Commit 0dc5f75f authored by incardon's avatar incardon
Browse files

Adding missing examples

parent d6a510d9
include ../../example.mk
CC=mpic++
LDIR =
OBJ_DORD = main.o
all: md_sym
%.o: %.cpp
$(CC) -fext-numeric-literals -O3 -g -c --std=c++11 $(OPT) -o $@ $< $(INCLUDE_PATH)
md_sym: $(OBJ_DORD)
$(CC) -o $@ $^ $(CFLAGS) $(LIBS_PATH) $(LIBS)
run: md_sym
source $$HOME/openfpm_vars; mpirun -np 3 ./md_sym
.PHONY: clean all run md_sym
clean:
rm -f *.o *~ core md_sym
#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"
/*!
* \page Vector_5_md_vl_sym Vector 5 molecular dynamic with symmetric Verlet list
*
*
* # Molecular dynamic with symmetric interactions # {#md_e5_sym}
*
* In a previous example we show how to build a parallel molecular dynamic simulation.
* We also show how it was possible to achive better performance using Verlet list.
*
* \see \ref e3_md_vl
*
* In this example we show how to improve even more our code using symmetric Verlet-list.
* If we look at the form of the Lennard-Jhones potential we will see that
* calculating the force that the particle **p** produce on **q** is equivalent to the force
* that **q** produce on **p**. This mean that when we use normal verlet-list we are redundantly
* doing double calculation. In order to avoid it we will use symmetric verlet-list. Symmetric
* verlet list have their feature in store the pair **p,q** only one time. If **p** store **q**
* as neighborhood than **q** does not store **p** as neighborhood. This Mean that when we calculate
* the contribution for of **q** to **p** we have to add such contribution also to **q**.
*
* The example is exactly equivalent to the non-symmetric with few differences in **calc_forces** and
* **calc_energies**
*
*
*/
//! \cond [constants] \endcond
constexpr int velocity = 0;
constexpr int force = 1;
//! \cond [constants] \endcond
/*!
*
* \page Vector_5_md_vl_sym Vector 5 molecular dynamic with symmetric Verlet list
*
* ## Calculate forces ## {#md_e5_calc_force}
*
* In this function we calculate the forces between particles. It require the vector of particles
* Cell list and sigma factor for the Lennard-Jhones potential. The function is exactly the same
* as the original
*
* \see \ref e3_md_vl_cf
*
* with the following changes
*
*
* * If we calculate the force for **p-q** we are also adding this force to **q-p**
* \snippet Vector/5_molecular_dynamic_sym/main.cpp add to q
*
* * At the end of the calculation we have to execute a ghost put
* \snippet Vector/5_molecular_dynamic_sym/main.cpp ghost_put
*
* ###Explanation### {#md_e5_sym_expl}
*
* The first point is given by the fact that if the pair is stored once, when we calculate
* the force, we have to add the contribution to both particles. The second instead is
* is given by the fact that **q** can be a ghost particles. In case **q** is a ghost particle
* we are adding the contribution to the ghost particle and not to the real one. To
* add the contribution to the real particle we have to use the function **ghost_put**.
* This function send back the information to the original processor, that will merge the
* information (in this case add_)
*
*
* \snippet Vector/5_molecular_dynamic_sym/main.cpp calc forces vl
*
*/
//! \cond [calc forces vl] \endcond
void calc_forces(vector_dist<3,double, aggregate<double[3],double[3]> > & vd, VerletList<3, double, FAST, shift<3, double> > & NN, double sigma12, double sigma6, double 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.getDomainIterator();
//! \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,double> 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.getKey());
// 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 q
Point<3,double> xq = vd.getPos(q);
// Get the distance between p and q
Point<3,double> r = xp - xq;
// take the norm of this vector
double rn = norm2(r);
if (rn > r_cut * r_cut) {++Np;continue;}
// Calculate the force, using pow is slower
Point<3,double> 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;
}
//! \cond [ghost_put] \endcond
// Sum the contribution to the real particles
vd.ghost_put<add_,force>();
//! \cond [ghost_put] \endcond
}
//! \cond [calc forces vl] \endcond
/*!
*
* \page Vector_5_md_vl_sym Vector 5 molecular dynamic with symmetric Verlet list
*
* ## Calculate energy ## {#md_e5_calc_ene}
*
* For the energy we use symmetric verlet-list in the same way as we did for calc_forces.
* Because the symmetric verlet-list span each couple one time, we have to remove the division by two
* (in this case we use the original factor 4.0 of the Lennard-Jhones potential rather than 2.0).
*
* \snippet Vector/5_molecular_dynamic_sym/main.cpp calc energy vl
*
*/
//! \cond [calc energy vl] \endcond
double calc_energy(vector_dist<3,double, aggregate<double[3],double[3]> > & vd, VerletList<3, double, FAST, shift<3, double> > & NN, double sigma12, double sigma6, double r_cut)
{
double E = 0.0;
double rc = r_cut*r_cut;
double shift = 4.0 * ( sigma12 / (rc*rc*rc*rc*rc*rc) - sigma6 / ( rc*rc*rc) );
// 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,double> xp = vd.getPos(p);
// Get an iterator over the neighborhood of the particle p
auto Np = NN.template getNNIterator<NO_CHECK>(p.getKey());
double 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.getKey()) {++Np; continue;};
// Get position of the particle q
Point<3,double> xq = vd.getPos(q);
// take the normalized direction
double 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;
}
// 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;
}
//! \cond [calc energy vl] \endcond
int main(int argc, char* argv[])
{
/*!
* \page Vector_5_md_vl_sym Vector 5 molecular dynamic with symmetric Verlet list
*
* ## Simulation ## {#md_e5_sym_sim}
*
* The simulation is equal to the simulation explained in the example molecular dynamic
*
* \see \ref e3_md_vl
*
* The difference is that we create a symmetric Verlet-list instead of a normal one
* \snippet Vector/5_molecular_dynamic_sym/main.cpp sim verlet
*
* The rest of the code remain unchanged
*
* \snippet Vector/5_molecular_dynamic_sym/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);
vector_dist<3,double, aggregate<double[3],double[3]> > vd(0,box,bc,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.getVerletSym(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_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<>(SKIP_LABELLING);
// 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 Vector 5 molecular dynamic with symmetric Verlet list
*
* ## Finalize ## {#finalize_v_e5_md_sym}
*
* At the very end of the program we have always to de-initialize the library
*
* \snippet Vector/5_molecular_dynamic_sym/main.cpp finalize
*
*/
//! \cond [finalize] \endcond
openfpm_finalize();
//! \cond [finalize] \endcond
/*!
* \page Vector_5_md_vl_sym Vector 5 molecular dynamic with symmetric Verlet list
*
* ## Full code ## {#full_code_v_e5_md_sym}
*
* \include Vector/5_molecular_dynamic_sym/main.cpp
*
*/
}
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