void MolecularDynamics::assign_velocities(Float temperature)
{
ParticleIndexes ips=get_simulation_particle_indexes();
setup_degrees_of_freedom(ips);
ParticlesTemp ps= IMP::internal::get_particle(get_model(), ips);
boost::normal_distribution<Float> mrng(0., 1.);
boost::variate_generator<RandomNumberGenerator&,
boost::normal_distribution<Float> >
sampler(random_number_generator, mrng);
for (ParticlesTemp::iterator iter = ps.begin();
iter != ps.end(); ++iter) {
Particle *p = *iter;
for (int i = 0; i < 3; ++i) {
p->set_value(vs_[i], sampler());
}
}
Float rescale = sqrt(temperature/
get_kinetic_temperature(get_kinetic_energy()));
for (ParticlesTemp::iterator iter = ps.begin();
iter != ps.end(); ++iter) {
Particle *p = *iter;
for (int i = 0; i < 3; ++i) {
Float velocity = p->get_value(vs_[i]);
velocity *= rescale;
p->set_value(vs_[i], velocity);
}
}
}
void MolecularDynamics::assign_velocities(Float temperature) {
ParticleIndexes ips = get_simulation_particle_indexes();
setup_degrees_of_freedom(ips);
ParticlesTemp ps = IMP::internal::get_particle(get_model(), ips);
boost::normal_distribution<Float> mrng(0., 1.);
boost::variate_generator<RandomNumberGenerator &,
boost::normal_distribution<Float> >
sampler(random_number_generator, mrng);
for (ParticlesTemp::iterator iter = ps.begin(); iter != ps.end();
++iter) {
Particle *p = *iter;
LinearVelocity(p).set_velocity(algebra::Vector3D(sampler(), sampler(),
sampler()));
}
Float rescale =
sqrt(temperature / get_kinetic_temperature(get_kinetic_energy()));
for (ParticlesTemp::iterator iter = ps.begin(); iter != ps.end();
++iter) {
Particle *p = *iter;
LinearVelocity v(p);
algebra::Vector3D velocity = v.get_velocity();
velocity *= rescale;
v.set_velocity(velocity);
}
}
int main (int argc, char *argv[])
{
int i, n_samples = 10;
if(argc == 2){
n_particles = atoi(argv[1]);
}
else{printf("usage: %s <n_particles>\n", argv[0] );return 1;}
ETA = 0.3;
double tmp, x = 0.0f, err = 0.0f;
printf("\nDIMENSION = %d\n\n", DIMENSION );
printf("N = %d\tETA = %f\n", n_particles, ETA );
for(i = 0; i < n_samples; i++){
init( ETA, 1.0f );
int t;for(t = 0; t < 50000; t++){ run(); if(t == 10000) reset(); } /* thermalization */
/* pressure */
tmp = SIGMA*dp/(2*get_kinetic_energy()*runtime);
x += tmp;
err += tmp*tmp;
}
char filename[64];
sprintf(filename,"data/%.2f_TL.dat",ETA);
FILE *file = fopen(filename,"a");
x /= n_samples;
err = sqrt((err/n_samples-x*x)/n_samples);
fprintf(file, "%e\t%e\t%e\n", ETA, x, err );
fclose(file);
return 0;
}
static double get_invariant_nvt(const struct md *md)
{
struct nvt_data *data = (struct nvt_data *)md->data;
double t_tau = cfg_get_double(md->state->cfg, "thermostat_tau");
double t_target = cfg_get_double(md->state->cfg, "temperature");
double kbt = BOLTZMANN * t_target;
double t_virt = kbt * md->n_freedom * (data->chi_dt +
data->chi * data->chi * t_tau * t_tau / 2.0);
return md->potential_energy + get_kinetic_energy(md) + t_virt;
}
double agent_body::get_sensor_value(agent_sensor_id const& sensor) const
{
switch(sensor)
{
case Position_X:
return get_position().x;
case Position_Y:
return get_position().y;
case WorldVelocity_X:
return get_linear_velocity().x;
case WorldVelocity_Y:
