static bool isFacet(ZMatrix const &g, int index)
{
bool ret;
dd_MatrixPtr M=NULL,M2=NULL,M3=NULL;
dd_colrange d;
dd_ErrorType err=dd_NoError;
dd_rowset redrows,linrows,ignoredrows, basisrows;
dd_colset ignoredcols, basiscols;
dd_DataFileType inputfile;
FILE *reading=NULL;
cddinitGmp();
M=ZMatrix2MatrixGmp(g, &err);
if (err!=dd_NoError) goto _L99;
d=M->colsize;
static dd_Arow temp;
dd_InitializeArow(g.getWidth()+1,&temp);
ret= !dd_Redundant(M,index+1,temp,&err);
dd_FreeMatrix(M);
dd_FreeArow(g.getWidth()+1,temp);
if (err!=dd_NoError) goto _L99;
return ret;
_L99:
assert(0);
return false;
}
MpMatrix promote(const ZMatrix& orgData)
{
const size_t rows = orgData.numberOfRows();
const size_t cols = orgData.numberOfColumns();
MpMatrix promoted(rows, cols);
for (size_t i = 0; i < rows; ++i) {
for (size_t j = 0; j < cols; ++j) {
ZMatrix::ScalarType scalar = orgData[i][j];
promoted[i][j] = (long) scalar; // for now it is enough, there is no support for long long.
// mpz_import(promoted[i][j].get_mpz_t(), 1, -1, sizeof(scalar), 0, 0, &scalar);
}
}
return promoted;
}
ZMatrix* FlyEm::ZBcfSet::load(const vector<string> &name)
{
ZMatrix *matrix = NULL;
for (vector<string>::const_iterator iter = name.begin(); iter != name.end();
++iter) {
ZHdf5Reader reader;
if (reader.open(m_featurePath + "/" + *iter + ".h5")) {
mylib::Array *array = reader.readArray(*iter);
if (matrix == NULL) {
matrix = new ZMatrix(array->dims[0], array->dims[1]);
matrix->copyValueFrom((double*) array->data);
} else {
int oldColumnNumber = matrix->getColumnNumber();
matrix->resize(matrix->getRowNumber(),
matrix->getColumnNumber() + array->dims[1]);
matrix->copyColumnValueFrom((double*) array->data, oldColumnNumber,
array->dims[1]);
}
mylib::Kill_Array(array);
reader.close();
} else {
cout << "Failed to open " << *iter << endl;
}
}
return matrix;
}
/*
Heuristic for checking if inequality of full dimensional cone is a
facet. If the routine returns true then the inequality is a
facet. If it returns false it is unknown.
*/
static bool fastIsFacetCriterion(ZMatrix const &normals, int i)
{
int n=normals.getWidth();
for(int j=0;j<n;j++)
if(normals[i][j].sign()!=0)
{
int sign=normals[i][j].sign();
bool isTheOnly=true;
for(int k=0;k<normals.getHeight();k++)
if(k!=i)
{
if(normals[i][j].sign()==sign)
{
isTheOnly=false;
break;
}
}
if(isTheOnly)return true;
}
return false;
}
ZMatrix* FlyEm::ZBcfSet::load(const std::string &name)
{
ZHdf5Reader reader;
ZMatrix *matrix = NULL;
if (reader.open(m_featurePath + "/" + name + ".h5")) {
mylib::Array *array = reader.readArray(name);
#ifdef _DEBUG_2
mylib::printArrayInfo(array);
cout << ((double*)array->data)[0] << endl;
#endif
matrix = new ZMatrix(array->dims[0], array->dims[1]);
matrix->copyValueFrom((double*) array->data);
mylib::Kill_Array(array);
reader.close();
}
return matrix;
}
void ZFlyEmMisc::NormalizeSimmat(ZMatrix &simmat)
{
for (int j = 0; j < simmat.getColumnNumber(); ++j) {
double maxC = simmat.getValue(j, j);
for (int i = 0; i < simmat.getRowNumber(); ++i) {
if (i != j) {
double maxR = simmat.getValue(i, i);
simmat.set(i, j, simmat.getValue(i, j) / dmax2(maxC, maxR));
}
}
}
simmat.setDiag(1);
}
// Export data to the specified file
bool MOPAC71ControlModelPlugin::exportData()
{
// Generate control lines
int charge = pluginOptions_.value("charge").toInt();
QString control1 = pluginOptions_.value("jobtype") + " " + pluginOptions_.value("hamiltonian") + " " + pluginOptions_.value("scftype") + " ";
if (charge != 0) control1 += QString::number(charge) + " ";
if (pluginOptions_.value("state") != "SINGLET") control1 += pluginOptions_.value("state") + " ";
if (toBool(pluginOptions_.value("precise"))) control1 += "PRECISE ";
if (toBool(pluginOptions_.value("campking"))) control1 += "KING ";
if (!pluginOptions_.value("extra").isEmpty()) control1 += "+";
// Write control and title lines
if (!fileParser_.writeLine(control1)) return false;
if (pluginOptions_.value("extra") != "") if (!fileParser_.writeLine(pluginOptions_.value("control2"))) return false;
if (!fileParser_.writeLine(targetModel()->name())) return false;
if (!fileParser_.writeLine("Coordinates churned out by Aten.")) return false;
// Write atoms
int fixedFlag;
// -- If there are only three atoms we *must* use a zmatrix
if (toBool(pluginOptions_.value("internal")) ||( targetModel()->nAtoms() <= 3))
{
ZMatrix* zmat = targetModel()->zMatrix();
double distance, angle, torsion;
int kk, jj, ll, count = 0;
for (ZMatrixElement* ii = zmat->elements(); ii != NULL; ii = ii->next)
{
// Reset vars
jj = 0;
kk = 0;
ll = 0;
distance = 0.0;
angle = 0.0;
torsion = 0.0;
// Grab ZMatrix data for element
if (ii->distanceAtom())
{
jj = ii->distanceAtom()->id() + 1;
distance = ii->distance();
}
if (ii->angleAtom())
{
kk = ii->angleAtom()->id() + 1;
angle = ii->angle();
}
if (ii->torsionAtom())
{
ll = ii->torsionAtom()->id() + 1;
torsion= ii->torsion();
}
// Write atom info
fixedFlag = ii->atom(0)->isPositionFixed() ? 0 : 1;
if (!fileParser_.writeLineF("%-3s %11.6f %i %11.6f %i %11.6f %i %i %i %i", ElementMap::symbol(ii->atom(0)->element()), distance, fixedFlag, angle, fixedFlag, torsion, jj, kk, ll)) return false;
}
}
else
{
for (Atom* i = targetModel()->atoms(); i != NULL; i = i->next)
{
fixedFlag = i->isPositionFixed() ? 0 : 1;
if (!fileParser_.writeLineF("%3s %12.6f %1i %12.6f %1i %12.6f %1i", ElementMap::symbol(i), i->r().x, fixedFlag, i->r().y, fixedFlag, i->r().z, fixedFlag)) return false;
}
}
// Write translation vector for cell
if (targetModel()->isPeriodic())
{
Matrix axes = targetModel()->cell().axes();
if (!fileParser_.writeLineF("Tv %12.6f 0 %12.6f 0 %12.6f 0\n", axes[0], axes[1], axes[2])) return false;
if (!fileParser_.writeLineF("Tv %12.6f 0 %12.6f 0 %12.6f 0\n", axes[4], axes[5], axes[6])) return false;
if (!fileParser_.writeLineF("Tv %12.6f 0 %12.6f 0 %12.6f 0\n", axes[8], axes[9], axes[10])) return false;
}
return true;
}