/** The method guarantees that the physical dimensions will not shrink.
* Moreover, if growth is necessary, it will be in geometrically increasing steps.
*/
void AutoMatrix::upSize ( const size_t rows, const size_t cols ) {
const size_t
physicalRows = rows <= countRows() ? countRows() : upperPowerOf2( rows ),
physicalCols = cols <= matrix.tda ? matrix.tda : upperPowerOf2( cols );
exactSize( physicalRows, physicalCols );
gslInit( rows, cols, matrix.data, matrix.tda );
}
Vector Matrix::superdiagonalVector ( const size_t offset ) {
// To circumvent GSL limitation to allow 0-dimensional vectors
// This use of static data relies on the immutability of 0-dim Vectors.
static Vector nullDimVector( 0, NULL, 0 );
if ( 0 == countRows() ) return nullDimVector;
return Vector( gsl_matrix_superdiagonal( &matrix, offset ) );
}
Matrix Matrix::subMatrix ( const size_t row, const size_t col, const size_t rows, const size_t cols ) {
// Circumvent GSL limitation to allow 0-row and/or 0-column matrices
if ( 0 == rows || 0 == cols ) {
assert( row + rows <= countRows() );
assert( col + cols <= countColumns() );
return Matrix( rows, cols, matrix.data + row * matrix.tda + col, matrix.tda );
} else {
return Matrix( gsl_matrix_submatrix( &matrix, row, col, rows, cols ) );
}
}
/** Note that GSL has rows and columns in C convention ordering. */
bool Matrix::gslInit ( const size_t rows, const size_t cols, double *base, const size_t tda ) {
bool invalidates
= base != matrix.data
|| rows < countRows()
|| cols < countColumns()
|| ( tda != matrix.tda && 1 < countRows() );
// Circumvent GSL limitation to allow 0-row and/or 0-column matrices
if ( 0 == rows || 0 == cols ) {
assert( 0 <= rows );
assert( 0 <= cols );
assert( cols <= tda );
matrix.data = base;
matrix.size1 = rows;
matrix.size2 = cols;
matrix.tda = tda;
} else {
*static_cast<gsl_matrix_view*>( this ) = gsl_matrix_view_array_with_tda( base, rows, cols, tda );
}
return invalidates;
}
void AutoMatrix::removeRow ( const size_t row ) {
const size_t
rows = countRows(),
cols = countColumns();
for ( size_t i = row + 1; i < rows; ++i ) {
const Vector rowSource = rowVector( i );
Vector rowTarget = rowVector( i - 1 );
rowTarget.copy( rowSource );
}
upSize( rows - 1, cols );
}
void AutoMatrix::removeColumn ( const size_t col ) {
const size_t
rows = countRows(),
cols = countColumns();
for ( size_t i = col + 1; i < cols; ++i ) {
const Vector colSource = columnVector( i );
Vector colTarget = columnVector( i - 1 );
colTarget.copy( colSource );
}
upSize( rows, cols - 1 );
}
void AutoMatrix::exactSize ( const size_t rows, const size_t cols ) {
const size_t required = calculateSize( rows, cols );
double *newArray;
if ( required == size ) { // Shortcut: no malloc necessary
if ( cols <= matrix.tda ) { // move towards begin
const size_t currentRows = countRows();
const size_t blockSize = cols * sizeof( double );
const double *source = matrix.data;
double *target = matrix.data;
for ( size_t row = 0; ++row < currentRows; ) {
// For row = 0, no copy is needed, so the pre-increment of row and pointers is what we want
memmove( target += cols, source += matrix.tda, blockSize );
}
} else { // move towards end requires opposite loop direction (new cols bigger, so new rows smaller)
const size_t currentCols = countColumns();
const size_t blockSize = currentCols * sizeof( double );
const double *source = &matrix.data[ matrix.tda * rows ];
double *target = &matrix.data[ rows * cols ];
// Guard against unsigned underflow
