void setScalarAsFloat(T* data, Vector3i position, Vector3i size, float value, uchar channel, uchar nrOfChannels) {
if(position.x() < 0 || position.y() < 0 || position.z() < 0 ||
position.x() > size.x()-1 || position.y() > size.y()-1 || position.z() > size.z()-1 || channel >= nrOfChannels)
throw OutOfBoundsException();
data[(position.x() + position.y()*size.x() + position.z()*size.x()*size.y())*nrOfChannels + channel] = value;
}
//----------------------------------------------------------------------------
void Texture::set(void* iPtr, const Vector3i& iS,
GLenum iInternalFormat,
GLenum iFormat,
GLenum iDataType)
{
vector<int> s(3, 0); s[0] = iS.x(); s[1] = iS.y(); s[2] = iS.z();
set( iPtr, s, iInternalFormat, iFormat, iDataType );
}
double Cube::value(const Vector3i &pos) const
{
unsigned int index = pos.x() * m_points.y() * m_points.z()
+ pos.y() * m_points.z() + pos.z();
if (index < m_data.size())
return m_data[index];
else
return 6969.0;
}
coord_t Box::volume() const {
if (!valid()) {
return 0;
}
Vector3i diagonal = this->diagonal();
return diagonal.x() * diagonal.y() * diagonal.z();
}
uint getOctreeDepthForBounding(const Vector3i& maxXYZ) {
coord_t max = ::std::max(maxXYZ.x(), ::std::max(maxXYZ.y(), maxXYZ.z()));
if (max < 0) {
throw ::std::runtime_error("Invalid bounding (all components must not be negative)");
}
// how many bits are required to store numbers from 0 to max
int requiredBits = getMostSignigicantSetBitPos(max) + 1;
return static_cast<uint>(requiredBits);
}
bool Cube::setLimits(const Vector3d &min_, const Vector3i &dim,
double spacing_)
{
Vector3d max_ = Vector3d(min_.x() + (dim.x()-1) * spacing_,
min_.y() + (dim.y()-1) * spacing_,
min_.z() + (dim.z()-1) * spacing_);
m_min = min_;
m_max = max_;
m_points = dim;
m_spacing = Vector3d(spacing_, spacing_, spacing_);
m_data.resize(m_points.x() * m_points.y() * m_points.z());
return true;
}
void AbstractTexture::storageImplementationDefault(GLenum target, GLsizei levels, AbstractTexture::InternalFormat internalFormat, const Vector3i& size) {
bindInternal();
/** @todo Re-enable when extension wrangler is available for ES2 */
#ifndef MAGNUM_TARGET_GLES2
glTexStorage3D(target, levels, GLenum(internalFormat), size.x(), size.y(), size.z());
#else
//glTexStorage3DEXT(target, levels, GLenum(internalFormat), size.x(), size.y(), size.z());
static_cast<void>(target);
static_cast<void>(levels);
static_cast<void>(internalFormat);
static_cast<void>(size);
#endif
}
bool Cube::setLimits(const Vector3 &min_, const Vector3i &dim,
const Vector3 &spacing_)
{
Vector3 max_ = Vector3(min_.x() + (dim.x()-1) * spacing_[0],
min_.y() + (dim.y()-1) * spacing_[1],
min_.z() + (dim.z()-1) * spacing_[2]);
m_min = min_;
m_max = max_;
m_points = dim;
m_spacing = spacing_;
m_data.resize(m_points.x() * m_points.y() * m_points.z());
return true;
}
bool Cube::setLimits(const Vector3 &min_, const Vector3 &max_,
const Vector3i &points)
{
// We can calculate all necessary properties and initialise our data
Vector3 delta = max_ - min_;
m_spacing = Vector3(delta.x() / (points.x()-1),
delta.y() / (points.y()-1),
delta.z() / (points.z()-1));
m_min = min_;
m_max = max_;
m_points = points;
m_data.resize(m_points.x() * m_points.y() * m_points.z());
return true;
}
void AbstractTexture::subImageImplementationDefault(GLenum target, GLint level, const Vector3i& offset, const Vector3i& size, AbstractImage::Format format, AbstractImage::Type type, const GLvoid* data) {
bindInternal();
/** @todo Get some extension wrangler instead to avoid linker errors to glTexSubImage3D() on ES2 */
#ifndef MAGNUM_TARGET_GLES2
glTexSubImage3D(target, level, offset.x(), offset.y(), offset.z(), size.x(), size.y(), size.z(), static_cast<GLenum>(format), static_cast<GLenum>(type), data);
#else
static_cast<void>(target);
static_cast<void>(level);
