void SPlaneSlicer::applySliceTranslation(vtkSmartPointer<vtkMatrix4x4> vtkMat) const
{
auto image = this->getInput< ::fwData::Image >(s_EXTENT_IN);
::fwData::Object::sptr index;
switch (m_orientation)
{
case ::fwDataTools::helper::MedicalImageAdaptor::Orientation::X_AXIS:
index = image->getField(::fwDataTools::fieldHelper::Image::m_sagittalSliceIndexId);
break;
case ::fwDataTools::helper::MedicalImageAdaptor::Orientation::Y_AXIS:
index = image->getField(::fwDataTools::fieldHelper::Image::m_frontalSliceIndexId);
break;
case ::fwDataTools::helper::MedicalImageAdaptor::Orientation::Z_AXIS:
index = image->getField(::fwDataTools::fieldHelper::Image::m_axialSliceIndexId);
break;
}
const int idx = ::fwData::Integer::dynamicCast(index)->value();
const auto& spacing = image->getSpacing();
const auto& origin = image->getOrigin();
const std::uint8_t axis = static_cast<std::uint8_t>(m_orientation);
const double trans = spacing[axis] * static_cast<double>(idx) + origin[axis];
vtkSmartPointer<vtkMatrix4x4> transMat = vtkSmartPointer<vtkMatrix4x4>::New();
transMat->Identity();
transMat->SetElement(axis, 3, trans);
vtkMatrix4x4::Multiply4x4(vtkMat, transMat, vtkMat);
}
void SPlaneSlicer::updating()
{
this->setReslicerExtent();
this->setReslicerAxes();
auto image = this->getInput< ::fwData::Image >(s_IMAGE_IN);
vtkSmartPointer<vtkImageData> vtkimg = vtkSmartPointer<vtkImageData>::New();
::fwVtkIO::toVTKImage(image, vtkimg.Get());
m_reslicer->SetInputData(vtkimg);
m_reslicer->Update();
auto slice = this->getInOut< ::fwData::Image >(s_SLICE_OUT);
::fwVtkIO::fromVTKImage(m_reslicer->GetOutput(), slice);
// HACK: Make output slice three-dimensional.
// We need to do so in order to visualize it with ::visuVTKAdaptor::SImageSlice.
// This is because the adaptor uses a vtkImageActor which doesn't handle 2d images.
auto size = slice->getSize();
slice->setSize({{size[0], size[1], 1}});
auto spacing = slice->getSpacing();
slice->setSpacing({{spacing[0], spacing[1], 0 }});
auto origin = slice->getOrigin();
slice->setOrigin({{origin[0], origin[1], 0}});
auto sig = slice->signal< ::fwData::Image::ModifiedSignalType >(::fwData::Image::s_MODIFIED_SIG);
sig->asyncEmit();
}
Module* PacketCountFilterCfg::getInstance()
{
if (!instance)
instance = new SystematicSampler(SYSTEMATIC_SAMPLER_COUNT_BASED,
getInterval(), getSpacing());
return (Module*)instance;
}
void HorizontalListLayout::setBoxes(Layouter::LayoutedWidgets &widgets)
{
float x = 0;
for(std::shared_ptr<PiH::Widget> &widget : widgets)
{
widget->setBoundingBox(x, getBoundingBox().y, widget->getBoundingBox().w, getBoundingBox().h);
x += widget->getBoundingBox().w + getSpacing();
}
}
void tmx::Tileset::tell() {
std::cout << "Name: " << getName() << "\n"
<< "Source: " << getSource() << "\n"
<< "First gID: " << getFirstGid() << "\n"
<< "Tile Width: " << getTileWidth() << "\n"
<< "Tile Height: " << getTileHeight() << "\n"
<< "Spacing: " << getSpacing() << "\n"
<< "Margin: " << getMargin() << std::endl;
}
void checkImages(cx::ImagePtr input, cx::ImagePtr expected)
{
{
INFO(getDim(input) << " == " << getDim(expected));
CHECK(cx::similar(getDim(input), getDim(expected)));
}
{
INFO(input->get_rMd() << "\n == \n" << expected->get_rMd());
CHECK(cx::similar(input->get_rMd(), expected->get_rMd()));
}
{
INFO(getSpacing(input) << " == " << getSpacing(expected));
CHECK(cx::similar(getSpacing(input), getSpacing(expected)));
}
CHECK(input->getParentSpace() == expected->getParentSpace());
// removed: image is not necessarily black. The size is what matters.
