Fixing missing example files

example/Vector/3_molecular_dynamic_gpu_opt/main_cpu.cpp

+#include "Vector/vector_dist.hpp"
+#include "Plot/GoogleChart.hpp"
+#include "Plot/util.hpp"
+#include "timer.hpp"
+
+#ifdef TEST_RUN
+size_t nstep = 100;
+#else
+size_t nstep = 1000;
+#endif
+
+typedef float real_number;
+
+constexpr int velocity = 0;
+constexpr int force = 1;
+
+
+template<typename CellList> void calc_forces(vector_dist<3,real_number, aggregate<real_number[3],real_number[3]> > & vd, CellList & NN, real_number sigma12, real_number sigma6, real_number r_cut2)
+{
+	vd.updateCellList(NN);
+
+	// Get an iterator over particles
+	auto it2 = vd.getDomainIterator();
+
+	// For each particle p ...
+	while (it2.isNext())
+	{
+		// ... get the particle p
+		auto p = it2.get();
+
+		// Get the position xp of the particle
+		Point<3,real_number> xp = vd.getPos(p);
+
+		// Reset the force counter
+		vd.template getProp<force>(p)[0] = 0.0;
+		vd.template getProp<force>(p)[1] = 0.0;
+		vd.template getProp<force>(p)[2] = 0.0;
+
+		// Get an iterator over the neighborhood particles of p
+		auto Np = NN.template getNNIterator<NO_CHECK>(NN.getCell(vd.getPos(p)));
+
+		// For each neighborhood particle ...
+		while (Np.isNext())
+		{
+			// ... q
+			auto q = Np.get();
+
+			// if (p == q) skip this particle
+			if (q == p.getKey())	{++Np; continue;};
+
+			// Get the position of p
+			Point<3,real_number> xq = vd.getPos(q);
+
+			// Get the distance between p and q
+			Point<3,real_number> r = xp - xq;
+
+			// take the norm of this vector
+			real_number rn = norm2(r);
+
+			if (rn > r_cut2)
+			{++Np; continue;};
+
+			// Calculate the force, using pow is slower
+			Point<3,real_number> f = 24.0*(2.0 *sigma12 / (rn*rn*rn*rn*rn*rn*rn) -  sigma6 / (rn*rn*rn*rn)) * r;
+
+			// we sum the force produced by q on p
+			vd.template getProp<force>(p)[0] += f.get(0);
+			vd.template getProp<force>(p)[1] += f.get(1);
+			vd.template getProp<force>(p)[2] += f.get(2);
+
+			// Next neighborhood
+			++Np;
+		}
+
+		// Next particle
+		++it2;
+	}
+}
+
+template<typename CellList> real_number calc_energy(vector_dist<3,real_number, aggregate<real_number[3],real_number[3]> > & vd, CellList & NN, real_number sigma12, real_number sigma6, real_number r_cut2)
+{
+	real_number rc = r_cut2;
+	real_number shift = 2.0 * ( sigma12 / (rc*rc*rc*rc*rc*rc) - sigma6 / ( rc*rc*rc) );
+
+	real_number E = 0.0;
+
+	// Get the iterator
+	auto it2 = vd.getDomainIterator();
+
+	// For each particle ...
+	while (it2.isNext())
+	{
+		// ... p
+		auto p = it2.get();
+
+		// Get the position of the particle p
+		Point<3,real_number> xp = vd.getPos(p);
+
+		// Get an iterator over the neighborhood of the particle p
+		auto Np = NN.template getNNIterator<NO_CHECK>(NN.getCell(vd.getPos(p)));
+
+		// For each neighborhood of the particle p
+		while (Np.isNext())
+		{
+			// Neighborhood particle q
+			auto q = Np.get();
+
+			// if p == q skip this particle
+			if (q == p.getKey())	{++Np; continue;};
+
+			// Get position of the particle q
+			Point<3,real_number> xq = vd.getPos(q);
+
+			// take the normalized direction
+			real_number rn = norm2(xp - xq);
+
+			if (rn > r_cut2)
+			{++Np;continue;}
+
+			// potential energy (using pow is slower)
+			E += 2.0 * ( sigma12 / (rn*rn*rn*rn*rn*rn) - sigma6 / ( rn*rn*rn) ) - shift;
+
+			// Next neighborhood
+			++Np;
+		}
+
+		// Kinetic energy of the particle given by its actual speed
+		E +=   (vd.template getProp<velocity>(p)[0]*vd.template getProp<velocity>(p)[0] +
+				vd.template getProp<velocity>(p)[1]*vd.template getProp<velocity>(p)[1] +
+				vd.template getProp<velocity>(p)[2]*vd.template getProp<velocity>(p)[2]) / 2;
+
+		// Next Particle
+		++it2;
+	}
+
+	return E;
+}
+
+//! \cond [calc energy2] \endcond
+
+int main(int argc, char* argv[])
+{
+	openfpm_init(&argc,&argv);
+
+	real_number sigma = 0.01;
+	real_number r_cut = 3.0*sigma;
+
+	// we will use it do place particles on a 10x10x10 Grid like
+	size_t sz[3] = {100,100,100};
+
+	// 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);
+
+	real_number dt = 0.00005;
+	real_number sigma12 = pow(sigma,12);
+	real_number sigma6 = pow(sigma,6);
+
+	openfpm::vector<real_number> x;
+	openfpm::vector<openfpm::vector<real_number>> y;
+
+	vector_dist<3,real_number, aggregate<real_number[3],real_number[3]> > vd(0,box,bc,ghost);
+
+	// We create the grid iterator
+	auto it = vd.getGridIterator(sz);
+
+	while (it.isNext())
+	{
+		// Create a new particle
+		vd.add();
+
+		// key contain (i,j,k) index of the grid
+		auto key = it.get();
+
+		// The index of the grid can be accessed with key.get(0) == i, key.get(1) == j ...