static_cast<void>(offset);
static_cast<void>(size);
static_cast<void>(format);
static_cast<void>(type);
static_cast<void>(data);
#endif
}
void AbstractTexture::subImageImplementationDSA(GLenum target, GLint level, const Vector3i& offset, const Vector3i& size, AbstractImage::Format format, AbstractImage::Type type, const GLvoid* data) {
glTextureSubImage3DEXT(_id, target, level, offset.x(), offset.y(), offset.z(), size.x(), size.y(), size.z(), static_cast<GLenum>(format), static_cast<GLenum>(type), data);
}
bool Box::contains(const Vector3i& point) const {
return point.x() >= m_llf.x() && point.y() >= m_llf.y() && point.z() >= m_llf.z() && m_urb.x() >= point.x() && m_urb.y() >= point.y() &&
m_urb.z() >= point.z();
}
bool MeshGenerator::marchingCube(const Vector3i &pos)
{
float afCubeValue[8];
Vector3f asEdgeVertex[12];
Vector3f asEdgeNorm[12];
// Calculate the position in the Cube
Vector3f fPos(pos.x() * m_stepSize + m_min.x(),
pos.y() * m_stepSize + m_min.y(),
pos.z() * m_stepSize + m_min.z());
//Make a local copy of the values at the cube's corners
for(int i = 0; i < 8; ++i) {
afCubeValue[i] = m_cube->value(Vector3i(pos + Vector3i(a2iVertexOffset[i])));
}
//Find which vertices are inside of the surface and which are outside
long iFlagIndex = 0;
for(int i = 0; i < 8; ++i) {
if(afCubeValue[i] <= m_iso) {
iFlagIndex |= 1<<i;
}
}
//Find which edges are intersected by the surface
long iEdgeFlags = aiCubeEdgeFlags[iFlagIndex];
// No intersections if the cube is entirely inside or outside of the surface
if(iEdgeFlags == 0) {
return false;
}
//Find the point of intersection of the surface with each edge
//Then find the normal to the surface at those points
for(int i = 0; i < 12; ++i) {
//if there is an intersection on this edge
if(iEdgeFlags & (1<<i)) {
float fOffset = offset(afCubeValue[a2iEdgeConnection[i][0]],
afCubeValue[a2iEdgeConnection[i][1]]);
asEdgeVertex[i] = Vector3f(
fPos.x() + (a2fVertexOffset[a2iEdgeConnection[i][0]][0]
+ fOffset * a2fEdgeDirection[i][0]) * m_stepSize,
fPos.y() + (a2fVertexOffset[a2iEdgeConnection[i][0]][1]
+ fOffset * a2fEdgeDirection[i][1]) * m_stepSize,
fPos.z() + (a2fVertexOffset[a2iEdgeConnection[i][0]][2]
+ fOffset * a2fEdgeDirection[i][2]) * m_stepSize);
/// FIXME Optimize this to only calculate normals when required
asEdgeNorm[i] = normal(asEdgeVertex[i]);
}
}
// Store the triangles that were found, there can be up to five per cube
for(int i = 0; i < 5; ++i) {
if(a2iTriangleConnectionTable[iFlagIndex][3*i] < 0)
break;
int iVertex = 0;
iEdgeFlags = a2iTriangleConnectionTable[iFlagIndex][3*i];
// Make sure we get the triangle winding the right way around!
if (!m_reverseWinding) {
for(int j = 0; j < 3; ++j) {
iVertex = a2iTriangleConnectionTable[iFlagIndex][3*i+j];
m_indices.push_back(m_vertices.size());
m_normals.push_back(asEdgeNorm[iVertex]);
m_vertices.push_back(asEdgeVertex[iVertex]);
}
}
else {
for(int j = 2; j >= 0; --j) {
iVertex = a2iTriangleConnectionTable[iFlagIndex][3*i+j];
m_indices.push_back(m_vertices.size());
m_normals.push_back(-asEdgeNorm[iVertex]);
m_vertices.push_back(asEdgeVertex[iVertex]);
}
}
}
return true;
}
void AbstractTexture::invalidateSubImplementationARB(GLint level, const Vector3i& offset, const Vector3i& size) {
glInvalidateTexSubImage(_id, level, offset.x(), offset.y(), offset.z(), size.x(), size.y(), size.z());
}
void AbstractTexture::imageImplementationDSA(GLenum target, GLint level, InternalFormat internalFormat, const Vector3i& size, AbstractImage::Format format, AbstractImage::Type type, const GLvoid* data) {
glTextureImage3DEXT(_id, target, level, GLint(internalFormat), size.x(), size.y(), size.z(), 0, static_cast<GLenum>(format), static_cast<GLenum>(type), data);
}
void AbstractTexture::storageImplementationDSA(GLenum target, GLsizei levels, AbstractTexture::InternalFormat internalFormat, const Vector3i& size) {