//CHECK(cxtest::Utilities::getFractionOfVoxelsAboveThreshold(input->getBaseVtkImageData(), 0) == Approx(0));
}
void VerticalListLayout::setBoxes(Layouter::LayoutedWidgets &widgets)
{
float x = getBoundingBox().x, y = getBoundingBox().y;
for(std::shared_ptr<PiH::Widget> &widget : widgets)
{
if(m_centered)
{
x = getBoundingBox().x + getBoundingBox().w / 2 - widget->getBoundingBox().w / 2;
}
widget->setBoundingBox(x, y, widget->getBoundingBox().w, widget->getBoundingBox().h);
y += widget->getBoundingBox().h + getSpacing();
}
}
/**
* Returns the dimensions of a particular character in the font.
* @param c Font character.
* @return Width and Height dimensions (X and Y are ignored).
*/
SDL_Rect Font::getCharSize(wchar_t c)
{
SDL_Rect size = { 0, 0, 0, 0 };
if (c != 1 && !isLinebreak(c) && !isSpace(c))
{
FontImage *image = &_images[_chars[c].first];
size.w = _chars[c].second.w + image->spacing;
size.h = _chars[c].second.h + image->spacing;
}
else
{
if (_monospace)
size.w = getWidth() + getSpacing();
else if (isNonBreakableSpace(c))
size.w = getWidth() / 4;
else
size.w = getWidth() / 2;
size.h = getHeight() + getSpacing();
}
// In case anyone mixes them up
size.x = size.w;
size.y = size.h;
return size;
}
//========================================================================
//
// NAME GFXFont::wrapStr
//
// DESCRIPTION
// modifies *str so that it will word wrap within the
// specified width. Carriage returns are removed
// and replaced with spaces or spaces are removed and
// replaced by carriage returns.
//
// ARGUMENTS
// str - String to be modified
// width - wrapping width in pixels
// RETURNS
//
// NOTES
// Tabs are not supported.
//
//========================================================================
void GFXFont::wrapStr(char *str, Int32 width)
{
Int32 spaceLen; // length of a space character
Int32 lineLen; // length of current line
Int32 wordLen; // length of current word
char *lastSpace;
spaceLen = getWidth(' ') + getSpacing();
lineLen = 0;
lastSpace = NULL;
while (*str)
{
// convert spaces
if (isspace(*str))
{
lineLen += spaceLen;
*str = ' ';
lastSpace = str;
str++;
}
else
{
wordLen = getWordWidth((void *)str);
if ((lineLen + wordLen) > width)
{
if (lastSpace)
{
*lastSpace = '\n';
lastSpace = NULL;
lineLen = 0;
}
}
lineLen += wordLen;
while (*str && (! isspace(*str)) )
str++;
}
}
}
RRect RLineCache::flush(class IRichCompositor* compositor)
{
RRect line_rect;
// no element yet, need not flush!