return get_linear_velocity().y;
case KineticEnergy:
return get_kinetic_energy();
default:
throw std::exception("Invalid Sensor Id");
}
}
static double get_invariant_npt(const struct md *md)
{
struct npt_data *data = (struct npt_data *)md->data;
double t_tau = cfg_get_double(md->state->cfg, "thermostat_tau");
double t_target = cfg_get_double(md->state->cfg, "temperature");
double p_tau = cfg_get_double(md->state->cfg, "barostat_tau");
double p_target = cfg_get_double(md->state->cfg, "pressure");
double kbt = BOLTZMANN * t_target;
double volume = get_volume(md);
double t_virt = kbt * md->n_freedom * (data->chi_dt +
data->chi * data->chi * t_tau * t_tau / 2.0);
double p_virt = p_target * volume + 3.0 * md->n_bodies * kbt *
data->eta * data->eta * p_tau * p_tau / 2.0;
return md->potential_energy + get_kinetic_energy(md) + t_virt + p_virt;
}
size_t composite_body::initialize_state_value_bindings_(sv_bindings_t& bindings, sv_accessors_t& accessors) const
{
auto initial_count = bindings.size();
auto bound_id = accessors.size();
bindings[s_sv_names.left.at(StateValue::PositionX)] = bound_id++;
accessors.push_back([this]
{
return get_com_position().x;
});
bindings[s_sv_names.left.at(StateValue::PositionY)] = bound_id++;
accessors.push_back([this]
{
return get_com_position().y;
});
bindings[s_sv_names.left.at(StateValue::LinVelX)] = bound_id++;
accessors.push_back([this]
{
return get_linear_velocity().x;
});
bindings[s_sv_names.left.at(StateValue::LinVelY)] = bound_id++;
accessors.push_back([this]
{
return get_linear_velocity().y;
});
bindings[s_sv_names.left.at(StateValue::KE)] = bound_id++;
accessors.push_back([this]
{
return get_kinetic_energy();
});
// TODO: what about joints added or removed dynamically? can these be supported?
for(auto const& rev : m_revolutes)
{
rev.rev->initialize_state_value_bindings_(bindings, accessors, rev.name);
}
return bindings.size() - initial_count;
}
Float HybridMonteCarlo::get_total_energy() const
{
return get_kinetic_energy()+get_potential_energy();
}
static double get_invariant_nve(const struct md *md)
{
return md->potential_energy + get_kinetic_energy(md);
}
static double get_temperature(const struct md *md)
{
double ke = get_kinetic_energy(md);
return 2.0 * ke / BOLTZMANN / md->n_freedom;
}
static void
time_integration_loop_hubble(Forceinfo *fi, Nbodyinfo *nb)
{
double zval; /* red shift at T=0 */
double tmpzz;
double t, t0, dt1, tpresent;
double W, K, E0, E, Q;
double cm[3], cmv[3];
int step = 0;
double tsnapout, timageout;
t = 0.0;
tpresent = 16.0; /* present time must be 16.0 */
zval = 24.0;
tmpzz = pow(1.0/(zval+1), 3.0/2.0);
t0 = tmpzz/(1.0-tmpzz)*tpresent;
fi->eps = (zval+1)*pow(t0/(tpresent+t0), 2.0/3.0)*eps0;
dt1 = dt0;
tsnapout = dtsnapout;
timageout = dtimageout;
PR(t0, f); PR(dt0, f); PRL(dt1, f);
PR(tstart,f); PR(tpresent,f); PR(dt,f); PRL(dtsnapout,f); PRL(dtimageout,f);
if (cputime_flag) {
vtc_turnon_cputime();
}
vtc_init_cputime();
vtc_print_cputime("initial vtc_get_force start at");
#if DIRECT /* direct sum */
if (grape_flag) {
vtc_set_scale(512.0, nb->m[0]);
fi->calculator = GRAPE_FORCEONLY;
vtc_get_force_direct(fi, nb);
#if CALCPOTENTIAL
fi->calculator = GRAPE_POTENTIALONLY;