glTextureStorage3DEXT(_id, target, levels, GLenum(internalFormat), size.x(), size.y(), size.z());
}
int main(int argc, char* argv[]){
gengetopt_args_info args_info;
string dumpFileName;
string outFileName;
//parse the command line option
if (cmdline_parser (argc, argv, &args_info) != 0) {
exit(1) ;
}
//get the dumpfile name and meta-data file name
if (args_info.input_given){
dumpFileName = args_info.input_arg;
} else {
strcpy( painCave.errMsg,
"No input file name was specified.\n" );
painCave.isFatal = 1;
simError();
}
if (args_info.output_given){
outFileName = args_info.output_arg;
} else {
strcpy( painCave.errMsg,
"No output file name was specified.\n" );
painCave.isFatal = 1;
simError();
}
Vector3i repeat = Vector3i(args_info.repeatX_arg,
args_info.repeatY_arg,
args_info.repeatZ_arg);
Mat3x3d repeatD = Mat3x3d(0.0);
repeatD(0,0) = repeat.x();
repeatD(1,1) = repeat.y();
repeatD(2,2) = repeat.z();
Vector3d translate = Vector3d(args_info.translateX_arg,
args_info.translateY_arg,
args_info.translateZ_arg);
//parse md file and set up the system
SimCreator oldCreator;
SimInfo* oldInfo = oldCreator.createSim(dumpFileName, false);
Globals* simParams = oldInfo->getSimParams();
std::vector<Component*> components = simParams->getComponents();
std::vector<int> nMol;
for (vector<Component*>::iterator i = components.begin();
i !=components.end(); ++i) {
int nMolOld = (*i)->getNMol();
int nMolNew = nMolOld * repeat.x() * repeat.y() * repeat.z();
nMol.push_back(nMolNew);
}
createMdFile(dumpFileName, outFileName, nMol);
SimCreator newCreator;
SimInfo* newInfo = newCreator.createSim(outFileName, false);
DumpReader* dumpReader = new DumpReader(oldInfo, dumpFileName);
int nframes = dumpReader->getNFrames();
DumpWriter* writer = new DumpWriter(newInfo, outFileName);
if (writer == NULL) {
sprintf(painCave.errMsg, "error in creating DumpWriter");
painCave.isFatal = 1;
simError();
}
SimInfo::MoleculeIterator miter;
Molecule::IntegrableObjectIterator iiter;
Molecule::RigidBodyIterator rbIter;
Molecule* mol;
StuntDouble* sd;
StuntDouble* sdNew;
RigidBody* rb;
Mat3x3d oldHmat;
Mat3x3d newHmat;
Snapshot* oldSnap;
Snapshot* newSnap;
Vector3d oldPos;
Vector3d newPos;
for (int i = 0; i < nframes; i++){
cerr << "frame = " << i << "\n";
dumpReader->readFrame(i);
oldSnap = oldInfo->getSnapshotManager()->getCurrentSnapshot();
newSnap = newInfo->getSnapshotManager()->getCurrentSnapshot();
newSnap->setID( oldSnap->getID() );
newSnap->setTime( oldSnap->getTime() );
oldHmat = oldSnap->getHmat();
newHmat = repeatD*oldHmat;
newSnap->setHmat(newHmat);
newSnap->setThermostat( oldSnap->getThermostat() );
newSnap->setBarostat( oldSnap->getBarostat() );
int newIndex = 0;
for (mol = oldInfo->beginMolecule(miter); mol != NULL;
mol = oldInfo->nextMolecule(miter)) {
for (int ii = 0; ii < repeat.x(); ii++) {
for (int jj = 0; jj < repeat.y(); jj++) {
for (int kk = 0; kk < repeat.z(); kk++) {
Vector3d trans = Vector3d(ii, jj, kk);
for (sd = mol->beginIntegrableObject(iiter); sd != NULL;
sd = mol->nextIntegrableObject(iiter)) {
oldPos = sd->getPos() + translate;
oldSnap->wrapVector(oldPos);
newPos = oldPos + trans * oldHmat;
sdNew = newInfo->getIOIndexToIntegrableObject(newIndex);
sdNew->setPos( newPos );
sdNew->setVel( sd->getVel() );
if (sd->isDirectional()) {
sdNew->setA( sd->getA() );
sdNew->setJ( sd->getJ() );
}
newIndex++;
}
}
}
}
}
//update atoms of rigidbody
for (mol = newInfo->beginMolecule(miter); mol != NULL;
mol = newInfo->nextMolecule(miter)) {
//change the positions of atoms which belong to the rigidbodies
for (rb = mol->beginRigidBody(rbIter); rb != NULL;
rb = mol->nextRigidBody(rbIter)) {
rb->updateAtoms();
rb->updateAtomVel();
}
}
writer->writeDump();
}
// deleting the writer will put the closing at the end of the dump file.
delete writer;
delete oldInfo;
}