element_list_t* line = getCachedElements();
if ( line->size() == 0 )
return line_rect;
// line mark
std::vector<element_list_t::iterator> line_marks;
std::vector<short> line_widths;
RRect zone = compositor->getMetricsState()->zone;
bool wrapline = m_rWrapLine;
// line width auto growth
if ( zone.size.w == 0 )
wrapline = false;
RMetricsState* mstate = compositor->getMetricsState();
RPos pen;
RRect temp_linerect;
short base_line_pos_y = 0;
element_list_t::iterator inner_start_it = line->begin();
line_marks.push_back(line->begin()); // push first line start
for ( element_list_t::iterator it = line->begin(); it != line->end(); it++ )
{
RMetrics* metrics = (*it)->getMetrics();
// prev composit event
(*it)->onCachedCompositBegin(this, pen);
// calculate baseline offset
short baseline_correct = 0;
if ( (*it)->needBaselineCorrect() )
{
baseline_correct = m_rBaselinePos;
}
// first element
if ( pen.x == 0 )
{
pen.x -= metrics->rect.min_x();
}
// set position
(*it)->setLocalPositionX(pen.x);
(*it)->setLocalPositionY(pen.y + baseline_correct);
RRect rect = metrics->rect;
rect.pos.x += pen.x;
rect.pos.y += baseline_correct;
temp_linerect.extend(rect);
// process wrapline
element_list_t::iterator next_it = it + 1;
if ( next_it == line->end() || // last element
(*next_it)->isNewlineBefore() || // line-break before next element
(*it)->isNewlineFollow() || // line-break after this element
( wrapline && pen.x != 0 // wrap line
&& pen.x + metrics->advance.x + (*next_it)->getMetrics()->rect.pos.x + (*next_it)->getMetrics()->rect.size.w + getPadding()*2 > zone.size.w
&& (*next_it)->canLinewrap() ) )
{
// correct out of bound correct
short y2correct = -temp_linerect.max_y();
for ( element_list_t::iterator inner_it = inner_start_it; inner_it != next_it; inner_it++ )
{
RPos pos = (*inner_it)->getLocalPosition();
(*inner_it)->setLocalPositionY(pos.y + y2correct);
(*inner_it)->setLocalPositionX(pos.x /*+ x2correct*/);
}
temp_linerect.pos.y = pen.y;
line_rect.extend(temp_linerect);
pen.y -= (temp_linerect.size.h + getSpacing());
pen.x = 0;
// push next line start
line_marks.push_back(next_it);
line_widths.push_back(temp_linerect.size.w);
inner_start_it = next_it;
temp_linerect = RRect();
}
else
{
pen.x += metrics->advance.x;
}
// post composit event
(*it)->onCachedCompositEnd(this, pen);
}
short align_correct_x = 0;
size_t line_mark_idx = 0;
if ( getHAlign() == e_align_left )
line_rect.size.w += getPadding() * 2;
else
line_rect.size.w = RMAX(zone.size.w, line_rect.size.w + getPadding() * 2); // auto rect
for ( element_list_t::iterator it = line->begin(); it != line->end(); it++ )
{
// prev composit event
(*it)->onCachedCompositBegin(this, pen);
if ( it == line_marks[line_mark_idx] )
{
short lwidth = line_widths[line_mark_idx];
// x correct
switch ( getHAlign() )
{
case e_align_left:
align_correct_x = getPadding();
break;
case e_align_center:
align_correct_x = ( line_rect.size.w - lwidth ) / 2;
break;
case e_align_right:
align_correct_x = line_rect.size.w - lwidth - getPadding();
break;
}
line_mark_idx++; // until next line
}
RPos pos = (*it)->getLocalPosition();
(*it)->setLocalPositionX(mstate->pen_x + pos.x + align_correct_x);
(*it)->setLocalPositionY(mstate->pen_y + pos.y);
// post composit event
(*it)->onCachedCompositEnd(this, pen);
}
line_rect.pos.y = mstate->pen_y;
// advance pen position
mstate->pen_y -= (line_rect.size.h + getSpacing());
mstate->pen_x = 0;
clear();
return line_rect;
}
RRect RHTMLTableCache::flush(class IRichCompositor* compositor)
{
RRect table_rect;
if ( m_rCached.empty())
{
return table_rect;
}
// table content size
std::vector<short> row_heights;
std::vector<short> col_widths;
std::vector<bool> width_set;
short max_row_width = 0;
short max_row_height = 0;
for ( element_list_t::iterator it = m_rCached.begin(); it != m_rCached.end(); it++ )
{
REleHTMLRow* row = dynamic_cast<REleHTMLRow*>(*it);
if ( !row )
{
CCLog("[CCRich] Table cache can only accept 'REleHTMLRow' element!");
continue;
}
short current_row_height = 0;
