/**Incorporates mass of each particle*/
double calc_mol_gyr_radius2(Molecule mol)
{
int i, id;
double rg=0.0, M=0.0, com[3], diff_vec[3];
calc_mol_center_of_mass(mol, com);
for(i=0; i<mol.part.n; i++) {
id = mol.part.e[i];
vecsub(partCfg[id].r.p, com, diff_vec);
rg += sqrlen(diff_vec);
M += PMASS(partCfg[id]);
}
return (rg/M);
}
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;
}
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;
}
void angularmomentum(int type, double *com)
{
int i, j;
double tmp[3];
double pre_factor;
com[0]=com[1]=com[2]=0.;
updatePartCfg(WITHOUT_BONDS);
for (j=0; j<n_part; j++)
{
if (type == partCfg[j].p.type)
{
vector_product(partCfg[j].r.p,partCfg[j].m.v,tmp);
pre_factor=PMASS(partCfg[j]);
for (i=0; i<3; i++) {
com[i] += tmp[i]*pre_factor;
}
}
}
return;
}
/* This is only done for the trapped molecules to save time */
void calc_local_mol_info (IntList *local_trapped_mols)
{
int mi, i,j, mol;
Particle *p;
int np, c;
Cell *cell;
int lm;
int fixed;
/* First reset all molecule masses,forces,centers of mass*/
for ( mi = 0 ; mi < n_molecules ; mi++ ) {
topology[mi].mass = 0;
for ( i = 0 ; i < 3 ; i++) {
topology[mi].f[i] = 0.0;
topology[mi].com[i] = 0.0;
topology[mi].v[i] = 0.0;
}
}
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++) {
mol = p[i].p.mol_id;
if ( mol >= n_molecules ) {
char *errtxt = runtime_error(128 + 3*TCL_INTEGER_SPACE);
ERROR_SPRINTF(errtxt, "{ 094 can't calculate molforces no such molecule as %d }",mol);
return;
}
/* Check to see if this molecule is fixed */
fixed =0;
for(j = 0; j < 3; j++) {
#ifdef EXTERNAL_FORCES
if (topology[mol].trap_flag & COORD_FIXED(j)) fixed = 1;
if (topology[mol].noforce_flag & COORD_FIXED(j)) fixed = 1;
#endif
}
if (fixed) {
topology[mol].mass += PMASS(p[i]);
/* Unfold the particle */
unfold_position(p[i].r.p,p[i].l.i);
for ( j = 0 ; j < 3 ; j++ ) {
topology[mol].f[j] += p[i].f.f[j];
topology[mol].com[j] += p[i].r.p[j]*PMASS(p[i]);
topology[mol].v[j] += p[i].m.v[j]*PMASS(p[i]);
}
/* Fold the particle back */
fold_position(p[i].r.p,p[i].l.i);
}
}
}
/* Final normalisation of centers of mass and velocity*/
for ( lm = 0 ; lm < local_trapped_mols->n; lm++ ) {
mi = local_trapped_mols->e[lm];
for ( i = 0 ; i < 3 ; i++) {
topology[mi].com[i] = topology[mi].com[i]/(double)(topology[mi].mass);
topology[mi].v[i] = topology[mi].v[i]/(double)(topology[mi].mass);
}
}
}
void analyze_rdfchain(double r_min, double r_max, int r_bins, double **_f1, double **_f2, double **_f3) {
int i, j, ind, c_i, c_j, mon;
double bin_width, inv_bin_width, factor, r_in, r_out, bin_volume, dist, chain_mass,
*cm=NULL, *min_d=NULL, *f1=NULL, *f2=NULL, *f3=NULL;
*_f1 = f1 = (double*)Utils::realloc(f1,r_bins*sizeof(double));
*_f2 = f2 = (double*)Utils::realloc(f2,r_bins*sizeof(double));