+		// We use getLastPos to set the position of the last particle added
+		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);
+
+		// We use getLastProp to set the property value of the last particle we added
+		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;
+	}
+
+	vd.map();
+	vd.ghost_get<>();
+
+	timer tsim;
+	tsim.start();
+
+	//! \cond [md steps] \endcond
+
+	// Get the Cell list structure
+	auto NN = vd.getCellList(r_cut);
+
+	// The standard
+	// auto NN = vd.getCellList(r_cut);
+
+	// calculate forces
+	calc_forces(vd,NN,sigma12,sigma6,r_cut*r_cut);
+	unsigned long int f = 0;
+
+	// MD time stepping
+	for (size_t i = 0; i < nstep ; i++)
+	{
+		timer t_s;
+		t_s.start();
+
+		// 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 moved the particles in space we have to map them and re-sync the ghost
+		vd.map();
+		vd.template ghost_get<>();
+
+		// calculate forces or a(tn + 1) Step 2
+		calc_forces(vd,NN,sigma12,sigma6,r_cut*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 configuration
+		if (i % 500 == 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
+			real_number energy = calc_energy(vd,NN,sigma12,sigma6,r_cut*r_cut);
+			auto & vcl = create_vcluster();
+			vcl.sum(energy);
+			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 << std::endl;
+
+			f++;
+		}
+
+		t_s.stop();
+
+		if (i % 100 == 0)
+		{
+			// resort the particle for better cache efficency
+			vd.reorder(5,reorder_opt::LINEAR);
+		}
+	}
+
+	tsim.stop();
+	std::cout << "Time: " << tsim.getwct() << std::endl;
+
+	// 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;
+
+	// Resolution in x
+	options.width = 1280;
+
+	// Resolution in y
+	options.heigh = 720;
+
+	// Add zoom capability
+	options.more = GC_ZOOM;
+
+	// 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");
+
+	openfpm_finalize();
+}
+
+
+
+

example/Vector/3_molecular_dynamic_gpu_opt/main_cpu_best.cpp

+#include "Vector/vector_dist.hpp"
+#include "Decomposition/CartDecomposition.hpp"
+#include "data_type/aggregate.hpp"
+#include "Plot/GoogleChart.hpp"
+#include "Plot/util.hpp"
+#include "timer.hpp"
+
+#ifdef TEST_RUN
+size_t nstep = 100;
+#else
+size_t nstep = 1000;
+#endif
+
+typedef float real_number;
+
+constexpr int velocity = 0;
+constexpr int force = 1;
+
+
+template<typename VerletList>
+void calc_forces(vector_dist<3,real_number, aggregate<real_number[3],real_number[3]> > & vd, VerletList & NN, real_number sigma12, real_number sigma6, real_number r_cut)
+{
+	// Reset force on the ghost
+
+	auto itg = vd.getDomainAndGhostIterator();
+
+	while (itg.isNext())
+	{
+		auto p = itg.get();
+
+		// Reset force
+		vd.getProp<force>(p)[0] = 0.0;
+		vd.getProp<force>(p)[1] = 0.0;
+		vd.getProp<force>(p)[2] = 0.0;
+
+		++itg;
+	}
+
+	//! \cond [real and ghost] \endcond
+
+	// Get an iterator over particles
+	auto it2 = vd.getParticleIteratorCRS(NN);
+
+	//! \cond [real and ghost] \endcond
+
+	// For each particle p ...
+	while (it2.isNext())
+	{
+		// ... get the particle p
+		auto p = it2.get();
+
+		// Get the position xp of the particle
+		Point<3,real_number> xp = vd.getPos(p);
+
+		// Get an iterator over the neighborhood particles of p
+		// Note that in case of symmetric
+		auto Np = NN.template getNNIterator<NO_CHECK>(p);
+
+		// For each neighborhood particle ...
