void adress_update_weights(){
Particle *p;
int i, np, c;
Cell *cell;
for (c = 0; c < local_cells.n; c++) {
cell = local_cells.cell[c];
p = cell->part;
np = cell->n;
for(i = 0; i < np; i++) {
if (ifParticleIsVirtual(&p[i])) {
p[i].p.adress_weight=adress_wf_vector((&p[i])->r.p);
//printf("LOCAL %f %f\n", p[i].r.p[0], p[i].p.adress_weight);
}
}
}
for (c = 0; c < local_cells.n; c++) {
cell = ghost_cells.cell[c];
p = cell->part;
np = cell->n;
for(i = 0; i < np; i++) {
if (ifParticleIsVirtual(&p[i])) {
p[i].p.adress_weight=adress_wf_vector((&p[i])->r.p);
//printf("GHOST %f %f\n", p[i].r.p[0], p[i].p.adress_weight);
}
}
}
}
void put_mol_force_on_parts(Particle *p_com){
int i,j,mol_id;
Particle *p;
double force[3],M;
#ifdef VIRTUAL_SITES_DEBUG
int count=0;
#endif
mol_id=p_com->p.mol_id;
for (i=0;i<3;i++){
force[i]=p_com->f.f[i];
p_com->f.f[i]=0.0;
}
#ifdef MASS
M=0;
for (i=0;i<topology[mol_id].part.n;i++){
p=local_particles[topology[mol_id].part.e[i]];
#ifdef VIRTUAL_SITES_DEBUG
if (p==NULL){
ostringstream msg;
msg <<"Particle does not exist in put_mol_force_on_parts! id= " << topology[mol_id].part.e[i] << "\n";
runtimeError(msg);
return;
}
#endif
if (ifParticleIsVirtual(p)) continue;
M+=PMASS(*p);
}
#else
M=topology[mol_id].part.n-1;
#endif
for (i=0;i<topology[mol_id].part.n;i++){
p=local_particles[topology[mol_id].part.e[i]];
#ifdef VIRTUAL_SITES_DEBUG
if (p==NULL){
ostringstream msg;
msg <<"Particle does not exist in put_mol_force_on_parts! id= " << topology[mol_id].part.e[i] << "\n";
runtimeError(msg);
return;
}
#endif
if (!ifParticleIsVirtual(p)) {
for (j=0;j<3;j++){
p->f.f[j]+=PMASS(*p)*force[j]/M;
}
#ifdef VIRTUAL_SITES_DEBUG
count++;
#endif
}
}
#ifdef VIRTUAL_SITES_DEBUG
if (count!=topology[mol_id].part.n-1){
ostringstream msg;
msg <<"There is more than one COM input_mol_force_on_parts! mol_id= " << mol_id << "\n";
runtimeError(msg);
return;
}
#endif
}
void put_mol_force_on_parts(Particle *p_com){
int i,j,mol_id;
Particle *p;
double force[3],M;
#ifdef VIRTUAL_SITES_DEBUG
int count=0;
#endif
mol_id=p_com->p.mol_id;
for (i=0;i<3;i++){
force[i]=p_com->f.f[i];
p_com->f.f[i]=0.0;
}
#ifdef MASS
M=0;
for (i=0;i<topology[mol_id].part.n;i++){
p=local_particles[topology[mol_id].part.e[i]];
#ifdef VIRTUAL_SITES_DEBUG
if (p==NULL){
char *errtxt = runtime_error(128 + 3*ES_INTEGER_SPACE);
ERROR_SPRINTF(errtxt,"Particle does not exist in put_mol_force_on_parts! id=%i\n",topology[mol_id].part.e[i]);
return;
}
#endif
if (ifParticleIsVirtual(p)) continue;
M+=PMASS(*p);
}
#else
M=topology[mol_id].part.n-1;
#endif
for (i=0;i<topology[mol_id].part.n;i++){
p=local_particles[topology[mol_id].part.e[i]];
#ifdef VIRTUAL_SITES_DEBUG
if (p==NULL){
char *errtxt = runtime_error(128 + 3*ES_INTEGER_SPACE);
ERROR_SPRINTF(errtxt,"Particle does not exist in put_mol_force_on_parts! id=%i\n",topology[mol_id].part.e[i]);
return;
}
#endif
if (!ifParticleIsVirtual(p)) {
for (j=0;j<3;j++){
p->f.f[j]+=PMASS(*p)*force[j]/M;
}
#ifdef VIRTUAL_SITES_DEBUG
count++;
#endif
}
}
#ifdef VIRTUAL_SITES_DEBUG
if (count!=topology[mol_id].part.n-1){
char *errtxt = runtime_error(128 + 3*ES_INTEGER_SPACE);
ERROR_SPRINTF(errtxt,"There is more than one COM input_mol_force_on_parts! mol_id=%i\n",mol_id);
return;
}
#endif
}
/** Calculate kinetic energies for one particle.