std::vector<class REleHTMLCell*>& cells = row->getCells();
for ( size_t i = 0; i < cells.size(); i++ )
{
CCAssert(i <= col_widths.size(), "");
if ( i == col_widths.size() )
{
col_widths.push_back(cells[i]->getMetrics()->rect.size.w + getPadding() * 2);
width_set.push_back(cells[i]->isWidthSet());
}
else
{
if (width_set[i])
{
if (cells[i]->isWidthSet())
{
col_widths[i] = RMAX(col_widths[i], cells[i]->getMetrics()->rect.size.w + getPadding() * 2);
}
else
{
// do nothing
}
}
else
{
if (cells[i]->isWidthSet())
{
col_widths[i] = cells[i]->getMetrics()->rect.size.w + getPadding() * 2;
width_set[i] = true;
}
else
{
// do nothing use the first row default width
//col_widths[i] = RMIN(col_widths[i], cells[i]->getMetrics()->rect.size.w + getPadding() * 2);
}
}
}
current_row_height = RMAX(current_row_height, cells[i]->getMetrics()->rect.size.h);
}
current_row_height += getPadding() * 2;
row_heights.push_back(current_row_height);
table_rect.size.h += current_row_height;
}
// max width
for ( size_t i = 0; i < col_widths.size(); i++ )
{
table_rect.size.w += col_widths[i];
}
// set content metrics
short spacing = getSpacing();
short pen_x = 0;
short pen_y = -m_rTable->m_rBorder;
size_t row_idx = 0;
for ( element_list_t::iterator it = m_rCached.begin(); it != m_rCached.end(); it++ )
{
REleHTMLRow* row = dynamic_cast<REleHTMLRow*>(*it);
if ( !row )
{
CCLog("[CCRich] Table cache can only accept 'REleHTMLRow' element!");
continue;
}
pen_x = m_rTable->m_rBorder;
// set row metrics
row->setLocalPositionX(pen_x);
row->setLocalPositionY(pen_y);
RMetrics* row_metrics = row->getMetrics();
row_metrics->rect.size.h = row_heights[row_idx];
row_metrics->rect.size.w = table_rect.size.w + spacing * (col_widths.size() - 1);
// process cells in row
short cell_pen_x = 0;
std::vector<class REleHTMLCell*>& cells = row->getCells();
for ( size_t i = 0; i < cells.size(); i++ )
{
cells[i]->setLocalPositionX(cell_pen_x);
cells[i]->setLocalPositionY(0);
RMetrics* cell_metrics = cells[i]->getMetrics();
cell_metrics->rect.size.w = col_widths[i];
cell_metrics->rect.size.h = row_heights[row_idx];
recompositCell(cells[i]);
cell_pen_x += col_widths[i];
cell_pen_x += spacing;
}
pen_y -= row_heights[row_idx];
pen_y -= spacing;
row_idx++;
}
table_rect.size.h += m_rTable->m_rBorder * 2 + spacing * (row_heights.size() - 1);
table_rect.size.w += m_rTable->m_rBorder * 2 + spacing * (col_widths.size() - 1);
m_rCached.clear();
return table_rect;
}
bool FieldPlane::accumulate(FieldPlane fp) {
return getCenter() == fp.getCenter() && getSpacing() == fp.getSpacing() ? accumulateSquare(fp.get()) : false;
}
bool FieldPlane::sum(FieldPlane fp) {
return getCenter() == fp.getCenter() && getSpacing() == fp.getSpacing() ? sum(fp.get()) : false;
}
int main(int argc, char* argv[])
{
/*!
* \page Vector_5_md_vl_sym_crs Vector 5 molecular dynamic with symmetric Verlet list crossing scheme
*
* ## Simulation ## {#md_e5_sym_sim_crs}
*
* The simulation is equal to the simulation explained in the example molecular dynamic
*
* \see \ref md_e5_sym
*
* The difference is that we create a symmetric Verlet-list for crossing scheme instead of a normal one
* \snippet Vector/5_molecular_dynamic_sym_crs/main.cpp sim verlet
*
* The rest of the code remain unchanged
*
* \snippet Vector/5_molecular_dynamic_sym_crs/main.cpp simulation
*
*/
//! \cond [simulation] \endcond
double dt = 0.00025;
double sigma = 0.1;
double r_cut = 3.0*sigma;
double r_gskin = 1.3*r_cut;
double sigma12 = pow(sigma,12);
double sigma6 = pow(sigma,6);
openfpm::vector<double> x;
openfpm::vector<openfpm::vector<double>> y;
openfpm_init(&argc,&argv);
Vcluster & v_cl = create_vcluster();
// we will use it do place particles on a 10x10x10 Grid like
size_t sz[3] = {10,10,10};
// domain
Box<3,float> box({0.0,0.0,0.0},{1.0,1.0,1.0});
// Boundary conditions
size_t bc[3]={PERIODIC,PERIODIC,PERIODIC};
// ghost, big enough to contain the interaction radius
Ghost<3,float> ghost(r_gskin);
ghost.setLow(0,0.0);
ghost.setLow(1,0.0);
ghost.setLow(2,0.0);
vector_dist<3,double, aggregate<double[3],double[3]> > vd(0,box,bc,ghost,BIND_DEC_TO_GHOST);
