Fixing getPos

CHANGELOG.md

@@ -4,7 +4,7 @@ All notable changes to this project will be documented in this file.
 ## [0.3.0] -
 
 ### Added
-- Nothing to report
+- Molacular Dynamic example
 
 ### Fixed
 - Nothing to report
@@ -13,6 +13,8 @@ All notable changes to this project will be documented in this file.
 - Eliminated global_v_cluster, init_global_v_cluster, delete_global_v_cluster, 
   substituted by 
   create_vcluster, openfpm_init, openfpm_delete
+- CartDecomposition parameter for the distributed structures is now optional
+- template getPos<0>(), substituted by getPos()
 
 ## [0.2.1] - 
 

example/Numerics/PSE/0_Derivative_approx_1D/main.cpp

@@ -127,7 +127,7 @@ int main(int argc, char* argv[])
 		auto key = it2.get();
 
 		// set the position of the particles
-		vd.template getPos<0>(key)[0] = (key.getKey() + base) * spacing;
+		vd.getPos(key)[0] = (key.getKey() + base) * spacing;
 		//set the property of the particles
 		vd.template getProp<0>(key) = f_xex2((key.getKey() + base) * spacing);
 
@@ -185,19 +185,19 @@ int main(int argc, char* argv[])
 		auto key = it.get();
 
 		// set the position of the particles
-		if (m_pad.isInsideNB(vd.template getPos<0>(key)) == true)
+		if (m_pad.isInsideNB(vd.getPos(key)) == true)
 		{
 			vd.add();
-			vd.template getLastPos<0>()[0] = - vd.template getPos<0>(key)[0];
+			vd.getLastPos()[0] = - vd.getPos(key)[0];
 			vd.template getLastProp<0>() = - vd.template getProp<0>(key);
 		}
 
 		// set the position of the particles
-		if (m_pad2.isInsideNB(vd.template getPos<0>(key)) == true)
+		if (m_pad2.isInsideNB(vd.getPos(key)) == true)
 		{
 			vd.add();
-			vd.template getLastPos<0>()[0] = 2.0 * box.getHigh(0) - vd.template getPos<0>(key)[0];
-			vd.template getLastProp<0>() = f_xex2(vd.template getLastPos<0>()[0]);
+			vd.getLastPos()[0] = 2.0 * box.getHigh(0) - vd.getPos(key)[0];
+			vd.template getLastProp<0>() = f_xex2(vd.getLastPos()[0]);
 		}
 
 		++it;
@@ -237,7 +237,7 @@ int main(int argc, char* argv[])
     	vect_dist_key_dx key = it_p.get();
 
     	// Get the position of the particles
-    	Point<1,double> p = vd.template getPos<0>(key);
+    	Point<1,double> p = vd.getPos(key);
 
     	// We are not interested in calculating out the domain
     	// note added padding particle are considered domain particles
@@ -261,7 +261,7 @@ int main(int argc, char* argv[])
     		if (nnp != key.getKey())
     		{
     			// W(x-y)
-    			double ker = lker.value(p,vd.template getPos<0>(nnp));
+    			double ker = lker.value(p,vd.getPos(nnp));
 
     			// f(y)
     			double prp_y = vd.template getProp<0>(nnp);

example/Numerics/PSE/1_Derivative_approx_1D_mp/main_float128.cpp

@@ -130,7 +130,7 @@ int main(int argc, char* argv[])
 		auto key = it2.get();
 
 		// set the position of the particles
-		vd.template getPos<0>(key)[0] = (key.getKey() + base) * spacing;
+		vd.getPos(key)[0] = (key.getKey() + base) * spacing;
 		//set the property of the particles
 		vd.template getProp<0>(key) = f_xex2((key.getKey() + base) * spacing);
 
@@ -188,19 +188,19 @@ int main(int argc, char* argv[])
 		auto key = it.get();
 
 		// set the position of the particles
-		if (m_pad.isInsideNB(vd.template getPos<0>(key)) == true)
+		if (m_pad.isInsideNB(vd.getPos(key)) == true)
 		{
 			vd.add();
-			vd.template getLastPos<0>()[0] = - vd.template getPos<0>(key)[0];
+			vd.getLastPos()[0] = - vd.getPos(key)[0];
 			vd.template getLastProp<0>() = - vd.template getProp<0>(key);
 		}
 
 		// set the position of the particles
-		if (m_pad2.isInsideNB(vd.template getPos<0>(key)) == true)
+		if (m_pad2.isInsideNB(vd.getPos(key)) == true)
 		{
 			vd.add();
-			vd.template getLastPos<0>()[0] = 2.0 * box.getHigh(0) - vd.template getPos<0>(key)[0];
-			vd.template getLastProp<0>() = f_xex2(vd.template getLastPos<0>()[0]);
+			vd.getLastPos()[0] = 2.0 * box.getHigh(0) - vd.getPos(key)[0];
+			vd.template getLastProp<0>() = f_xex2(vd.getLastPos()[0]);
 		}
 