@param p1 particle for which to calculate energies
*/
inline void add_kinetic_energy(Particle *p1)
{
#ifdef VIRTUAL_SITES
if (ifParticleIsVirtual(p1)) return;
#endif
/* kinetic energy */
energy.data.e[0] += (SQR(p1->m.v[0]) + SQR(p1->m.v[1]) + SQR(p1->m.v[2]))*PMASS(*p1);
#ifdef ROTATION
#ifdef ROTATION_PER_PARTICLE
if (p1->p.rotation)
#endif
{
#ifdef ROTATIONAL_INERTIA
/* the rotational part is added to the total kinetic energy;
Here we use the rotational inertia */
energy.data.e[0] += (SQR(p1->m.omega[0])*p1->p.rinertia[0] +
SQR(p1->m.omega[1])*p1->p.rinertia[1] +
SQR(p1->m.omega[2])*p1->p.rinertia[2])*time_step*time_step;
#else
/* the rotational part is added to the total kinetic energy;
at the moment, we assume unit inertia tensor I=(1,1,1) */
energy.data.e[0] += (SQR(p1->m.omega[0]) + SQR(p1->m.omega[1]) + SQR(p1->m.omega[2]))*time_step*time_step;
#endif
}
#endif
}
// Calculates center of mass of a particle
int calc_mol_pos_cfg(Particle *p_com,double r_com[3]){
int i,j,mol_id;
double M=0;
Particle *p;
#ifdef VIRTUAL_SITES_DEBUG
int count=0;
#endif
for (i=0;i<3;i++){
r_com[i]=0.0;
}
mol_id=p_com->p.mol_id;
for (i=0;i<topology[mol_id].part.n;i++){
p=&partCfg[topology[mol_id].part.e[i]];
if (ifParticleIsVirtual(p)) continue;
for (j=0;j<3;j++){
r_com[j] += PMASS(*p)*p->r.p[j];
}
M+=PMASS(*p);
#ifdef VIRTUAL_SITES_DEBUG
count++;
#endif
}
for (j=0;j<3;j++){
r_com[j] /= M;
}
#ifdef VIRTUAL_SITES_DEBUG
if (count!=topology[mol_id].part.n-1){
fprintf(stderr,"There is more than one COM in calc_mol_pos_cfg! mol_id=%i\n",mol_id);
return 0;
}
#endif
return 1;
}
/** initialize the forces for a ghost particle */
MDINLINE void init_ghost_force(Particle *part)
{
#ifdef ADRESS
if (ifParticleIsVirtual(part)) {
part->p.adress_weight=adress_wf_vector(part->r.p);
}
#endif
part->f.f[0] = 0;
part->f.f[1] = 0;
part->f.f[2] = 0;
#ifdef ROTATION
{
double scale;
/* set torque to zero */
part->f.torque[0] = 0;
part->f.torque[1] = 0;
part->f.torque[2] = 0;
/* and rescale quaternion, so it is exactly of unit length */
scale = sqrt( SQR(part->r.quat[0]) + SQR(part->r.quat[1]) +
SQR(part->r.quat[2]) + SQR(part->r.quat[3]));
part->r.quat[0]/= scale;
part->r.quat[1]/= scale;
part->r.quat[2]/= scale;
part->r.quat[3]/= scale;
}
#endif
}
/* momentum update step of ghmc */
void simple_momentum_update()
{
int i, j, c, np;
Particle *part;
double sigmat, sigmar;
sigmat = sqrt(temperature); sigmar = sqrt(temperature);
for (c = 0; c < local_cells.n; c++) {
np = local_cells.cell[c]->n;
part = local_cells.cell[c]->part;
for (i = 0; i < np; i++) {
#ifdef VIRTUAL_SITES
if (ifParticleIsVirtual(&part[i])) continue;
#endif
#ifdef MASS
sigmat = sqrt(temperature / PMASS(part[i]));
#endif
for (j = 0; j < 3; j++) {
part[i].m.v[j] = sigmat*gaussian_random()*time_step;
#ifdef ROTATION
#ifdef ROTATIONAL_INERTIA
sigmar = sqrt(temperature / part[i].p.rinertia[j]);
#endif
part[i].m.omega[j] = sigmar*gaussian_random();
#endif
}
}
}
//fprintf(stderr,"%d: temp after simple update: %f\n",this_node,calc_local_temp());
}
Particle *get_mol_com_particle(Particle *calling_p){
int mol_id;
int i;
Particle *p;
mol_id=calling_p->p.mol_id;
if (mol_id < 0) {
char *errtxt = runtime_error(128 + 3*ES_INTEGER_SPACE);
ERROR_SPRINTF(errtxt,"Particle does not have a mol id! pnr=%i\n",
calling_p->p.identity);
return NULL;
}
for (i=0;i<topology[mol_id].part.n;i++){
p=local_particles[topology[mol_id].part.e[i]];
if (p==NULL){
char *errtxt = runtime_error(128 + 3*ES_INTEGER_SPACE);
ERROR_SPRINTF(errtxt,"Particle does not exist in put_mol_force_on_parts! id=%i\n",topology[mol_id].part.e[i]);
return NULL;
}
if (ifParticleIsVirtual(p)) {
return p;
}
}
char *errtxt = runtime_error(128 + 3*ES_INTEGER_SPACE);
ERROR_SPRINTF(errtxt,"No com found in get_mol_com_particleParticle does not exist in put_mol_force_on_parts! pnr=%i\n",calling_p->p.identity);
return NULL;
return calling_p;
}
Particle *get_mol_com_particle(Particle *calling_p) {
int mol_id;
int i;
Particle *p;
mol_id=calling_p->p.mol_id;
for (i=0; i<topology[mol_id].part.n; i++) {
p=local_particles[topology[mol_id].part.e[i]];
#ifdef VIRTUAL_SITES_DEBUG