vtc_get_force_direct(fi, nb);
fi->calculator = GRAPE_FORCEONLY;
#endif
}
else {
vtc_get_force_direct(fi, nb);
}
#else /* tree */
if (grape_flag) {
fi->calculator = GRAPE_FORCEONLY;
vtc_get_force_tree(fi, nb);
#if CALCPOTENTIAL
fi->calculator = GRAPE_POTENTIALONLY;
vtc_get_force_tree(fi, nb);
fi->calculator = GRAPE_FORCEONLY;
#endif
}
else {
vtc_get_force_tree(fi, nb);
}
#endif /* direct/tree */
vtc_print_cputime("initial vtc_get_force end at");
fprintf(stderr, "ninteraction: %e list_len_avg: %6.5f nwalk: %d\n",
fi->ninteraction, (double)fi->ninteraction/nb->n, fi->nwalk);
K = get_kinetic_energy(nb);
#if CALCPOTENTIAL
W = get_potential_energy(nb);
E = E0 = W+K;
PR(E0, f); PR(W, f);
#endif
PRL(K, f);
plot_nbody(t, nb);
/* calculate force at T=0 and quit */
if (snapout_flag && dtsnapout == 0.0) {
static int nout = 0;
char fn[255];
snapout_acc_flag = 1;
sprintf(fn, snapoutfile, nout);
PRL(fn, s);
if (ionemo_flag) {
write_binary(fn, t, nb);
}
else if (usepob_flag) {
write_pob(fn, t, nb);
}
else {
write_ascii(fn, t, nb);
}
vtc_print_cputime("exit at");
return;
}
while (t < tend) {
if (fi->eps < eps) {
double eps1;
eps1 = (zval+1)*pow((t+t0)/(tpresent+t0), 2.0/3.0)*eps0;
fi->eps = (eps1 < eps ? eps1 : eps);
}
else {
fi->eps = eps;
}
if (dt1 < dt) {
dt1 = dt0*(t+t0)/t0;
}
else {
dt1 = dt;
}
if (step%outlogstep == outlogstep - 1 && cputime_flag) {
vtc_turnon_cputime();
}
else {
vtc_turnoff_cputime();
}
push_velocity(0.5*dt1, nb);
push_position(dt1, nb);
vtc_init_cputime();
#if DIRECT /* direct sum */
vtc_get_force_direct(fi, nb);
#else /* tree */
vtc_get_force_tree(fi, nb);
#endif /* direct/tree */
vtc_print_cputime("vtc_get_force end at");
push_velocity(0.5*dt1, nb);
vtc_print_cputime("integration end at");
plot_nbody(t, nb);
if (step%outlogstep == outlogstep - 1) {
fprintf(stderr, "ninteraction: %e list_len_avg: %6.5f nwalk: %d\n",
fi->ninteraction, fi->ninteraction/nb->n, fi->nwalk);
K = get_kinetic_energy(nb);
#if CALCPOTENTIAL
if (grape_flag) {
fi->calculator = GRAPE_POTENTIALONLY;
#if DIRECT /* direct sum */
vtc_get_force_direct(fi, nb);
#else /* tree */
vtc_get_force_tree(fi, nb);
#endif /* direct/tree */
fi->calculator = GRAPE_FORCEONLY;
}
W = get_potential_energy(nb);
E = W+K;
Q = K/(K-E);
fprintf(stderr, "\nT= %f K= %f Q= %f E= %f Eerr= %f Eabserr= %f\n",
t, K, Q, E, (E0-E)/E0, E0-E);
#else
fprintf(stderr, "\nT= %f K= %f\n", t, K);
#endif
fprintf(stderr, "step: %d\n", step);
fprintf(stderr, "T: %f current eps: %f dt: %f\n",
t, fi->eps, dt1);
get_cmterms(nb, cm, cmv);
fprintf(stderr, "CM %15.13e %15.13e %15.13e\n",
cm[0], cm[1], cm[2]);
fprintf(stderr, "CMV %15.13e %15.13e %15.13e\n",
cmv[0], cmv[1], cmv[2]);
}
if (tsnapout < t && snapout_flag) {
static int nout = 0;
char fn[255];
char cmd[255];
sprintf(fn, snapoutfile, nout);
PRL(fn, s);
if (ionemo_flag) {
write_binary(fn, t, nb);
}
else if (usepob_flag) {
write_pob(fn, t, nb);
}
else {
write_ascii(fn, t, nb);
}
if (command_exec_flag) {
sprintf(cmd, "%s %s %03d", command_name, fn, nout);
fprintf(stderr, "execute %s\n", cmd);
system(cmd);
}
nout++;
PR(t, f); PRL(fn, s);
tsnapout += dtsnapout;
}
if (timageout < t && imageout_flag) {
static int nout = 0;