if ( 0 < rows ) {
for ( size_t row = rows; --row >= 1; ) {
memmove( target -= cols, source -= matrix.tda, blockSize );
}
}
}
newArray = matrix.data;
} else {
newArray = static_cast<double*>( malloc( required ) );
assert( NULL != newArray );
const size_t copyRows = min( rows, countRows() );
const size_t blockSize = min( cols, countColumns() ) * sizeof( double );
for ( size_t row = 0; row < copyRows; ++row ) {
memcpy( &newArray[ cols * row ], &matrix.data[ matrix.tda * row ], blockSize );
}
free( matrix.data );
size = required;
}
gslInit( rows, cols, newArray, cols ); // update GSL struct variables
}
void Matrix::fill ( const double *array ) {
const size_t cols = countColumns();
const size_t rows = countRows();
if ( matrix.tda == cols || 1 >= rows ) { // packed is copied as one lump
const size_t blockSize = rows * cols * sizeof( double );
memcpy( matrix.data, array, blockSize );
} else {
const size_t blockSize = cols * sizeof( double );
double *target = matrix.data;
for ( size_t row = 0; row < rows; ++row ) {
memcpy( target, array, blockSize );
array += cols;
target += matrix.tda;
}
}
}
void RowLoader::triggerRowCountDetermination(int token)
{
std::unique_lock<std::mutex> lk(m);
num_tasks++;
nosync_ensureDbAccess();
// do a count query to get the full row count in a fast manner
row_counter = std::async(std::launch::async, [this, token]() {
auto nrows = countRows();
if(nrows >= 0)
emit rowCountComplete(token, nrows);
std::lock_guard<std::mutex> lk(m);
nosync_taskDone();
});
}
//---------------------------------------------------------------------------
int32_t CSVFile::afterOpen(void)
{
//-------------------------------------------------------
// Check if we opened this with CREATE and write the
// FITini Header and position to Write Start.
if(fileMode == CREATE && parent == nullptr)
{
STOP(("Cannot write CSV files at present."));
}
else
{
//------------------------------------------------------
// Find out how many Rows and cols we have
totalRows = countRows();
totalCols = countCols();
}
return(NO_ERROR);
}
void
GLFont::drawText(const std::string &text, bool hcentered, bool vcentered) const
{
if (vcentered) {
unsigned rows=countRows(text);
glTranslatef(0,float(rows)/2.0f-1.0f,0);
}
std::string::size_type pos(text.find_first_of('\n'));
if (pos!=std::string::npos) {
std::string row(text,0,pos);
drawTextRow(row,hcentered);
if (pos+1<text.size()) {
glTranslatef(0,-1,0);
drawText(std::string(text,pos+1),hcentered);
}
return;
}
drawTextRow(text,hcentered);
}
void Matrix::extractQ ( const Vector& tau, const Matrix& qr ) {
const size_t
rows = countRows(),
cols = countColumns(),
qrRows = qr.countRows(),
qrCols = qr.countColumns(),
tauDims = tau.countDimensions();
assert( qrRows >= qrCols );
assert( qrCols == tauDims );
assert( rows == qrRows );
assert( cols == qrCols || cols == qrRows );
fill( 0.0 );
Vector diagonal = diagonalVector();
diagonal.fill( 1.0 );
for ( size_t col = qrCols; 0 < col--; ) {
Matrix affected = subMatrix( col, col, rows - col, cols - col );
affected.householderTransform(
tau.get( col ),
const_cast<Matrix&>( qr ).columnVector( col ).subVector( col, rows - col )
);
}
}
AutoMatrix::AutoMatrix ( const AutoMatrix& original ) : Matrix(
original.countRows(),
original.countColumns(),
static_cast<double*>( malloc( original.size ) ),
original.matrix.tda
), size( original.size ) {
const size_t
rows = countRows(),
cols = countColumns();
if ( cols == matrix.tda ) {
// copy one big lump