if (p==NULL) {
char *errtxt = runtime_error(128 + 3*TCL_INTEGER_SPACE);
ERROR_SPRINTF(errtxt,"Particle does not exist in put_mol_force_on_parts! id=%i\n",topology[mol_id].part.e[i]);
return NULL;
}
#endif
if (ifParticleIsVirtual(p)) {
return p;
}
}
#ifdef VIRTUAL_SITES_DEBUG
char *errtxt = runtime_error(128 + 3*TCL_INTEGER_SPACE);
ERROR_SPRINTF(errtxt,"No com found in get_mol_com_particleParticle does not exist in put_mol_force_on_parts! pnr=%i\n",calling_p->p.identity);
return NULL;
#endif
return calling_p;
}
Particle *get_mol_com_particle(Particle *calling_p){
int mol_id;
int i;
Particle *p;
mol_id=calling_p->p.mol_id;
if (mol_id < 0) {
ostringstream msg;
msg <<"Particle does not have a mol id! pnr= " << calling_p->p.identity << "\n";
runtimeError(msg);
return NULL;
}
for (i=0;i<topology[mol_id].part.n;i++){
p=local_particles[topology[mol_id].part.e[i]];
if (p==NULL){
ostringstream msg;
msg <<"Particle does not exist in put_mol_force_on_parts! id= " << topology[mol_id].part.e[i] << "\n";
runtimeError(msg);
return NULL;
}
if (ifParticleIsVirtual(p)) {
return p;
}
}
ostringstream msg;
msg <<"No com found in get_mol_com_particleParticle does not exist in put_mol_force_on_parts! pnr= " << calling_p->p.identity << "\n";
runtimeError(msg);
return NULL;
return calling_p;
}
/* momentum update step of ghmc with temperature scaling */
void tscale_momentum_update()
{
int i, j, c, np;
Particle *part;
//fprintf(stderr,"%d: temp before update: %f\n",this_node,calc_local_temp());
save_last_state();
simple_momentum_update();
//fprintf(stderr,"%d: temp after simple update: %f\n",this_node,calc_local_temp());
double tempt, tempr;
calc_kinetic(&tempt, &tempr);
tempt /= (1.5*n_total_particles);
tempr /= (1.5*n_total_particles);
double scalet = sqrt(temperature / tempt);
#ifdef ROTATION
double scaler = sqrt(temperature / tempr);
#endif
for (c = 0; c < local_cells.n; c++) {
np = local_cells.cell[c]->n;
part = local_cells.cell[c]->part;
for (i = 0; i < np; i++) {
for (j = 0; j < 3; j++) {
part[i].m.v[j] *= scalet;
#ifdef ROTATION
part[i].m.omega[j] *= scaler;
#endif
}
}
}
//fprintf(stderr,"%d: temp after scale: %f\n",this_node,calc_local_temp());
for (c = 0; c < local_cells.n; c++) {
np = local_cells.cell[c]->n;
part = local_cells.cell[c]->part;
for (i = 0; i < np; i++) {
#ifdef VIRTUAL_SITES
if (ifParticleIsVirtual(&part[i])) continue;
#endif
for (j = 0; j < 3; j++) {
part[i].m.v[j] = cosp*(part[i].l.m_ls.v[j])+sinp*(part[i].m.v[j]);
#ifdef ROTATION
part[i].m.omega[j] = cosp*(part[i].l.m_ls.omega[j])+sinp*(part[i].m.omega[j]);
#endif
}
}
}
//fprintf(stderr,"%d : temp after partial update: %f\n",this_node,calc_local_temp());
}
bool steepest_descent_step(void) {
Cell *cell;
Particle *p;
int c, i, j, np;
double f_max = -std::numeric_limits<double>::max();
double f;
/* Verlet list criterion */
const double skin2 = SQR(0.5*skin);
double f_max_global;
double dx[3], dx2;
const double max_dx2 = SQR(params->max_displacement);
for (c = 0; c < local_cells.n; c++) {
cell = local_cells.cell[c];
p = cell->part;
np = cell->n;
for(i = 0; i < np; i++) {
f = 0.0;
dx2 = 0.0;
#ifdef VIRTUAL_SITES
if (ifParticleIsVirtual(&p[i])) continue;
#endif
for(j=0; j < 3; j++){
#ifdef EXTERNAL_FORCES
if (!(p[i].p.ext_flag & COORD_FIXED(j)))
#endif
{
f += SQR(p[i].f.f[j]);
dx[j] = params->gamma * p[i].f.f[j];
dx2 += SQR(dx[j]);
MINIMIZE_ENERGY_TRACE(printf("part %d dim %d dx %e gamma*f %e\n", i, j, dx[j], params->gamma * p[i].f.f[j]));
}
#ifdef EXTERNAL_FORCES
else {
dx[j] = 0.0;
}
#endif
}
if(dx2 <= max_dx2) {
p[i].r.p[0] += dx[0];
p[i].r.p[1] += dx[1];
p[i].r.p[2] += dx[2];
} else {
const double c = params->max_displacement/std::sqrt(dx2);
p[i].r.p[0] += c*dx[0];
p[i].r.p[1] += c*dx[1];
p[i].r.p[2] += c*dx[2];
}
if(distance2(p[i].r.p,p[i].l.p_old) > skin2 ) resort_particles = 1;
f_max = std::max(f_max, f);
}
}
MINIMIZE_ENERGY_TRACE(printf("f_max %e resort_particles %d\n", f_max, resort_particles));
announce_resort_particles();
MPI_Allreduce(&f_max, &f_max_global, 1, MPI_DOUBLE, MPI_MAX, comm_cart);
return (sqrt(f_max_global) < params->f_max);
}
void rescale_forces_propagate_vel()
