void calc_f_dev(int natoms,real charge[],rvec x[],rvec f[],
t_idef *idef,real *xiH,real *xiS)
{
enum { wwwO, wwwH1, wwwH2, wwwS, wwwNR };
int lj_index[wwwNR] = { 0, 4, 4, 8 };
real rmsf,dFH,dFS,dFO,dr_14;
real q[wwwNR],c6[wwwNR],c12[wwwNR],c12ratio;
rvec fff[2],dx;
int i,j,aj;
for(i=0; (i<wwwNR); i++) {
q[i] = charge[i];
c12[i] = idef->iparams[lj_index[i]].lj.c12;
c6[i] = idef->iparams[lj_index[i]].lj.c6;
}
calc_force(natoms,f,fff);
rmsf = norm(fff[0]);
dFS = 0;
dFH = 0;
dFO = 0;
for(i=0; (i<4); i++) {
for(j=4; (j<8); j++) {
if (c12[i] != 0) {
rvec_sub(x[i],x[j],dx);
aj = j % 4;
dr_14 = pow(iprod(dx,dx),-7);
c12ratio = -12*sqrt(c12[aj]/c12[i])*dr_14*iprod(fff[0],dx);
switch (i) {
case wwwH1:
case wwwH2:
dFH += c12ratio;
break;
case wwwS:
dFS += c12ratio;
break;
case wwwO:
dFS += c12ratio;
break;
}
}
}
}
if (debug) {
fprintf(debug,"FFF: dFS=%10.3e, dFH=%10.3e, dFO=%10.3e, rmsf=%10.3e\n",
dFS,dFH,dFO,rmsf);
}
if (dFH == 0)
*xiH = 1;
else
*xiH=rmsf/(10*c12[wwwH1]*dFH);
if (dFS == 0)
*xiS = 1;
else
*xiS=rmsf/(10*c12[wwwS]*dFS);
}
/* Utility Function: cell_neighbor
* Calculate forces between all atoms of cell1 and cell2
* and return potential energy
*/
double calc_pair_interactions(Cell* cell1, Cell* cell2, const SimParams* params)
{
double potentialEnergy = 0.0;
int i,j;
for(i=0;i<cell1->n_atoms;i++)
for(j=0;j<cell2->n_atoms;j++) {
potentialEnergy += calc_force(&(cell1->atoms[i]), &(cell2->atoms[j]), params);
}
return potentialEnergy;
}
/*Utility Function: calc_self_interactions
*/
double calc_self_interactions(Cell* this_cell, const SimParams* params)
{
double potentialEnergy = 0.0;
int i,j;
for(i=0;i<this_cell->n_atoms;i++)
for(j=i+1;j<this_cell->n_atoms;j++) {
potentialEnergy += calc_force(&(this_cell->atoms[i]),
&(this_cell->atoms[j]), params);
}
return potentialEnergy;
}
int main(int argc, char** argv)
{
const char filename[]="10.txt";
// Determine the number of atoms
Natoms = get_natoms(filename);
// Initialize the positions !
init(Natoms, filename);
// Loop over timesteps
std::ofstream simFile,enerFile;
simFile.open("LDmj_sim.xyz");
enerFile.open("LDmj_sim.ener");
enerFile << "Time step" << std::setw(15) << "time"
<< std::setw(15) << "PE" << std::setw(15) << "KE"
<< std::setw(15) << "TE" << std::setw(15) << "Px"
<< std::setw(15) << "Py" << std::setw(15)
<< "Pz" << std::setw(15) << std::endl;
for(int k=0; k<=1000; k++) {
elapsed_time = dt*double(k);
// Calculate pair-energy and forces
if(k==0) calc_force();
calc_kenergy();
TE=U+KE;
std::cout << std::setw(8) << k << std::setw(15) << elapsed_time
<< std::setw(15) << U << std::setw(15) << KE
<< std::setw(15) << TE << std::setw(15) << px
<< std::setw(15) << py << std::setw(15) << pz
<< std::setw(15) << std::endl;
calc_momentum();
write_xyz(simFile, k);
dump_stats(enerFile, k);
// parameters are computed for (i+1)
vv_scheme();
}
simFile.close();
enerFile.close();
return 0;
}
void vv_scheme()
{
double tfact;
// TODO : Perform openMP.
// reinitialize all the temp variables to zero.
for(int i=0; i<Natoms; i++){
r_old[i][0] = r[i][0];
r_old[i][1] = r[i][1];
r_old[i][2] = r[i][2];
v_old[i][0] = v[i][0];
v_old[i][1] = v[i][1];
v_old[i][2] = v[i][2];
f_old[i][0] = f[i][0];
f_old[i][1] = f[i][1];
f_old[i][2] = f[i][2];
}
for(int i=0; i<Natoms; i++){
tfact = dt/(2.0*m[i]);
// Step 1. v(t+0.5dt)
v[i][0] = v_old[i][0] + f_old[i][0]*tfact;
v[i][1] = v_old[i][1] + f_old[i][1]*tfact;
v[i][2] = v_old[i][2] + f_old[i][2]*tfact;
v_old[i][0] = v[i][0];
v_old[i][1] = v[i][1];
v_old[i][2] = v[i][2];
// Step 2. r(t+dt)
r[i][0] = r_old[i][0] + v_old[i][0]*dt;
r[i][1] = r_old[i][1] + v_old[i][1]*dt;
r[i][2] = r_old[i][2] + v_old[i][2]*dt;
}
calc_pairenergy();
calc_force();
for(int i=0; i<Natoms; i++){
// Step 3. v(t+dt)
v[i][0] = v_old[i][0] + f[i][0]*tfact;
v[i][1] = v_old[i][1] + f[i][1]*tfact;
v[i][2] = v_old[i][2] + f[i][2]*tfact;
}
}
void run_simulation(simulation_t *simulation) {
collide_particles(simulation->src_buf, simulation->count);
// iterate through each particle and addup all forces
for (unsigned int i = 0; i < simulation->count; i++) {
particle_t *a = &simulation->src_buf[i];
particle_t *a2 = &simulation->dst_buf[i];
vec3f forces;
forces.x = forces.y = forces.z = 0;
for (unsigned int j = 0; j < simulation->count; j++) {
if (i != j) {
particle_t *b = &simulation->src_buf[j];
forces = vec_add(forces, calc_force(a, b));
}
}
// a = F / m
vec3f acc = vec_scale(forces, 1 / a->mass);
integrate(a, a2, acc, simulation->dt);
}
// swap buffers
particle_t *tmp = simulation->src_buf;
simulation->src_buf = simulation->dst_buf;
simulation->dst_buf = tmp;
}
