void turn_body(int direction, double length){
int a = current_step % 10;
if(a < 5)
move_body(0, length);
else
rotate_body(direction, length);
}
static void update_step_nve(struct md *md)
{
double dt = cfg_get_double(md->state->cfg, "time_step");
for (size_t i = 0; i < md->n_bodies; i++) {
struct body *body = md->bodies + i;
body->vel.x += 0.5 * body->force.x * dt / body->mass;
body->vel.y += 0.5 * body->force.y * dt / body->mass;
body->vel.z += 0.5 * body->force.z * dt / body->mass;
body->angmom.x += 0.5 * body->torque.x * dt;
body->angmom.y += 0.5 * body->torque.y * dt;
body->angmom.z += 0.5 * body->torque.z * dt;
body->pos.x += body->vel.x * dt;
body->pos.y += body->vel.y * dt;
body->pos.z += body->vel.z * dt;
rotate_body(body, dt);
}
compute_forces(md);
for (size_t i = 0; i < md->n_bodies; i++) {
struct body *body = md->bodies + i;
body->vel.x += 0.5 * body->force.x * dt / body->mass;
body->vel.y += 0.5 * body->force.y * dt / body->mass;
body->vel.z += 0.5 * body->force.z * dt / body->mass;
body->angmom.x += 0.5 * body->torque.x * dt;
body->angmom.y += 0.5 * body->torque.y * dt;
body->angmom.z += 0.5 * body->torque.z * dt;
}
}
/*
* Reference
*
* Simone Melchionna, Giovanni Ciccotti, Brad Lee Holian
*
* Hoover NPT dynamics for systems varying in shape and size
*
* Mol. Phys. 78, 533 (1993)
*/
static void update_step_npt(struct md *md)
{
struct npt_data *data = (struct npt_data *)md->data;
double dt = cfg_get_double(md->state->cfg, "time_step");
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 t_tau2 = t_tau * t_tau;
double p_tau2 = p_tau * p_tau;
double kbt = BOLTZMANN * t_target;
double t0 = get_temperature(md);
double p0 = get_pressure(md);
double v0 = get_volume(md);
for (size_t i = 0; i < md->n_bodies; i++) {
struct body *body = md->bodies + i;
body->vel.x += 0.5 * dt * (body->force.x / body->mass -
body->vel.x * (data->chi + data->eta));
body->vel.y += 0.5 * dt * (body->force.y / body->mass -
body->vel.y * (data->chi + data->eta));
body->vel.z += 0.5 * dt * (body->force.z / body->mass -
body->vel.z * (data->chi + data->eta));
body->angmom.x += 0.5 * dt * (body->torque.x -
body->angmom.x * data->chi);
body->angmom.y += 0.5 * dt * (body->torque.y -
body->angmom.y * data->chi);
body->angmom.z += 0.5 * dt * (body->torque.z -
body->angmom.z * data->chi);
rotate_body(body, dt);
}
data->chi += 0.5 * dt * (t0 / t_target - 1.0) / t_tau2;
data->chi_dt += 0.5 * dt * data->chi;
data->eta += 0.5 * dt * v0 * (p0 - p_target) / md->n_bodies / kbt / p_tau2;
vec_t com = get_system_com(md);
vec_t pos_init[md->n_bodies];
for (size_t i = 0; i < md->n_bodies; i++)
pos_init[i] = md->bodies[i].pos;
for (size_t iter = 1; iter <= MAX_ITER; iter++) {
bool done = true;
for (size_t i = 0; i < md->n_bodies; i++) {
struct body *body = md->bodies + i;
vec_t pos = wrap(md, &body->pos);
vec_t v = {
data->eta * (pos.x - com.x),
data->eta * (pos.y - com.y),
data->eta * (pos.z - com.z)
};
vec_t new_pos = {
pos_init[i].x + dt * (body->vel.x + v.x),
pos_init[i].y + dt * (body->vel.y + v.y),
pos_init[i].z + dt * (body->vel.z + v.z)
};
done = done && vec_dist(&body->pos, &new_pos) < EPSILON;
body->pos = new_pos;
}
if (done)
break;
if (iter == MAX_ITER)
msg("WARNING: NPT UPDATE DID NOT CONVERGE\n\n");
}
vec_scale(&md->box, exp(dt * data->eta));
check_fail(efp_set_periodic_box(md->state->efp, md->box.x, md->box.y, md->box.z));
compute_forces(md);
double chi_init = data->chi, eta_init = data->eta;
vec_t angmom_init[md->n_bodies], vel_init[md->n_bodies];
for (size_t i = 0; i < md->n_bodies; i++) {
angmom_init[i] = md->bodies[i].angmom;
vel_init[i] = md->bodies[i].vel;
}
for (size_t iter = 1; iter <= MAX_ITER; iter++) {
double chi_prev = data->chi;