{
Cell *cell;
Particle *p;
int i, j, np, c;
double scale;
#ifdef NPT
if(integ_switch == INTEG_METHOD_NPT_ISO){
nptiso.p_vel[0] = nptiso.p_vel[1] = nptiso.p_vel[2] = 0.0;}
#endif
scale = 0.5 * time_step * time_step;
INTEG_TRACE(fprintf(stderr,"%d: rescale_forces_propagate_vel:\n",this_node));
for (c = 0; c < local_cells.n; c++) {
cell = local_cells.cell[c];
p = cell->part;
np = cell->n;
for(i = 0; i < np; i++) {
check_particle_force(&p[i]);
/* Rescale forces: f_rescaled = 0.5*dt*dt * f_calculated * (1/mass) */
p[i].f.f[0] *= scale/PMASS(p[i]);
p[i].f.f[1] *= scale/PMASS(p[i]);
p[i].f.f[2] *= scale/PMASS(p[i]);
ONEPART_TRACE(if(p[i].p.identity==check_id) fprintf(stderr,"%d: OPT: SCAL f = (%.3e,%.3e,%.3e) v_old = (%.3e,%.3e,%.3e)\n",this_node,p[i].f.f[0],p[i].f.f[1],p[i].f.f[2],p[i].m.v[0],p[i].m.v[1],p[i].m.v[2]));
#ifdef VIRTUAL_SITES
// Virtual sites are not propagated during integration
if (ifParticleIsVirtual(&p[i])) continue;
#endif
for(j = 0; j < 3 ; j++) {
#ifdef EXTERNAL_FORCES
if (!(p[i].l.ext_flag & COORD_FIXED(j))) {
#endif
#ifdef NPT
if(integ_switch == INTEG_METHOD_NPT_ISO && ( nptiso.geometry & nptiso.nptgeom_dir[j] )) {
nptiso.p_vel[j] += SQR(p[i].m.v[j])*PMASS(p[i]);
p[i].m.v[j] += p[i].f.f[j] + friction_therm0_nptiso(p[i].m.v[j])/PMASS(p[i]);
}
else
#endif
/* Propagate velocity: v(t+dt) = v(t+0.5*dt) + 0.5*dt * f(t+dt) */
{ p[i].m.v[j] += p[i].f.f[j]; }
#ifdef EXTERNAL_FORCES
}
#endif
}
ONEPART_TRACE(if(p[i].p.identity==check_id) fprintf(stderr,"%d: OPT: PV_2 v_new = (%.3e,%.3e,%.3e)\n",this_node,p[i].m.v[0],p[i].m.v[1],p[i].m.v[2]));
}
}
#ifdef NPT
finalize_p_inst_npt();
#endif
}
void update_mol_vel_particle(Particle *p){
int j;
double v_com[3];
if (ifParticleIsVirtual(p)) {
calc_mol_vel(p,v_com);
for (j=0;j<3;j++){
p->m.v[j] = v_com[j];
}
}
}
void update_mol_pos_particle(Particle *p){
int j;
double r_com[3];
if (ifParticleIsVirtual(p)) {
calc_mol_pos(p,r_com);
for (j=0;j<3;j++){
p->r.p[j] = r_com[j];
}
}
}
/** propagate angular velocities and quaternions \todo implement for
fixed_coord_flag */
void propagate_omega_quat()
{
Particle *p;
Cell *cell;
int c,i,j, np;
double lambda, dt2, dt4, dtdt, dtdt2;
dt2 = time_step*0.5;
dt4 = time_step*0.25;
dtdt = time_step*time_step;
dtdt2 = dtdt*0.5;
INTEG_TRACE(fprintf(stderr,"%d: propagate_omega_quat:\n",this_node));
for (c = 0; c < local_cells.n; c++) {
cell = local_cells.cell[c];
p = cell->part;
np = cell->n;
for(i = 0; i < np; i++) {
double Qd[4], Qdd[4], S[3], Wd[3];
#ifdef VIRTUAL_SITES
// Virtual sites are not propagated in the integration step
if (ifParticleIsVirtual(&p[i]))
continue;
#endif
define_Qdd(&p[i], Qd, Qdd, S, Wd);
lambda = 1 - S[0]*dtdt2 - sqrt(1 - dtdt*(S[0] + time_step*(S[1] + dt4*(S[2]-S[0]*S[0]))));
for(j=0; j < 3; j++){
p[i].m.omega[j]+= dt2*Wd[j];
}
ONEPART_TRACE(if(p[i].p.identity==check_id) fprintf(stderr,"%d: OPT: PV_1 v_new = (%.3e,%.3e,%.3e)\n",this_node,p[i].m.v[0],p[i].m.v[1],p[i].m.v[2]));
p[i].r.quat[0]+= time_step*(Qd[0] + dt2*Qdd[0]) - lambda*p[i].r.quat[0];
p[i].r.quat[1]+= time_step*(Qd[1] + dt2*Qdd[1]) - lambda*p[i].r.quat[1];
p[i].r.quat[2]+= time_step*(Qd[2] + dt2*Qdd[2]) - lambda*p[i].r.quat[2];
p[i].r.quat[3]+= time_step*(Qd[3] + dt2*Qdd[3]) - lambda*p[i].r.quat[3];
// Update the director
convert_quat_to_quatu(p[i].r.quat, p[i].r.quatu);
#ifdef DIPOLES
// When dipoles are enabled, update dipole moment
convert_quatu_to_dip(p[i].r.quatu, p[i].p.dipm, p[i].r.dip);
#endif
ONEPART_TRACE(if(p[i].p.identity==check_id) fprintf(stderr,"%d: OPT: PPOS p = (%.3f,%.3f,%.3f)\n",this_node,p[i].r.p[0],p[i].r.p[1],p[i].r.p[2]));
}
}
}
Particle *get_mol_com_particle_from_molid_cfg(int mol_id){
int i;
Particle *p;
for (i=0;i<topology[mol_id].part.n;i++){
p=&partCfg[topology[mol_id].part.e[i]];
if (ifParticleIsVirtual(p)){
return p;
}
}
#ifdef VIRTUAL_SITES_DEBUG
fprintf(stderr,"No com found in get_mol_com_particle_from_molid_cfg ! mol_id=%i\n",mol_id);
#endif
return NULL;
}
void update_mol_pos()
{
Particle *p;
int i, np, c;
Cell *cell;
for (c = 0; c < local_cells.n; c++) {
cell = local_cells.cell[c];
p = cell->part;