memcpy( matrix.data, original.matrix.data, calculateSize( rows, cols ) );
} else {
// copy row by row
const size_t blockSize = cols * sizeof( double );
const double *source = original.matrix.data;
double *target = matrix.data;
for ( size_t row = 0; row < rows; ++row ) {
memcpy( target, source, blockSize );
source += original.matrix.tda;
target += matrix.tda;
}
}
}
main(int argc, char *argv[]) {
int rows = countRows(argv[1]);
int columns = countColumns(argv[1]);
printf("Rows : %d\n", rows);
printf("Columns: %d\n", columns);
float tableau[rows][columns];
/* DIAGNOSTICS */
int i,j;
int count = 1; // contatore Tableau
/* Print Tableau */
printf("\n=== PRINT TABLEAU BEFORE IMPORT [MAIN] ===\n");
for (i = 0; i < rows; i++) {
for (j = 0; j < columns; j++)
printf("(%d,%d): %.3f\t", i, j, tableau[i][j]);
printf("\n");
}
printf("\nTableau Address: %p\n", tableau);
/* Memory Addresses */
printf("\n=== MEMORY ADDRESSES BEFORE IMPORT [MAIN]===\n");
for (i = 0; i < rows; i++) {
for (j = 0; j < columns; j++)
printf("(%d,%d): %p\t", i, j, &(tableau[i][j]));
printf("\n");
}
import(rows,columns,tableau);
/* Memory Addresses */
printf("\n=== MEMORY ADDRESSES AFTER IMPORT [MAIN]===\n");
for (i = 0; i < rows; i++) {
for (j = 0; j < columns; j++)
printf("(%d,%d): %p\t", i, j, &(tableau[i][j]));
printf("\n");
}
/* Print Tableau */
printf("\n=== PRINT TABLEAU AFTER IMPORT [MAIN] ===\n");
for (i = 0; i < rows; i++) {
for (j = 0; j < columns; j++)
printf("(%d,%d): %.3f\t", i, j, tableau[i][j]);
printf("\n");
}
/* === SIMPLEX === */
int unbounded = 0;
int optimal = 0;
float theta,ratio;
int k,h,sw;
while ((optimal < (columns - 1)) && (unbounded < (rows - 1))) {
for (j = 1; j < columns; j++)
if (tableau[0][j] >= 0)
optimal++; // se tutti i costi ridotti sono > 0, allora siamo nell'ottimo
else { // altrimenti scelgo una variabile fuori base con costo ridotto < 0 (Bland)
optimal = 0;
h = j; // salvo l'indice della colonna della variabile fuori base scelta
for (i = 1; i < rows; i++)
if (tableau[i][h] <= 0) // se ogni riga della colonna della variabile fuori base e' <= 0, allora e' illimitato
unbounded++;
else {
unbounded = 0;
sw = 0;
for (i = 1; i < rows; i++) { // altrimenti calcola i rapporti ed il theta
if (tableau[i][h] > 0 && sw == 0) {
theta = tableau[i][0] / tableau[i][h];
k = i;
sw++;
}
else if (tableau[i][h] > 0) {
ratio = tableau[i][0] / tableau[i][h];
if (ratio < theta) {
theta = ratio;
k = i;
}
}
}
}
pivot(k, h, rows, columns, tableau);
printf("\n=== PRINT TABLEAU %d ===\n", count++);
for (i = 0; i < rows; i++) {
for (j = 0; j < columns; j++)
printf("(%d,%d): %.3f\t", i, j, tableau[i][j]);
printf("\n");
}
}
}
return 0;
}
void tva::Doc::slSolveStaticTask()
{
//tva::util::showMsg("slSolveStaticTask");
slMakeMatrises();
//
//if (!model.gM.hasM)
//{
// tva::util::showMsg("matr M not ready");
// return;
//}
if (!model.gM.hasK)
{
tva::util::showMsg("matr K not ready");
return;
}
auto K2=model.gM.getK();
{//correction K
static const double multStuck=100.0;
K2.getElem(0,0) *= multStuck;
//K2.getElem(0,1) *= multStuck;
//K2.getElem(1,0) *= multStuck;
}
//make F_outer
tva::tMatr F_outer;
F_outer.resize(K2.countRows(),1);
{
static const double F_r=-1.0;
F_outer.fill(0.0);
F_outer.getElem(K2.countRows()-1,0) = F_r;
}
//solve
auto b=K2.getSolve(F_outer);
//
tva::postProc::MatrToWidgetTable(b, tableWidget_23);
//extract vector
std::vector<double> stdX,stdB;
for(int i=0; i<b.countRows(); ++i)
{
stdX.push_back(i);
stdB.push_back(b.getElem(i,0));