+		while (Np.isNext())
+		{
+			// ... q
+			auto q = Np.get();
+
+			// if (p == q) skip this particle
+			if (q == p)	{++Np; continue;};
+
+			// Get the position of q
+			Point<3,real_number> xq = vd.getPos(q);
+
+			// Get the distance between p and q
+			Point<3,real_number> r = xp - xq;
+
+			// take the norm of this vector
+			real_number rn = norm2(r);
+
+			if (rn > r_cut * r_cut) {++Np;continue;}
+
+			// Calculate the force, using pow is slower
+			Point<3,real_number> f = 24.0*(2.0 *sigma12 / (rn*rn*rn*rn*rn*rn*rn) -  sigma6 / (rn*rn*rn*rn)) * r;
+
+			// we sum the force produced by q on p
+			vd.template getProp<force>(p)[0] += f.get(0);
+			vd.template getProp<force>(p)[1] += f.get(1);
+			vd.template getProp<force>(p)[2] += f.get(2);
+
+			//! \cond [add to q] \endcond
+
+			// we sum the force produced by p on q
+			vd.template getProp<force>(q)[0] -= f.get(0);
+			vd.template getProp<force>(q)[1] -= f.get(1);
+			vd.template getProp<force>(q)[2] -= f.get(2);
+
+			//! \cond [add to q] \endcond
+
+			// Next neighborhood
+			++Np;
+		}
+
+		// Next particle
+		++it2;
+	}
+
+	// Sum the contribution to the real particles
+	vd.ghost_put<add_,force>();
+}
+
+
+template<typename VerletList>
+real_number calc_energy(vector_dist<3,real_number, aggregate<real_number[3],real_number[3]> > & vd, VerletList & NN, real_number sigma12, real_number sigma6, real_number r_cut)
+{
+	real_number E = 0.0;
+
+	real_number rc = r_cut*r_cut;
+	real_number shift = 4.0 * ( sigma12 / (rc*rc*rc*rc*rc*rc) - sigma6 / ( rc*rc*rc) );
+
+	// Get an iterator over particles
+	auto it2 = vd.getParticleIteratorCRS(NN);
+
+	// For each particle ...
+	while (it2.isNext())
+	{
+		// ... p
+		auto p = it2.get();
+
+		// Get the position of the particle p
+		Point<3,real_number> xp = vd.getPos(p);
+
+		// Get an iterator over the neighborhood particles of p
+		auto Np = NN.template getNNIterator<NO_CHECK>(p);
+
+		real_number Ep = E;
+
+		// For each neighborhood of the particle p
+		while (Np.isNext())
+		{
+			// Neighborhood particle q
+			auto q = Np.get();
+
+			// if p == q skip this particle
+			if (q == p)	{++Np; continue;};
+
+			// Get position of the particle q
+			Point<3,real_number> xq = vd.getPos(q);
+
+			// take the normalized direction
+			real_number rn = norm2(xp - xq);
+
+			if (rn >= r_cut*r_cut)	{++Np;continue;}
+
+			// potential energy (using pow is slower)
+			E += 4.0 * ( sigma12 / (rn*rn*rn*rn*rn*rn) - sigma6 / ( rn*rn*rn) ) - shift;
+
+			// Next neighborhood
+			++Np;
+		}
+
+		// To note that the crossing scheme go across the domain particles +
+		// some ghost particles. This mean that we have to filter out the ghost
+		// particles otherwise we count real_number energies
+		//
+		if (p < vd.size_local())
+		{
+			// Kinetic energy of the particle given by its actual speed
+			E += (vd.template getProp<velocity>(p)[0]*vd.template getProp<velocity>(p)[0] +
+					vd.template getProp<velocity>(p)[1]*vd.template getProp<velocity>(p)[1] +
+					vd.template getProp<velocity>(p)[2]*vd.template getProp<velocity>(p)[2]) / 2;
+		}
+
+		// Next Particle
+		++it2;
+	}
+
+	// Calculated energy
+	return E;
+}
+
+int main(int argc, char* argv[])
+{
+	real_number dt = 0.00005;
+	real_number sigma = 0.01;
+	real_number r_cut = 3.0*sigma;
+	real_number r_gskin = 1.3*r_cut;
+	real_number sigma12 = pow(sigma,12);
+	real_number sigma6 = pow(sigma,6);
+
+	openfpm::vector<real_number> x;
+	openfpm::vector<openfpm::vector<real_number>> 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] = {100,100,100};
+
+	// 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,real_number, aggregate<real_number[3],real_number[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();
+
+	// Get the Cell list structure
+	auto NN = vd.getVerletCrs(r_gskin);;
+
+	// calculate forces
+	calc_forces(vd,NN,sigma12,sigma6,r_cut);
+	unsigned long int f = 0;
+
+	int cnt = 0;
+	real_number max_disp = 0.0;
+
+	// MD time stepping
+	for (size_t i = 0; i < nstep ; i++)
+	{
+		// Get the iterator
+		auto it3 = vd.getDomainIterator();
+
+		real_number 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,real_number> 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
+			real_number 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;
+
+	// 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");
+
+	openfpm_finalize();
+}