np = cell->n;
for(i = 0; i < np; i++) {
if (ifParticleIsVirtual(&p[i]))
update_mol_pos_particle(&p[i]);
}
//only for real particles
}
}
// Distribute forces that have accumulated on virtual particles to the
// associated real particles
void distribute_mol_force()
{
// Iterate over all the particles in the local cells
Particle *p;
int i, np, c;
Cell *cell;
for (c = 0; c < local_cells.n; c++) {
cell = local_cells.cell[c];
p = cell->part;
np = cell->n;
for(i = 0; i < np; i++) {
// We only care about virtual particles
if (ifParticleIsVirtual(&p[i])) {
update_mol_pos_particle(&p[i]);
// First obtain the real particle responsible for this virtual particle:
Particle *p_real = vs_relative_get_real_particle(&p[i]);
// Get distance vector pointing from real to virtual particle, respecting periodic boundary i
// conditions
double d[3];
get_mi_vector(d,p[i].r.p,p_real->r.p);
// The rules for transfering forces are:
// F_realParticle +=F_virtualParticle
// T_realParticle +=f_realParticle \times (r_virtualParticle-r_realParticle)
// Calculate torque to be added on real particle
double tmp[3];
vector_product(d,p[i].f.f,tmp);
// Add forces and torques
int j;
// printf("Particle %d gets torque from %f %f %f of particle %d\n",p_real->p.identity, p[i].f.f[0], p[i].f.f[1],p[i].f.f[2], p[i].p.identity);
for (j=0;j<3;j++) {
p_real->f.torque[j]+=tmp[j];
// printf("%f ",tmp[j]);
p_real->f.f[j]+=p[i].f.f[j];
// Clear forces on virtual particle
p[i].f.f[j]=0;
}
}
}
}
}
void update_mol_vel()
{
#ifndef VIRTUAL_SITES_NO_VELOCITY
Particle *p;
int i, np, c;
Cell *cell;
for (c = 0; c < local_cells.n; c++) {
cell = local_cells.cell[c];
p = cell->part;
np = cell->n;
for(i = 0; i < np; i++) {
if (ifParticleIsVirtual(&p[i]))
update_mol_vel_particle(&p[i]);
}
}
#endif
}
/* but p_com is a real particle */
void calc_mol_pos(Particle *p_com,double r_com[3]){
int i,j,mol_id;
double M=0;
double vec12[3];
Particle *p;
#ifdef VIRTUAL_SITES_DEBUG
int count=0;
#endif
for (i=0;i<3;i++){
r_com[i]=0.0;
}
mol_id=p_com->p.mol_id;
for (i=0;i<topology[mol_id].part.n;i++){
p=local_particles[topology[mol_id].part.e[i]];
#ifdef VIRTUAL_SITES_DEBUG
if (p==NULL){
ostringstream msg;
msg <<"Particle does not exist in calc_mol_pos! id= " << topology[mol_id].part.e[i] << "\n";
runtimeError(msg);
return;
}
#endif
if (ifParticleIsVirtual(p)) continue;
get_mi_vector(vec12,p->r.p, p_com->r.p);
for (j=0;j<3;j++){
r_com[j] += PMASS(*p)*vec12[j];
}
M+=PMASS(*p);
#ifdef VIRTUAL_SITES_DEBUG
count++;
#endif
}
for (j=0;j<3;j++){
r_com[j] /= M;
r_com[j] += p_com->r.p[j];
}
#ifdef VIRTUAL_SITES_DEBUG
if (count!=topology[mol_id].part.n-1){
ostringstream msg;
msg <<"There is more than one COM in calc_mol_pos! mol_id= " << mol_id << "\n";
runtimeError(msg);
return;
}
#endif
}
void distribute_mol_force()
{
Particle *p;
int i, np, c;
Cell *cell;
for (c = 0; c < local_cells.n; c++) {
cell = local_cells.cell[c];
p = cell->part;
np = cell->n;
for(i = 0; i < np; i++) {
if (ifParticleIsVirtual(&p[i])) {
if (sqrlen(p[i].f.f)!=0){
put_mol_force_on_parts(&p[i]);
}
}
}
}
}
// Rigid body conribution to scalar pressure and stress tensor
void vs_relative_pressure_and_stress_tensor(double* pressure, double* stress_tensor)
{
// Division by 3 volume is somewhere else. (pressure.cpp after all presure calculations)
// Iterate over all the particles in the local cells
Particle *p;
int i, np, c;
Cell *cell;
for (c = 0; c < local_cells.n; c++) {
cell = local_cells.cell[c];
p = cell->part;
np = cell->n;
for(i = 0; i < np; i++) {
// We only care about virtual particles
if (!ifParticleIsVirtual(&p[i]))
continue;
update_mol_pos_particle(&p[i]);
// First obtain the real particle responsible for this virtual particle:
Particle *p_real = vs_relative_get_real_particle(&p[i]);
// Get distance vector pointing from real to virtual particle, respecting periodic boundary i
// conditions
double d[3];
get_mi_vector(d,p_real->r.p,p[i].r.p);
// Stress tensor conribution
for (int k =0; k<3;k++)
for (int l =0;l<3;l++)
stress_tensor[k*3+l] +=p[i].f.f[k] *d[l];
// Pressure = 1/3 trace of stress tensor
// but the 1/3 is applied somewhere else.