size_t k = 0;
size_t start = vd.accum();
auto it = vd.getGridIterator(sz);
while (it.isNext())
{
vd.add();
auto key = it.get();
vd.getLastPos()[0] = key.get(0) * it.getSpacing(0);
vd.getLastPos()[1] = key.get(1) * it.getSpacing(1);
vd.getLastPos()[2] = key.get(2) * it.getSpacing(2);
vd.template getLastProp<velocity>()[0] = 0.0;
vd.template getLastProp<velocity>()[1] = 0.0;
vd.template getLastProp<velocity>()[2] = 0.0;
vd.template getLastProp<force>()[0] = 0.0;
vd.template getLastProp<force>()[1] = 0.0;
vd.template getLastProp<force>()[2] = 0.0;
k++;
++it;
}
vd.map();
vd.ghost_get<>();
timer tsim;
tsim.start();
//! \cond [sim verlet] \endcond
// Get the Cell list structure
auto NN = vd.getVerletCrs(r_gskin);;
//! \cond [sim verlet] \endcond
// calculate forces
calc_forces(vd,NN,sigma12,sigma6,r_cut);
unsigned long int f = 0;
int cnt = 0;
double max_disp = 0.0;
// MD time stepping
for (size_t i = 0; i < 10000 ; i++)
{
// Get the iterator
auto it3 = vd.getDomainIterator();
double max_displ = 0.0;
// integrate velicity and space based on the calculated forces (Step1)
while (it3.isNext())
{
auto p = it3.get();
// here we calculate v(tn + 0.5)
vd.template getProp<velocity>(p)[0] += 0.5*dt*vd.template getProp<force>(p)[0];
vd.template getProp<velocity>(p)[1] += 0.5*dt*vd.template getProp<force>(p)[1];
vd.template getProp<velocity>(p)[2] += 0.5*dt*vd.template getProp<force>(p)[2];
Point<3,double> disp({vd.template getProp<velocity>(p)[0]*dt,vd.template getProp<velocity>(p)[1]*dt,vd.template getProp<velocity>(p)[2]*dt});
// here we calculate x(tn + 1)
vd.getPos(p)[0] += disp.get(0);
vd.getPos(p)[1] += disp.get(1);
vd.getPos(p)[2] += disp.get(2);
if (disp.norm() > max_displ)
max_displ = disp.norm();
++it3;
}
if (max_disp < max_displ)
max_disp = max_displ;
// Because we moved the particles in space we have to map them and re-sync the ghost
if (cnt % 10 == 0)
{
vd.map();
vd.template ghost_get<>();
// Get the Cell list structure
vd.updateVerlet(NN,r_gskin,VL_CRS_SYMMETRIC);
}
else
{
vd.template ghost_get<>(SKIP_LABELLING);
}
cnt++;
// calculate forces or a(tn + 1) Step 2
calc_forces(vd,NN,sigma12,sigma6,r_cut);
// Integrate the velocity Step 3
auto it4 = vd.getDomainIterator();
while (it4.isNext())
{
auto p = it4.get();
// here we calculate v(tn + 1)
vd.template getProp<velocity>(p)[0] += 0.5*dt*vd.template getProp<force>(p)[0];
vd.template getProp<velocity>(p)[1] += 0.5*dt*vd.template getProp<force>(p)[1];
vd.template getProp<velocity>(p)[2] += 0.5*dt*vd.template getProp<force>(p)[2];
++it4;
}
// After every iteration collect some statistic about the confoguration
if (i % 100 == 0)
{
// We write the particle position for visualization (Without ghost)
vd.deleteGhost();
vd.write("particles_",f);
// we resync the ghost
vd.ghost_get<>();
// We calculate the energy
double energy = calc_energy(vd,NN,sigma12,sigma6,r_cut);
auto & vcl = create_vcluster();
vcl.sum(energy);
vcl.max(max_disp);
vcl.execute();
// we save the energy calculated at time step i c contain the time-step y contain the energy
x.add(i);
y.add({energy});
// We also print on terminal the value of the energy
// only one processor (master) write on terminal
if (vcl.getProcessUnitID() == 0)
std::cout << "Energy: " << energy << " " << max_disp << " " << std::endl;
max_disp = 0.0;
f++;
}
}
tsim.stop();
std::cout << "Time: " << tsim.getwct() << std::endl;
//! \cond [simulation] \endcond
// Google charts options, it store the options to draw the X Y graph
GCoptions options;
// Title of the graph
options.title = std::string("Energy with time");
// Y axis name
options.yAxis = std::string("Energy");
// X axis name
options.xAxis = std::string("iteration");
// width of the line
options.lineWidth = 1.0;
// Object that draw the X Y graph
GoogleChart cg;
// Add the graph
// The graph that it produce is in svg format that can be opened on browser
cg.AddLinesGraph(x,y,options);
// Write into html format
cg.write("gc_plot2_out.html");
//! \cond [google chart] \endcond
/*!