char fn[255];
char cmd[255];
sprintf(fn, snapoutfile, nout);
strcat(fn, ".gif");
PRL(fn, s);
vtc_plotstar(nb->x, nb->n, t, image_scale, fn);
nout++;
PR(t, f); PRL(fn, s);
timageout += dtimageout;
}
t += dt1;
step++;
vtc_print_cputime("exit at");
} /* main loop */
}
static void
time_integration_loop(Forceinfo *fi, Nbodyinfo *nb)
{
int i, nstep;
int outsnapstep, outimagestep;
double W, K, E0, E, Q;
double cm[3], cmv[3];
double t = tstart;
nstep = (int)((tend-tstart)/dt+0.1);
dt = (tend-tstart)/nstep;
outsnapstep = (int) (dtsnapout/dt+0.1);
outimagestep = (int) (dtimageout/dt+0.1);
PR(tstart,f); PR(tend,f); PR(dt,f); PRL(dtsnapout,f); PRL(dtimageout,f);
if (cputime_flag) {
vtc_turnon_cputime();
}
vtc_init_cputime();
vtc_print_cputime("initial vtc_get_force start at");
#if DIRECT /* direct sum */
if (grape_flag) {
vtc_set_scale(512.0, nb->m[0]);
#if MDGRAPE2
fi->calculator = GRAPE_FORCEONLY;
#else
fi->calculator = GRAPE;
#endif /* MDGRAPE2 */
vtc_get_force_direct(fi, nb);
#if CALCPOTENTIAL && MDGRAPE2
fi->calculator = GRAPE_POTENTIALONLY;
vtc_get_force_direct(fi, nb);
fi->calculator = GRAPE_FORCEONLY;
#endif /* CALCPOTENTIAL && MDGRAPE2 */
}
else {
#if CALCPOTENTIAL
fi->calculator = HOST;
#endif /* CALCPOTENTIAL */
vtc_get_force_direct(fi, nb);
}
#else /* tree */
if (grape_flag) {
#if NOFORCE
fi->calculator = NOCALCULATOR;
#elif MDGRAPE2
fi->calculator = GRAPE_FORCEONLY;
#else
fi->calculator = GRAPE;
#endif /* NOFORCE */
vtc_get_force_tree(fi, nb);
#if CALCPOTENTIAL && MDGRAPE2
fi->calculator = GRAPE_POTENTIALONLY;
vtc_get_force_tree(fi, nb);
fi->calculator = GRAPE_FORCEONLY;
#endif /* CALCPOTENTIAL && MDGRAPE2 */
}
else {
#if CALCPOTENTIAL
fi->calculator = HOST;
#endif /* CALCPOTENTIAL */
vtc_get_force_tree(fi, nb);
}
#endif
vtc_print_cputime("initial vtc_get_force end at");
fprintf(stderr, "ninteraction: %e list_len_avg: %6.5f nwalk: %d\n",
fi->ninteraction, (double)fi->ninteraction/nb->n, fi->nwalk);
K = get_kinetic_energy(nb);
#if CALCPOTENTIAL
W = get_potential_energy(nb);
E = E0 = W+K;
PR(E0, 20.17f); PR(W, 20.17f);
#endif
PRL(K, f);
plot_nbody(t, nb);
/* calculate force at T=0 and quit */
if (snapout_flag && dtsnapout == 0.0) {
static int nout = 0;
char fn[255];
snapout_acc_flag = 1;
sprintf(fn, snapoutfile, nout);
PRL(fn, s);
if (ionemo_flag) {
write_binary(fn, t, nb);
}
else if (usepob_flag) {
write_pob(fn, t, nb);
}
else {
write_ascii(fn, t, nb);
}
vtc_print_cputime("exit at");
#if USE_GM_API
fprintf(stderr, "will m2_gm_finalize...\n");
m2_gm_finalize();
fprintf(stderr, "done m2_gm_finalize.\n");
#endif /* USE_GM_API */
}
for (i = 0; i < nstep; i++) {
if (i%outlogstep == outlogstep - 1 && cputime_flag) {
vtc_turnon_cputime();
}
else {
vtc_turnoff_cputime();
}
fprintf(stderr, "step %d\n", i);
push_velocity(0.5*dt, nb);
push_position(dt, nb);
t = tstart+(i+1)*dt;
vtc_init_cputime();
#if DIRECT /* direct sum */
vtc_get_force_direct(fi, nb);
#else /* tree */
vtc_get_force_tree(fi, nb);
#endif
vtc_print_cputime("vtc_get_force end at");
push_velocity(0.5*dt, nb);
vtc_print_cputime("integration end at");
plot_nbody(t, nb);
if (i%outlogstep == outlogstep - 1) {
fprintf(stderr, "ninteraction: %e list_len_avg: %6.5f nwalk: %d\n",