*pressure +=(p[i].f.f[0] *d[0] +p[i].f.f[1] *d[1] +p[i].f.f[2] *d[2]);
}
}
*pressure/=0.5*time_step*time_step;
for (i=0;i<9;i++)
stress_tensor[i]/=0.5*time_step*time_step;
}
void calc_kinetic(double *ek_trans , double *ek_rot)
{
int i, c, np;
Particle *part;
double et = 0.0, er = 0.0;
for (c = 0; c < local_cells.n; c++) {
np = local_cells.cell[c]->n;
part = local_cells.cell[c]->part;
for (i = 0; i < np; i++) {
#ifdef VIRTUAL_SITES
if (ifParticleIsVirtual(&part[i])) continue;
#endif
/* kinetic energy */
et += (SQR(part[i].m.v[0]) + SQR(part[i].m.v[1]) + SQR(part[i].m.v[2]))*PMASS(part[i]);
/* rotational energy */
#ifdef ROTATION
#ifdef ROTATIONAL_INERTIA
er += SQR(part[i].m.omega[0])*part[i].p.rinertia[0] +
SQR(part[i].m.omega[1])*part[i].p.rinertia[1] +
SQR(part[i].m.omega[2])*part[i].p.rinertia[2];
#else
er += SQR(part[i].m.omega[0]) + SQR(part[i].m.omega[1]) + SQR(part[i].m.omega[2]);
#endif
#endif
}
}
MPI_Allreduce(MPI_IN_PLACE, &et, 1, MPI_DOUBLE, MPI_SUM, comm_cart);
MPI_Allreduce(MPI_IN_PLACE, &er, 1, MPI_DOUBLE, MPI_SUM, comm_cart);
et /= (2.0*time_step*time_step);
#ifdef ROTATION
er /= 2.0;
#endif
*ek_trans=et;
*ek_rot=er;
}
/* but p_com is a real particle */
void calc_mol_pos(Particle *p_com,double r_com[3]){
int i,j,mol_id;
double M=0;
double vec12[3];
Particle *p;
#ifdef VIRTUAL_SITES_DEBUG
int count=0;
#endif
for (i=0;i<3;i++){
r_com[i]=0.0;
}
mol_id=p_com->p.mol_id;
for (i=0;i<topology[mol_id].part.n;i++){
p=local_particles[topology[mol_id].part.e[i]];
#ifdef VIRTUAL_SITES_DEBUG
if (p==NULL){
char *errtxt = runtime_error(128 + 3*ES_INTEGER_SPACE);
ERROR_SPRINTF(errtxt,"Particle does not exist in calc_mol_pos! id=%i\n",topology[mol_id].part.e[i]);
return;
}
#endif
if (ifParticleIsVirtual(p)) continue;
get_mi_vector(vec12,p->r.p, p_com->r.p);
for (j=0;j<3;j++){
r_com[j] += PMASS(*p)*vec12[j];
}
M+=PMASS(*p);
#ifdef VIRTUAL_SITES_DEBUG
count++;
#endif
}
for (j=0;j<3;j++){
r_com[j] /= M;
r_com[j] += p_com->r.p[j];
}
#ifdef VIRTUAL_SITES_DEBUG
if (count!=topology[mol_id].part.n-1){
char *errtxt = runtime_error(128 + 3*ES_INTEGER_SPACE);
ERROR_SPRINTF(errtxt,"There is more than one COM in calc_mol_pos! mol_id=%i\n",mol_id);
return;
}
#endif
}
void calc_dipole_of_molecule(int mol_id,double dipole[4]){
int j,k;
Particle *p,*p_first=NULL;
double vec12[3];
dipole[0]=dipole[1]=dipole[2]=dipole[3]=0.0;
for (j=0;j<topology[mol_id].part.n;j++){
p=&partCfg[topology[mol_id].part.e[j]];
if (ifParticleIsVirtual(p)) continue;
if (p_first==NULL){
p_first=p;
}
else
{
get_mi_vector(vec12,p->r.p, p_first->r.p);
for (k=0;k<3;k++){
dipole[k] += p->p.q*vec12[k];
}
}
dipole[3]+=p->p.q;
}
}
double calc_energy_kinetic_mol(int type){
double E_kin=0;
int i;
Particle *p_com;
for (i=0;i<n_molecules;i++){
if (topology[i].type == type){
p_com=get_mol_com_particle_from_molid_cfg(i);
#ifdef VIRTUAL_SITES_DEBUG
if (p_com==NULL){
return -(i);
}
if (!ifParticleIsVirtual(p_com)){
return -(i);
}
#endif
E_kin+=PMASS(*p_com)*sqrlen(p_com->m.v);
}
}
E_kin*=0.5/time_step/time_step;
return E_kin;
}
int tclcommand_analyze_parse_and_print_check_mol(Tcl_Interp *interp,int argc, char **argv){
int j,count=0;
double dist;
char buffer[TCL_DOUBLE_SPACE];
Particle p;
updatePartCfg(WITHOUT_BONDS);
for(j=0; j<n_total_particles; j++){
if (!ifParticleIsVirtual(&partCfg[j])) continue;
get_particle_data(j,&p);
//dist=min_distance(partCfg[j].r.p,p.r.p);