double eta_prev = data->eta;
double t_cur = get_temperature(md);
double p_cur = get_pressure(md);
double v_cur = get_volume(md);
data->chi = chi_init + 0.5 * dt * (t_cur / t_target - 1.0) / t_tau2;
data->eta = eta_init + 0.5 * dt * v_cur * (p_cur - p_target) /
md->n_bodies / kbt / p_tau2;
for (size_t i = 0; i < md->n_bodies; i++) {
struct body *body = md->bodies + i;
body->vel.x = vel_init[i].x + 0.5 * dt *
(body->force.x / body->mass -
vel_init[i].x * (data->chi + data->eta));
body->vel.y = vel_init[i].y + 0.5 * dt *
(body->force.y / body->mass -
vel_init[i].y * (data->chi + data->eta));
body->vel.z = vel_init[i].z + 0.5 * dt *
(body->force.z / body->mass -
vel_init[i].z * (data->chi + data->eta));
body->angmom.x = angmom_init[i].x + 0.5 * dt *
(body->torque.x - angmom_init[i].x * data->chi);
body->angmom.y = angmom_init[i].y + 0.5 * dt *
(body->torque.y - angmom_init[i].y * data->chi);
body->angmom.z = angmom_init[i].z + 0.5 * dt *
(body->torque.z - angmom_init[i].z * data->chi);
}
if (fabs(data->chi - chi_prev) < EPSILON &&
fabs(data->eta - eta_prev) < EPSILON)
break;
if (iter == MAX_ITER)
msg("WARNING: NPT UPDATE DID NOT CONVERGE\n\n");
}
data->chi_dt += 0.5 * dt * data->chi;
}
/*
* NVT with Nose-Hoover thermostat:
*
* William G. Hoover
*
* Canonical dynamics: Equilibrium phase-space distributions
*
* Phys. Rev. A 31, 1695 (1985)
*/
static void update_step_nvt(struct md *md)
{
struct nvt_data *data = (struct nvt_data *)md->data;
double dt = cfg_get_double(md->state->cfg, "time_step");
double target = cfg_get_double(md->state->cfg, "temperature");
double tau = cfg_get_double(md->state->cfg, "thermostat_tau");
double t0 = get_temperature(md);
for (size_t i = 0; i < md->n_bodies; i++) {
struct body *body = md->bodies + i;
body->vel.x += 0.5 * dt * (body->force.x / body->mass -
body->vel.x * data->chi);
body->vel.y += 0.5 * dt * (body->force.y / body->mass -
body->vel.y * data->chi);
body->vel.z += 0.5 * dt * (body->force.z / body->mass -
body->vel.z * data->chi);
body->angmom.x += 0.5 * dt * (body->torque.x -
body->angmom.x * data->chi);
body->angmom.y += 0.5 * dt * (body->torque.y -
body->angmom.y * data->chi);
body->angmom.z += 0.5 * dt * (body->torque.z -
body->angmom.z * data->chi);
body->pos.x += body->vel.x * dt;
body->pos.y += body->vel.y * dt;
body->pos.z += body->vel.z * dt;
rotate_body(body, dt);
}
data->chi += 0.5 * dt * (t0 / target - 1.0) / tau / tau;
data->chi_dt += 0.5 * dt * data->chi;
compute_forces(md);
double chi_init = data->chi;
vec_t angmom_init[md->n_bodies], vel_init[md->n_bodies];
for (size_t i = 0; i < md->n_bodies; i++) {
angmom_init[i] = md->bodies[i].angmom;
vel_init[i] = md->bodies[i].vel;
}
for (size_t iter = 1; iter <= MAX_ITER; iter++) {
double chi_prev = data->chi;
double ratio = get_temperature(md) / target;
data->chi = chi_init + 0.5 * dt * (ratio - 1.0) / tau / tau;
for (size_t i = 0; i < md->n_bodies; i++) {
struct body *body = md->bodies + i;
body->vel.x = vel_init[i].x + 0.5 * dt *
(body->force.x / body->mass - vel_init[i].x * data->chi);
body->vel.y = vel_init[i].y + 0.5 * dt *
(body->force.y / body->mass - vel_init[i].y * data->chi);
body->vel.z = vel_init[i].z + 0.5 * dt *
(body->force.z / body->mass - vel_init[i].z * data->chi);
body->angmom.x = angmom_init[i].x + 0.5 * dt *
(body->torque.x - angmom_init[i].x * data->chi);
body->angmom.y = angmom_init[i].y + 0.5 * dt *
(body->torque.y - angmom_init[i].y * data->chi);
body->angmom.z = angmom_init[i].z + 0.5 * dt *
(body->torque.z - angmom_init[i].z * data->chi);
}
if (fabs(data->chi - chi_prev) < EPSILON)
break;
if (iter == MAX_ITER)
msg("WARNING: NVT UPDATE DID NOT CONVERGE\n\n");
}
data->chi_dt += 0.5 * dt * data->chi;
}