* \page Vector_5_md_vl_sym_crs Vector 5 molecular dynamic with symmetric Verlet list crossing scheme
*
* ## Finalize ## {#finalize_v_e5_md_sym_crs}
*
* At the very end of the program we have always to de-initialize the library
*
* \snippet Vector/5_molecular_dynamic_sym_crs/main.cpp finalize
*
*/
//! \cond [finalize] \endcond
openfpm_finalize();
//! \cond [finalize] \endcond
/*!
* \page Vector_5_md_vl_sym_crs Vector 5 molecular dynamic with symmetric Verlet list crossing scheme
*
* ## Full code ## {#full_code_v_e5_md_sym_crs}
*
* \include Vector/5_molecular_dynamic_sym_crs/main.cpp
*
*/
}
int main(int argc, char* argv[])
{
/*!
*
* \page Vector_4_comp_reo Vector 4 computational reordering and cache friendliness
*
* ## Initialization ##
*
* The initialization is the same as the molecular dynamic example. The differences are in the
* parameters. We will use a bigger system, with more particles. The delta time for integration
* is chosen in order to keep the system stable.
*
* \see \ref e3_md_init
*
* \snippet Vector/4_reorder/main_comp_ord.cpp vect create
*
*/
//! \cond [vect create] \endcond
double dt = 0.0001;
float r_cut = 0.03;
double sigma = r_cut/3.0;
double sigma12 = pow(sigma,12);
double sigma6 = pow(sigma,6);
openfpm::vector<double> x;
openfpm::vector<openfpm::vector<double>> y;
openfpm_init(&argc,&argv);
Vcluster & v_cl = create_vcluster();
// we will use it do place particles on a 40x40x40 Grid like
size_t sz[3] = {40,40,40};
// domain
Box<3,float> box({0.0,0.0,0.0}, {1.0,1.0,1.0});
// Boundary conditions
size_t bc[3]= {PERIODIC,PERIODIC,PERIODIC};
// ghost, big enough to contain the interaction radius
Ghost<3,float> ghost(r_cut);
vector_dist<3,double, aggregate<double[3],double[3]> > vd(0,box,bc,ghost);
//! \cond [vect create] \endcond
/*!
* \page Vector_4_comp_reo Vector 4 computational reordering and cache friendliness
*
* ## Particles on a grid like position ##
*
* Here we place the particles on a grid like manner
*
* \see \ref e3_md_gl
*
* \snippet Vector/4_reorder/main_comp_ord.cpp vect grid
*
*/
//! \cond [vect grid] \endcond
auto it = vd.getGridIterator(sz);
while (it.isNext())
{
vd.add();
auto key = it.get();
vd.getLastPos()[0] = key.get(0) * it.getSpacing(0);
vd.getLastPos()[1] = key.get(1) * it.getSpacing(1);
vd.getLastPos()[2] = key.get(2) * it.getSpacing(2);
vd.template getLastProp<velocity>()[0] = 0.0;
vd.template getLastProp<velocity>()[1] = 0.0;
vd.template getLastProp<velocity>()[2] = 0.0;
vd.template getLastProp<force>()[0] = 0.0;
vd.template getLastProp<force>()[1] = 0.0;
vd.template getLastProp<force>()[2] = 0.0;
++it;
}
//! \cond [vect grid] \endcond
/*!