unfold_position(p.r.p,p.l.i);
dist=distance(partCfg[j].r.p,p.r.p);
if (dist > 0.01){
if (count==0) Tcl_AppendResult(interp,"BEGIN Particle Missmatch: \n", (char *)NULL);
sprintf(buffer,"%i",j);
Tcl_AppendResult(interp,"Particle ",buffer, (char *)NULL);
Tcl_PrintDouble(interp,partCfg[j].r.p[0] , buffer);
Tcl_AppendResult(interp," partCfg x ",buffer, (char *)NULL);
Tcl_PrintDouble(interp,partCfg[j].r.p[1] , buffer);
Tcl_AppendResult(interp," y ",buffer, (char *)NULL);
Tcl_PrintDouble(interp,partCfg[j].r.p[2] , buffer);
Tcl_AppendResult(interp," z ",buffer, (char *)NULL);
Tcl_PrintDouble(interp,p.r.p[0] , buffer);
Tcl_AppendResult(interp," my_partCfg x ",buffer, (char *)NULL);
Tcl_PrintDouble(interp,p.r.p[1] , buffer);
Tcl_AppendResult(interp," y ",buffer, (char *)NULL);
Tcl_PrintDouble(interp,p.r.p[2] , buffer);
Tcl_AppendResult(interp," z ",buffer, (char *)NULL);
Tcl_PrintDouble(interp, dist, buffer);
Tcl_AppendResult(interp," dist ",buffer,"\n", (char *)NULL);
count++;
}
}
if (count!=0){
Tcl_AppendResult(interp,"END Particle Missmatch\n", (char *)NULL);
return(TCL_ERROR);
}
return(TCL_OK);
}
void propagate_press_box_pos_and_rescale_npt()
{
#ifdef NPT
if(integ_switch == INTEG_METHOD_NPT_ISO) {
Cell *cell;
Particle *p;
int i, j, np, c;
double scal[3]={0.,0.,0.}, L_new=0.0;
/* finalize derivation of p_inst */
finalize_p_inst_npt();
/* adjust \ref nptiso_struct::nptiso.volume; prepare pos- and vel-rescaling */
if (this_node == 0) {
nptiso.volume += nptiso.inv_piston*nptiso.p_diff*0.5*time_step;
scal[2] = SQR(box_l[nptiso.non_const_dim])/pow(nptiso.volume,2.0/nptiso.dimension);
nptiso.volume += nptiso.inv_piston*nptiso.p_diff*0.5*time_step;
if (nptiso.volume < 0.0) {
char *errtxt = runtime_error(128 + 3*TCL_DOUBLE_SPACE);
ERROR_SPRINTF(errtxt, "{015 your choice of piston=%g, dt=%g, p_diff=%g just caused the volume to become negative, decrease dt} ",
nptiso.piston,time_step,nptiso.p_diff);
nptiso.volume = box_l[0]*box_l[1]*box_l[2];
scal[2] = 1;
}
L_new = pow(nptiso.volume,1.0/nptiso.dimension);
// printf(stdout,"Lnew, %f: volume, %f: dim, %f: press, %f \n", L_new, nptiso.volume, nptiso.dimension,nptiso.p_inst );
// fflush(stdout);
scal[1] = L_new/box_l[nptiso.non_const_dim];
scal[0] = 1/scal[1];
}
MPI_Bcast(scal, 3, MPI_DOUBLE, 0, MPI_COMM_WORLD);
/* propagate positions while rescaling positions and velocities */
for (c = 0; c < local_cells.n; c++) {
cell = local_cells.cell[c]; p = cell->part; np = cell->n;
for(i = 0; i < np; i++) {
#ifdef VIRTUAL_SITES
if (ifParticleIsVirtual(&p[i])) continue;
#endif
for(j=0; j < 3; j++){
#ifdef EXTERNAL_FORCES
if (!(p[i].l.ext_flag & COORD_FIXED(j))) {
#endif
if(nptiso.geometry & nptiso.nptgeom_dir[j]) {
p[i].r.p[j] = scal[1]*(p[i].r.p[j] + scal[2]*p[i].m.v[j]);
p[i].l.p_old[j] *= scal[1];
p[i].m.v[j] *= scal[0];
} else {
p[i].r.p[j] += p[i].m.v[j];
}
#ifdef EXTERNAL_FORCES
}
#endif
}
ONEPART_TRACE(if(p[i].p.identity==check_id) fprintf(stderr,"%d: OPT:PV_1 v_new=(%.3e,%.3e,%.3e)\n",this_node,p[i].m.v[0],p[i].m.v[1],p[i].m.v[2]));
ONEPART_TRACE(if(p[i].p.identity==check_id) fprintf(stderr,"%d: OPT:PPOS p=(%.3f,%.3f,%.3f)\n",this_node,p[i].r.p[0],p[i].r.p[1],p[i].r.p[2]));
#ifdef ADDITIONAL_CHECKS
force_and_velocity_check(&p[i]);
#endif
}
}
resort_particles = 1;
/* Apply new volume to the box-length, communicate it, and account for necessary adjustments to the cell geometry */