 		++it;
@@ -241,7 +241,7 @@ int main(int argc, char* argv[])
     	vect_dist_key_dx key = it_p.get();
 
     	// Get the position of the particles
-    	Point<1,float128> p = vd.template getPos<0>(key);
+    	Point<1,float128> p = vd.getPos(key);
 
     	// We are not interested in calculating out the domain
     	// note added padding particle are considered domain particles
@@ -265,7 +265,7 @@ int main(int argc, char* argv[])
     		if (nnp != key.getKey())
     		{
     			// W(x-y)
-    			float128 ker = lker.value(p,vd.template getPos<0>(nnp));
+    			float128 ker = lker.value(p,vd.getPos(nnp));
 
     			// f(y)
     			float128 prp_y = vd.template getProp<0>(nnp);

example/Numerics/PSE/1_Diffusion_1D/main.cpp

@@ -74,7 +74,7 @@ template<typename CellL> double calcLap(Point<1,double> p, vect_dist_key_dx key,
 		if (nnp != key.getKey())
 		{
 			// W(x-y)
-			double ker = lker.value(p,vd.template getPos<0>(nnp));
+			double ker = lker.value(p,vd.getPos(nnp));
 
 			// f(y)
 			double prp_y = vd.template getProp<0>(nnp);
@@ -180,7 +180,7 @@ int main(int argc, char* argv[])
 		auto key = it2.get();
 
 		// set the position of the particles
-		vd.template getPos<0>(key)[0] = (key.getKey() + base) * spacing;
+		vd.getPos(key)[0] = (key.getKey() + base) * spacing;
 		//set the property of the particles
 		vd.template getProp<0>(key) = f_xex2((key.getKey() + base) * spacing);
 
@@ -238,19 +238,19 @@ int main(int argc, char* argv[])
 		auto key = it.get();
 
 		// set the position of the particles
-		if (m_pad.isInsideNB(vd.template getPos<0>(key)) == true)
+		if (m_pad.isInsideNB(vd.getPos(key)) == true)
 		{
 			vd.add();
-			vd.template getLastPos<0>()[0] = - vd.template getPos<0>(key)[0];
+			vd.getLastPos()[0] = - vd.getPos(key)[0];
 			vd.template getLastProp<0>() = - vd.template getProp<0>(key);
 		}
 
 		// set the position of the particles
-		if (m_pad2.isInsideNB(vd.template getPos<0>(key)) == true)
+		if (m_pad2.isInsideNB(vd.getPos(key)) == true)
 		{
 			vd.add();
-			vd.template getLastPos<0>()[0] = 2.0 * box.getHigh(0) - vd.template getPos<0>(key)[0];
-			vd.template getLastProp<0>() = f_xex2(vd.template getLastPos<0>()[0]);
+			vd.getLastPos()[0] = 2.0 * box.getHigh(0) - vd.getPos(key)[0];
+			vd.template getLastProp<0>() = f_xex2(vd.getLastPos()[0]);
 		}
 
 		++it;
@@ -284,7 +284,7 @@ int main(int argc, char* argv[])
     		// key
     		vect_dist_key_dx key = it_p.get();
 
-    		Point<1,double> p = vd.template getPos<0>(key);
+    		Point<1,double> p = vd.getPos(key);
 
     		// We are not interested in calculating out the domain
     		// note added padding particle are considered domain particles

example/SE/0_classes/main.cpp

@@ -98,7 +98,7 @@ int main(int argc, char* argv[])
 		try
         {
 			vect_dist_key_dx vt(5048);
-			auto it = vd.getPos<0>(vt);
+			auto it = vd.getPos(vt);
         }
 		catch (size_t e)
 		{
@@ -185,7 +185,7 @@ int main(int argc, char* argv[])
 	try
     {
 		vect_dist_key_dx vt(0);
-		auto it = vd1->getPos<0>(vt);
+		auto it = vd1->getPos(vt);
     }
 	catch (size_t e)
 	{

example/Vector/0_simple/main.cpp

@@ -91,8 +91,8 @@ int main(int argc, char* argv[])
 	{
 		auto key = it.get();
 
-		vd.template getPos<s::x>(key)[0] = ud(eg);
-		vd.template getPos<s::x>(key)[1] = ud(eg);
+		vd.getPos(key)[0] = ud(eg);
+		vd.getPos(key)[1] = ud(eg);
 