fi->ninteraction, fi->ninteraction/nb->n, fi->nwalk);
K = get_kinetic_energy(nb);
#if CALCPOTENTIAL
#if MDGRAPE2
if (grape_flag) {
fi->calculator = GRAPE_POTENTIALONLY;
#if DIRECT /* direct sum */
vtc_get_force_direct(fi, nb);
#else /* tree */
vtc_get_force_tree(fi, nb);
#endif /* direct/tree */
fi->calculator = GRAPE_FORCEONLY;
}
#endif /* MDGRAPE2 */
W = get_potential_energy(nb);
E = W+K;
Q = K/(K-E);
fprintf(stderr, "\nT= %f K= %20.17f Q= %20.17f E= %20.17f Eerr= %20.17f Eabserr= %20.17f\n",
t, K, Q, E, (E0-E)/E0, E0-E);
#else /* CALCPOTENTIAL */
fprintf(stderr, "\nT= %f K= %20.17f\n", t, K);
#endif /* CALCPOTENTIAL */
fprintf(stderr, "step: %d\n", i);
get_cmterms(nb, cm, cmv);
fprintf(stderr, "CM %15.13e %15.13e %15.13e\n",
cm[0], cm[1], cm[2]);
fprintf(stderr, "CMV %15.13e %15.13e %15.13e\n",
cmv[0], cmv[1], cmv[2]);
}
if (i%outsnapstep == outsnapstep - 1 && snapout_flag) {
static int nout = 0;
char fn[255];
char cmd[255];
sprintf(fn, snapoutfile, nout);
PRL(fn, s);
if (ionemo_flag) {
write_binary(fn, t, nb);
}
else if (usepob_flag) {
write_pob(fn, t, nb);
}
else {
write_ascii(fn, t, nb);
}
if (command_exec_flag) {
sprintf(cmd, "%s %s %03d", command_name, fn, nout);
fprintf(stderr, "execute %s\n", cmd);
system(cmd);
}
nout++;
PR(t, f); PRL(fn, s);
}
if (i%outimagestep == outimagestep - 1 && imageout_flag) {
static int nout = 0;
char fn[255];
char cmd[255];
char msg[255];
double center[2];
sprintf(fn, snapoutfile, nout);
strcat(fn, ".gif");
PRL(fn, s);
sprintf(msg, "t: %5.3f", t);
center[0] = 0.0;
center[1] = 0.0;
// vtc_plotstar(fn, nb, msg, image_scale, center, 1e10, NULL, NULL);
// vtc_plotstar(nb->x, nb->m, nb->n, t, image_scale, fn);
nout++;
PR(t, f); PRL(fn, s);
}
vtc_print_cputime("exit at");
} /* i loop */
}
int main()
{
int i;
dt = 1e-13;
H = 5e4;
t_max = 500.0*100.*dt;
Lx = Ly = Lz = pow(50.0/1e10,0.333333);
assert(N % 2 == 0 );
srand(time(NULL));
rx[0] = 0.5 * Lx + 100.0 * 100.0 * a0;
vx[0] = 0.0;
ry[0] = 0.5 * Ly;
vy[0] = sqrt(e*e / (me * 100.0 * 100.0 * a0));
rz[0] = 0.5 * Lz;
vz[0] = 0.0;
m[0] = me; q[0] = -e; type[0] = 1;
rx[1] = 0.5 * Lx;
vx[1] = 0.0;
ry[1] = 0.5 * Ly;
vy[1] = 0.0;
rz[1] = 0.5 * Lz;
vz[1] = 0.0;
m[1] = mp; q[1] = e; type[1] = 2;
U = K = KelXY = KelZ = KpXY = KpZ = 0.0;
for(i = 0; i < N; ++i) {get_kinetic_energy(i);}
update_forces();
E = K + U;
initK = K;
initU = U;
initE = E;
int st = 0;
double t;
double dx, dy, dz;
FILE* f_en = fopen("energy","w");
FILE* f_pos = fopen("part_pos", "w");
get_distance_vector(0, 1, &dx, &dy, &dz);
fprintf(f_pos,"%d\t%g\t%g\t%g\t%g\t%g\n",st, rx[0]/Lx, ry[0]/Ly, rx[1]/Lx, ry[1]/Ly, sqrt(dx*dx + dy*dy + dz*dz));
fprintf(f_en,"%d\t%g\t%g\t%g\n", st, E, initE, (1.0 - fabs(E/initE)));
for(t = 0.0; t < t_max; t += dt)
{
U = K = KelXY = KelZ = KpXY = KpZ = 0.0;
/*VV_step(dt);*/
B_step(dt);
E = U + K;
st++;
get_distance_vector(0, 1, &dx, &dy, &dz);
fprintf(f_pos,"%d\t%g\t%g\t%g\t%g\t%g\n",st, rx[0]/Lx, ry[0]/Ly, rx[1]/Lx, ry[1]/Ly, sqrt(dx*dx + dy*dy + dz*dz));
fprintf(f_en,"%d\t%g\t%g\t%g\n", st, E, initE, (1.0 - fabs(E/initE)));
if(initE != 0.0 && fabs(initE - E) > 0.1 * fabs(initE))
{
fprintf(stderr,"!\n");
return EXIT_FAILURE;
}
}
return EXIT_SUCCESS;
}