}
//
//auto p = std::make_pair(stdX, stdB);
{//plot staticTask
typedef tva::chartSetup::chartStyle chStyle;
//
chStyle style;
//
tva::chartSetup::axisStyle asX;
tva::chartSetup::axisStyle asY;
asX.title = "index";
asY.title = "staticDef";
{
tva::chartSetup::opPair limY;
const auto& providerData = stdB;
limY.first =tva::util::getMinElement(stdB);
limY.second = tva::util::getMaxElement(stdB);
if (limY.second.isSettled())
{
//limY.second = limY.second.get()*(1+percentLimitCorrection);
}
tva::chartSetup::opPair limX;
limX.first = 0;//tva::util::getMinElement(model.Omega);
limX.second = stdX.size()+1;
asY.lim = limY;
asX.lim = limX;
}
style.axStyleX = asX;
style.axStyleY = asY;
//
//tva::chartSetup::opChartStyle loc_style;
//
tva::chartSetup::lineStyle lStyle;
lStyle.color = QColor(0,85,0);
//
bool needClear(true);
bool leftAxis(true);
postProc::policyChart policy;
policy.style = style;
policy.lStyle = lStyle;
policy.needClear = needClear;
policy.leftAxis = leftAxis;
//
tva::postProc::vec2Chart( policy, stdX, stdB, plotStaticTask.get() );
}
}
void loadTOP(char* filename){
int i;
printf("Reading topology.\n");
FILE* topFile = fopen(filename, "r");
char buffer[buf_size];
if (topFile != NULL ){
while(fgets(buffer, buf_size, topFile) != NULL){
if(strncmp(buffer, "[ atoms ]", 9) == 0){
printf("Counting atoms...\n");
sop.aminoCount = countRows(topFile);
printf("%d found.\n", sop.aminoCount);
}
if(strncmp(buffer, "[ bonds ]", 9) == 0){
printf("Counting covalent bonds...\n");
sop.bondCount = countRows(topFile);
printf("%d found.\n", sop.bondCount);
}
if(strncmp(buffer, "[ native ]", 10) == 0){
printf("Counting native contacts...\n");
sop.nativeCount = countRows(topFile);
printf("%d found.\n", sop.nativeCount);
}
if(strncmp(buffer, "[ pairs ]", 9) == 0){
printf("Counting pairs...\n");
sop.pairCount = countRows(topFile);
printf("%d found.\n", sop.pairCount);
}
}
} else {
printf("ERROR: cant find topology file '%s'.\n", filename);
exit(0);
}
sop.aminos = (Atom*)calloc(sop.aminoCount, sizeof(Atom));
sop.bonds = (CovalentBond*)calloc(sop.bondCount, sizeof(CovalentBond));
sop.natives = (NativeContact*)calloc(sop.nativeCount, sizeof(NativeContact));
sop.pairs = (PossiblePair*)calloc(sop.pairCount, sizeof(PossiblePair));
rewind(topFile);
while(fgets(buffer, buf_size, topFile) != NULL){
if(strncmp(buffer, "[ atoms ]", 9) == 0){
fgets(buffer, buf_size, topFile);
for(i = 0; i < sop.aminoCount; i++){
readAtom(&sop.aminos[i], topFile);
}
}
if(strncmp(buffer, "[ bonds ]", 9) == 0){
fgets(buffer, buf_size, topFile);
for(i = 0; i < sop.bondCount; i++){
TOPPair pair = readPair(topFile);
sop.bonds[i].i = pair.i;
sop.bonds[i].j = pair.j;
sop.bonds[i].r0 = pair.c0;
}
}
if(strncmp(buffer, "[ native ]", 10) == 0){
fgets(buffer, buf_size, topFile);
for(i = 0; i < sop.nativeCount; i++){
TOPPair pair = readPair(topFile);
sop.natives[i].i = pair.i;
sop.natives[i].j = pair.j;
sop.natives[i].r0 = pair.c0;
sop.natives[i].eh = pair.c1;
}
}
if(strncmp(buffer, "[ pairs ]", 9) == 0){
fgets(buffer, buf_size, topFile);
for(i = 0; i < sop.pairCount; i++){
TOPPair pair = readPair(topFile);
sop.pairs[i].i = pair.i;
sop.pairs[i].j = pair.j;
}
}
}
fclose(topFile);
printf("Done reading topology.\n");
}
Vector AutoMatrix::newColumn () {
const size_t col = countColumns();
upSize( countRows(), col + 1 );
return columnVector( col );
}
Vector AutoMatrix::newRow () {
const size_t row = countRows();
upSize( row + 1, countColumns() );
return rowVector( row );
}