 		++it;
 	}
@@ -121,7 +121,7 @@ int main(int argc, char* argv[])
 		auto key = it.get();
 
 		// The template parameter is unuseful and will probably disappear
-		if (ct.isLocal(vd.template getPos<0>(key)) == false)
+		if (ct.isLocal(vd.getPos(key)) == false)
 			std::cerr << "Error particle is not local" << "\n";
 
 		// set the all the properties to 0.0

example/Vector/1_celllist/main.cpp

@@ -103,9 +103,9 @@ int main(int argc, char* argv[])
 
 		auto key = it.get();
 
-		vd.template getLastPos<0>()[0] = key.get(0) * it.getSpacing(0);
-		vd.template getLastPos<0>()[1] = key.get(1) * it.getSpacing(1);
-		vd.template getLastPos<0>()[2] = key.get(2) * it.getSpacing(2);
+		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);
 
 		++it;
 	}
@@ -133,9 +133,9 @@ int main(int argc, char* argv[])
 	{
 		auto p = it2.get();
 
-		Point<3,float> xp = vd.getPos<0>(p);
+		Point<3,float> xp = vd.getPos(p);
 
-		auto Np = NN.getIterator(NN.getCell(vd.getPos<0>(p)));
+		auto Np = NN.getIterator(NN.getCell(vd.getPos(p)));
 
 		while (Np.isNext())
 		{
@@ -143,7 +143,7 @@ int main(int argc, char* argv[])
 
 			// repulsive
 
-			Point<3,float> xq = vd.getPos<0>(q);
+			Point<3,float> xq = vd.getPos(q);
 			Point<3,float> f = (xp - xq);
 
 			// we sum the distance of all the particles

example/Vector/1_verlet/main.cpp

@@ -102,9 +102,9 @@ int main(int argc, char* argv[])
 
 		auto key = it.get();
 
-		vd.template getLastPos<0>()[0] = key.get(0) * it.getSpacing(0);
-		vd.template getLastPos<0>()[1] = key.get(1) * it.getSpacing(1);
-		vd.template getLastPos<0>()[2] = key.get(2) * it.getSpacing(2);
+		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);
 
 		++it;
 	}
@@ -138,14 +138,14 @@ int main(int argc, char* argv[])
 	for (size_t i = 0 ; i < verlet.size() ; i++)
 	{
 
-		Point<3,float> p = vd.getPos<0>(i);
+		Point<3,float> p = vd.getPos(i);
 
 		// for each neighborhood particle
 		for (size_t j = 0 ; j < verlet.get(i).size() ; j++)
 		{
 			auto & NN = verlet.get(i);
 
-			Point<3,float> q = vd.getPos<0>(NN.get(j));
+			Point<3,float> q = vd.getPos(NN.get(j));
 
 			// some non-sense calculation as usage demo
 

example/Vector/2_molecular_dynamic/Makefile

+include ../../example.mk
+
+CC=mpic++
+
+LDIR =
+
+OBJ = main.o
+
+%.o: %.cpp
+	$(CC) -O3 -g -c --std=c++11 -o $@ $< $(INCLUDE_PATH)
+
+md_dyn: $(OBJ)
+	$(CC) -o $@ $^ $(CFLAGS) $(LIBS_PATH) $(LIBS)
+
+all: cell
+
+.PHONY: clean all
+
+clean:
+	rm -f *.o *~ core md_dyn
+

example/Vector/2_molecular_dynamic/config.cfg

+[pack]
+files = main.cpp Makefile

example/Vector/2_molecular_dynamic/gc_plot2_out.html

+<html>
+  <head>
+    <script type="text/javascript" src="https://www.gstatic.com/charts/loader.js"></script>
+    <script type="text/javascript">
+      google.charts.load('current', {'packages':['corechart']});
+      google.charts.setOnLoadCallback(drawVisualization);
+
+
+      function drawVisualization() {
+var data0 = new google.visualization.DataTable();
+data0.addColumn('number','iteration');
+data0.addColumn('number','line0');
+data0.addRows([
+[0,18010.3],
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+[9700,20237.4],
+[9800,20089.2],
+[9900,20061.7],
+]);
+var options0= {
+title : 'Energy with time',
+vAxis: {title: 'Energy'},
+hAxis: {title: 'iteration'},
+curveType: 'function',
+lineWidth: 1,
+intervals: { 'style':'area' },
+};
+var chart = new google.visualization.ComboChart(document.getElementById('chart_div0'));chart.draw(data0, options0);
+}</script>
+</head>
+<body>
+<div id="chart_div0" style="width: 900px; height: 500px;"></div>
+</body>
+</html>