*
* \page Vector_4_comp_reo Vector 4 computational reordering and cache friendliness
*
* ## Molecular dynamic steps ##
*
* Here we do 30000 MD steps using verlet integrator the cycle is the same as the
* molecular dynamic example. with the following changes.
*
* ### Cell lists ###
*
* Instead of getting the normal cell list we get an hilbert curve cell-list. Such cell list has a
* function called **getIterator** used inside the function **calc_forces** and **calc_energy**
* that iterate across all the particles but in a smart-way. In practice
* given an r-cut a cell-list is constructed with the provided spacing. Suppose to have a cell-list
* \f$ m \times n \f$, an hilbert curve \f$ 2^k \times 2^k \f$ is contructed with \f$ k = ceil(log_2(max(m,n))) \f$.
* Cell-lists are explored according to this Hilbert curve, If a cell does not exist is simply skipped.
*
*
* \verbatim
+------+------+------+------+ Example of Hilbert curve running on a 3 x 3 Cell
| | | | | An hilbert curve of k = ceil(log_2(3)) = 4
| X+---->X | X +---> X |
| ^ | + | ^ | + |
***|******|******|****---|--+ *******
* + | v | + * v | * *
* 7 | 8+---->9 * X | * * = Domain
* ^ | | * + | * *
*--|-----------------*---|--+ *******
* + | | * v |
* 4<----+5 | 6<---+ X |
* | ^ | + * |
*---------|-------|--*------+
* | + | v * |
* 1+---->2 | 3+---> X |
* | | * |
**********************------+
this mean that we will iterate the following cells
1,2,5,4,7,8,9,6,3
Suppose now that the particles are ordered like described
Particles id Cell
0 1
1 7
2 8
3 1
4 9
5 9
6 6
7 7
8 3
9 2
10 4
11 3
The iterator of the cell-list will explore the particles in the following way
Cell 1 2 5 4 7 8 9 6 3
| | | | | | | | | |
0,3,9,,10,1,7,2,4,5,6,8
* \endverbatim
*
* We cannot explain here what is a cache, but in practice is a fast memory in the CPU able
* to store chunks of memory. The cache in general is much smaller than RAM, but the big advantage
* is its speed. Retrieve data from the cache is much faster than RAM. Unfortunately the factors
* that determine what is on cache and what is not are multiples: Type of cache, algorithm ... .
* Qualitatively all caches will tend to load chunks of data that you read multiple-time, or chunks
* of data that probably you will read based on pattern analysis. A small example is a linear memory copy where
* you read consecutively memory and you write on consecutive memory.
* Modern CPU recognize such pattern and decide to load on cache the consecutive memory before
* you actually require it.
*
*
* Iterating the vector in the way described above has the advantage that when we do computation on particles
* and its neighborhood with the sequence described above it will happen that:
*
* * If to process a particle A we read some neighborhood particles to process the next particle A+1
* we will probably read most of the previous particles.
*
*
* In order to show in practice what happen we first show the graph when we do not reorder
*
* \htmlinclude Vector/4_reorder/no_reorder.html
*
* The measure has oscillation but we see an asymptotic behavior from 0.04 in the initial condition to
* 0.124 . Below we show what happen when we use iterator from the Cell list hilbert
*
* \htmlinclude Vector/4_reorder/comp_reord.html
*
* In cases where particles does not move or move very slowly consider to use data-reordering, because it can
* give **8-10% speedup**
*
* \see \ref e4_reo
*
* ## Timers ##
*
* In order to collect the time of the force calculation we insert two timers around the function
* calc_force. The overall performance is instead calculated with another timer around the time stepping
*
* \snippet Vector/4_reorder/main_data_ord.cpp timer start
* \snippet Vector/4_reorder/main_data_ord.cpp timer stop
*
* \see \ref e3_md_vi
*
*
*/
//! \cond [md steps] \endcond
// Get the Cell list structure
auto NN = vd.getCellList_hilb(r_cut);
// calculate forces
calc_forces(vd,NN,sigma12,sigma6);
