*row ] = aduvec[iTemp];
iTemp++;
}
else
adUmat[row + n*iCol ] = *adw;
}
adevec[iCol] = 0;
i++ ;
}
/*
4. Recompute Gap
DualityGap = -n + trace(Sigma*Xk) + rho*(sum(sum(abs(Xk))));
*/
dCurrGap = - n + cblasR_ddot((n*n), adSigmat,incx, adXmat, incx) + dRho*(cblasR_dasum((n*n), adXmat,incx));
dRelGap = dCurrGap/dOrigGap;
}
free(adTempVec);
free(adevec);
free(adhvec);
free(adfvec);
free(adVinmat);
free(aduo);
free(adwo);
free(aduvec);
free(adw);
free(adbvec);
free(buffveca);
free(buffvecb);
free(buffmat);
return dRelGap;
}