example/Vector/2_molecular_dynamic/main.cpp

+
+#include "Vector/vector_dist.hpp"
+#include "Decomposition/CartDecomposition.hpp"
+#include "data_type/aggregate.hpp"
+#include "Plot/GoogleChart.hpp"
+#include "Plot/util.hpp"
+
+/*
+ * ### WIKI 1 ###
+ *
+ * ## Molecular Dynamic with Lennard-Jones potential
+ *
+ * This example show a simple Lennard-Jones molecular dynamic simulation in a stable regime
+ *
+ * ### WIKI END ###
+ *
+ */
+
+constexpr int velocity = 0;
+constexpr int force = 1;
+
+/* ### WIKI 11 ###
+ *
+ * The function to calculate the forces between particles. It require the vector of particles
+ * Cell list and scaling factor.
+ *
+ */
+void calc_forces(vector_dist<3,double, aggregate<double[3],double[3]> > & vd, CellList<3, double, FAST, shift<3, double> > & NN, double L)
+{
+
+	// ### WIKI 12 ###
+	//
+	// Update the cell list from the actual particle configuration
+	//
+	//
+	vd.updateCellList(NN);
+
+	// ### WIKI 13 ###
+	//
+	// Calculate the forces
+	//
+	auto it2 = vd.getDomainIterator();
+	while (it2.isNext())
+	{
+		auto p = it2.get();
+
+		Point<3,double> xp = vd.getPos<0>(p);
+
+		vd.template getProp<force>(p)[0] = 0.0;
+		vd.template getProp<force>(p)[1] = 0.0;
+		vd.template getProp<force>(p)[2] = 0.0;
+
+		// For each neighborhood particle
+		auto Np = NN.template getNNIterator<NO_CHECK>(NN.getCell(vd.getPos<0>(p)));
+
+		while (Np.isNext())
+		{
+			// Neighborhood particle q
+			auto q = Np.get();
+
+			if (q == p.getKey())	{++Np; continue;};
+
+			// repulsive
+			Point<3,double> xq = vd.getPos<0>(q);
+			Point<3,double> r = xp - xq;
+
+			// take the norm, normalize
+			float rn = r.norm();
+			r /= rn;
+			rn *= L;
+
+			// Calculate the force, using pow is slower
+			Point<3,double> f = 24.0*(2.0 / (rn*rn*rn*rn*rn*rn*rn*rn*rn*rn*rn*rn*rn) -  1.0 / (rn*rn*rn*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);
+
+			++Np;
+		}
+
+		++it2;
+	}
+}
+
+/* ### WIKI 14 ###
+ *
+ * The function to calculate the total energy. It require the same parameter as calculate forces
+ *
+ */
+double calc_energy(vector_dist<3,double, aggregate<double[3],double[3]> > & vd, CellList<3, double, FAST, shift<3, double> > & NN, double L)
+{
+	// ### WIKI 15 ###
+	//
+	// Reset the counter for the energy and
+	// update the cell list from the actual particle configuration
+	//
+	//
+	double E = 0.0;
+	vd.updateCellList(NN);
+
+	// ### WIKI 16 ###
+	//
+	// Calculate the forces
+	//
+	auto it2 = vd.getDomainIterator();
+	while (it2.isNext())
+	{
+		auto p = it2.get();
+
+		Point<3,double> xp = vd.getPos<0>(p);
+
+		vd.template getProp<force>(p)[0] = 0.0;
+		vd.template getProp<force>(p)[1] = 0.0;
+		vd.template getProp<force>(p)[2] = 0.0;
+
+		// For each neighborhood particle
+		auto Np = NN.template getNNIterator<NO_CHECK>(NN.getCell(vd.getPos<0>(p)));
+
+		while (Np.isNext())
+		{
+			// Neighborhood particle q
+			auto q = Np.get();
+
+			if (q == p.getKey())	{++Np; continue;};
+
+			Point<3,double> xq = vd.getPos<0>(q);
+			Point<3,double> r = xp - xq;
+
+			// take the normalized direction
+			float rn = r.norm();
+			r /= rn;
+
+			rn *= L;
+
+			// potential energy (using pow is slower)
+			E += 4.0 * ( 1.0 / (rn*rn*rn*rn*rn*rn*rn*rn*rn*rn*rn*rn) + 1.0 / ( rn*rn*rn*rn*rn*rn) );
+
+			// Kinetic energy
+			E += sqrt(vd.template getProp<force>(p)[0]*vd.template getProp<force>(p)[0] +
+					vd.template getProp<force>(p)[1]*vd.template getProp<force>(p)[1] +
+					vd.template getProp<force>(p)[2]*vd.template getProp<force>(p)[2]);
+
+			++Np;
+		}
+
+		++it2;
+	}
+