if (this_node == 0) {
for ( i = 0 ; i < 3 ; i++ ){
if ( nptiso.geometry & nptiso.nptgeom_dir[i] ) {
box_l[i] = L_new;
} else if ( nptiso.cubic_box ) {
box_l[i] = L_new;
}
}
}
MPI_Bcast(box_l, 3, MPI_DOUBLE, 0, MPI_COMM_WORLD);
on_NpT_boxl_change();
}
/** initialize the forces for a real particle */
MDINLINE void init_local_particle_force(Particle *part)
{
#ifdef ADRESS
double new_weight;
if (ifParticleIsVirtual(part)) {
new_weight = adress_wf_vector(part->r.p);
#ifdef ADRESS_INIT
double old_weight = part->p.adress_weight;
if(new_weight>0 && old_weight==0){
double rand_cm_pos[3], rand_cm_vel[3], rand_weight, new_pos, old_pos;
int it, dim, this_mol_id=part->p.mol_id, rand_mol_id, rand_type;
int n_ats_this_mol=topology[this_mol_id].part.n, n_ats_rand_mol;
//look for a random explicit particle
rand_type=-1;
rand_weight=-1;
rand_mol_id=-1;
n_ats_rand_mol=-1;
while(rand_type != part->p.type || rand_weight != 1 || n_ats_rand_mol != n_ats_this_mol){
rand_mol_id = i_random(n_molecules);
rand_type = local_particles[(topology[rand_mol_id].part.e[0])]->p.type;
rand_weight = local_particles[(topology[rand_mol_id].part.e[0])]->p.adress_weight;
n_ats_rand_mol = topology[rand_mol_id].part.n;
if(!ifParticleIsVirtual(local_particles[(topology[rand_mol_id].part.e[0])]))
fprintf(stderr,"No virtual site found on molecule %d, with %d total molecules.\n",rand_mol_id, n_molecules);
}
//store CM position and velocity
for(dim=0;dim<3;dim++){
rand_cm_pos[dim]=local_particles[(topology[rand_mol_id].part.e[0])]->r.p[dim];
rand_cm_vel[dim]=local_particles[(topology[rand_mol_id].part.e[0])]->m.v[dim];
}
//assign new positions and velocities to the atoms
for(it=0;it<n_ats_this_mol;it++){
if (!ifParticleIsVirtual(local_particles[topology[rand_mol_id].part.e[it]])) {
for(dim=0;dim<3;dim++){
old_pos = local_particles[topology[this_mol_id].part.e[it]]->r.p[dim];
new_pos = local_particles[topology[rand_mol_id].part.e[it]]->r.p[dim]-rand_cm_pos[dim]+part->r.p[dim];
//MAKE SURE THEY ARE IN THE SAME BOX
while(new_pos-old_pos>box_l[dim]*0.5)
new_pos=new_pos-box_l[dim];
while(new_pos-old_pos<-box_l[dim]*0.5)
new_pos=new_pos+box_l[dim];
local_particles[(topology[this_mol_id].part.e[it])]->r.p[dim] = new_pos;
local_particles[(topology[this_mol_id].part.e[it])]->m.v[dim] = local_particles[(topology[rand_mol_id].part.e[it])]->m.v[dim]-rand_cm_vel[dim]+part->m.v[dim];
}
}
}
}
#endif
part->p.adress_weight=new_weight;
}
#endif
if ( thermo_switch & THERMO_LANGEVIN )
friction_thermo_langevin(part);
else {
part->f.f[0] = 0;
part->f.f[1] = 0;
part->f.f[2] = 0;
}
#ifdef EXTERNAL_FORCES
if(part->l.ext_flag & PARTICLE_EXT_FORCE) {
part->f.f[0] += part->l.ext_force[0];
part->f.f[1] += part->l.ext_force[1];
part->f.f[2] += part->l.ext_force[2];
}
#endif
#ifdef ROTATION
{
double scale;
/* set torque to zero */
part->f.torque[0] = 0;
part->f.torque[1] = 0;
part->f.torque[2] = 0;
/* and rescale quaternion, so it is exactly of unit length */
scale = sqrt( SQR(part->r.quat[0]) + SQR(part->r.quat[1]) +
SQR(part->r.quat[2]) + SQR(part->r.quat[3]));
part->r.quat[0]/= scale;
part->r.quat[1]/= scale;
part->r.quat[2]/= scale;
part->r.quat[3]/= scale;
}
#endif
#ifdef ADRESS
/* #ifdef THERMODYNAMIC_FORCE */
if(ifParticleIsVirtual(part))
if(part->p.adress_weight > 0 && part->p.adress_weight < 1)
add_thermodynamic_force(part);
/* #endif */
#endif
}