unsigned long int f = 0;
timer time2;
time2.start();
#ifndef TEST_RUN
size_t Nstep = 30000;
#else
size_t Nstep = 300;
#endif
// MD time stepping
for (size_t i = 0; i < Nstep ; i++)
{
// Get the iterator
auto it3 = vd.getDomainIterator();
// integrate velicity and space based on the calculated forces (Step1)
while (it3.isNext())
{
auto p = it3.get();
// here we calculate v(tn + 0.5)
vd.template getProp<velocity>(p)[0] += 0.5*dt*vd.template getProp<force>(p)[0];
vd.template getProp<velocity>(p)[1] += 0.5*dt*vd.template getProp<force>(p)[1];
vd.template getProp<velocity>(p)[2] += 0.5*dt*vd.template getProp<force>(p)[2];
// here we calculate x(tn + 1)
vd.getPos(p)[0] += vd.template getProp<velocity>(p)[0]*dt;
vd.getPos(p)[1] += vd.template getProp<velocity>(p)[1]*dt;
vd.getPos(p)[2] += vd.template getProp<velocity>(p)[2]*dt;
++it3;
}
// Because we mooved the particles in space we have to map them and re-sync the ghost
vd.map();
vd.template ghost_get<>();
timer time;
if (i % 10 == 0)
time.start();
// calculate forces or a(tn + 1) Step 2
calc_forces(vd,NN,sigma12,sigma6);
if (i % 10 == 0)
{
time.stop();
x.add(i);
y.add({time.getwct()});
}
// Integrate the velocity Step 3
auto it4 = vd.getDomainIterator();
while (it4.isNext())
{
auto p = it4.get();
// here we calculate v(tn + 1)
vd.template getProp<velocity>(p)[0] += 0.5*dt*vd.template getProp<force>(p)[0];
vd.template getProp<velocity>(p)[1] += 0.5*dt*vd.template getProp<force>(p)[1];
vd.template getProp<velocity>(p)[2] += 0.5*dt*vd.template getProp<force>(p)[2];
++it4;
}
// After every iteration collect some statistic about the confoguration
if (i % 100 == 0)
{
// We write the particle position for visualization (Without ghost)
vd.deleteGhost();
vd.write("particles_",f);
// we resync the ghost
vd.ghost_get<>();
// We calculate the energy
double energy = calc_energy(vd,NN,sigma12,sigma6);
auto & vcl = create_vcluster();
vcl.sum(energy);
vcl.execute();
// We also print on terminal the value of the energy
// only one processor (master) write on terminal
if (vcl.getProcessUnitID() == 0)
std::cout << std::endl << "Energy: " << energy << std::endl;
f++;
}
}
time2.stop();
std::cout << "Performance: " << time2.getwct() << std::endl;
//! \cond [md steps] \endcond
/*!
* \page Vector_4_comp_reo Vector 4 computational reordering and cache friendliness
*
* ## Plotting graphs ##
*
* After we terminate the MD steps our vector x contains at which iteration we benchmark the force
* calculation time, while y contains the measured time at that time-step. We can produce a graph X Y
*
* \note The graph produced is an svg graph that can be view with a browser. From the browser we can
* also easily save the graph into pure svg format
*
* \snippet Vector/4_reorder/main_comp_ord.cpp google chart
*
*/
//! \cond [google chart] \endcond
// Google charts options, it store the options to draw the X Y graph
GCoptions options;
// Title of the graph
options.title = std::string("Force calculation time");
// Y axis name
options.yAxis = std::string("Time");
// X axis name
options.xAxis = std::string("iteration");
// width of the line
options.lineWidth = 1.0;
// Object that draw the X Y graph
GoogleChart cg;
// Add the graph
// The graph that it produce is in svg format that can be opened on browser
cg.AddLinesGraph(x,y,options);
// Write into html format
cg.write("gc_plot2_out.html");
//! \cond [google chart] \endcond
/*!
*
* \page Vector_4_comp_reo Vector 4 computational reordering and cache friendliness
*
* ## Finalize ##
*
* At the very end of the program we have always to de-initialize the library
*
* \snippet Vector/4_reorder/main_comp_ord.cpp finalize
*
*/
//! \cond [finalize] \endcond
openfpm_finalize();
//! \cond [finalize] \endcond
/*!
*
* \page Vector_4_comp_reo Vector 4 computational reordering and cache friendliness
*
* # Full code #
*
* \include Vector/4_reorder/main_comp_ord.cpp
*
*/
}