*_f3 = f3 = (double*)Utils::realloc(f3,r_bins*sizeof(double));
cm = (double*)Utils::realloc(cm,(chain_n_chains*3)*sizeof(double));
min_d = (double*)Utils::realloc(min_d,(chain_n_chains*chain_n_chains)*sizeof(double));
for(i=0; i<r_bins; i++) {
f1[i] = f2[i] = f3[i] = 0.0;
}
bin_width = (r_max-r_min) / (double)r_bins;
inv_bin_width = 1.0 / bin_width;
for(c_i=0; c_i<chain_n_chains; c_i++) {
cm[3*c_i] = cm[3*c_i+1] = cm[3*c_i+2] = 0.0;
for(c_j=(c_i+1); c_j<chain_n_chains; c_j++) {
min_d[c_i*chain_n_chains+c_j] = box_l[0] + box_l[1] + box_l[2];
}
}
for(c_i=0; c_i<chain_n_chains; c_i++) {
for(i=0; i<chain_length; i++) {
mon = chain_start + c_i*chain_length + i;
cm[3*c_i]+= partCfg[mon].r.p[0]*PMASS(partCfg[mon]);
cm[3*c_i+1]+= partCfg[mon].r.p[1]*PMASS(partCfg[mon]);
cm[3*c_i+2]+= partCfg[mon].r.p[2]*PMASS(partCfg[mon]);
for(c_j=(c_i+1); c_j<chain_n_chains; c_j++) {
for(j=0; j<chain_length; j++) {
dist = min_distance(partCfg[mon].r.p, partCfg[chain_start + c_j*chain_length+j].r.p);
if ((dist > r_min) && (dist < r_max)) {
ind = (int) ( (dist - r_min)*inv_bin_width );
f1[ind]+= 1.0;
}
if (dist<min_d[c_i*chain_n_chains+c_j]) min_d[c_i*chain_n_chains+c_j] = dist;
}
}
}
}
chain_mass = 0;
for(i=0; i<chain_length; i++) chain_mass+= PMASS(partCfg[i]);
for(c_i=0; c_i<chain_n_chains; c_i++) {
cm[3*c_i]/= chain_mass;
cm[3*c_i+1]/= chain_mass;
cm[3*c_i+2]/= chain_mass;
for(c_j=(c_i+1); c_j<chain_n_chains; c_j++) {
dist = min_d[c_i*chain_n_chains+c_j];
if ((dist > r_min) && (dist < r_max)) {
ind = (int) ( (dist - r_min)*inv_bin_width );
f3[ind]+= 1.0;
}
}
}
for(c_i=0; c_i<chain_n_chains; c_i++) {
for(c_j=(c_i+1); c_j<chain_n_chains; c_j++) {
dist = min_distance(&cm[3*c_i],&cm[3*c_j]);
if ((dist > r_min) && (dist < r_max)) {
ind = (int) ( (dist - r_min)*inv_bin_width );
f2[ind]+= 1.0;
}
}
}
/* normalization */
factor = box_l[0]*box_l[1]*box_l[2] *1.5/PI/(chain_n_chains*(chain_n_chains-1));
for(i=0; i<r_bins; i++) {
r_in = i*bin_width + r_min;
r_out = r_in + bin_width;
bin_volume = r_out*r_out*r_out - r_in*r_in*r_in;
f1[i] *= factor / (bin_volume * chain_length*chain_length);
f2[i] *= factor / bin_volume;
f3[i] *= factor / bin_volume;
}
}
/** Calculate Random Force and Friction Force acting between particle
p1 and p2 and add them to their forces. */
inline void add_dpd_thermo_pair_force(Particle *p1, Particle *p2, double d[3], double dist, double dist2)
{
extern double dpd_gamma,dpd_pref1, dpd_pref2,dpd_r_cut,dpd_r_cut_inv;
extern int dpd_wf;
#ifdef TRANS_DPD
extern double dpd_tgamma, dpd_pref3, dpd_pref4,dpd_tr_cut,dpd_tr_cut_inv;
extern int dpd_twf;
#endif
int j;
// velocity difference between p1 and p2
double vel12_dot_d12=0.0;
// inverse distance
double dist_inv;
// weighting functions for friction and random force
double omega,omega2;// omega = w_R/dist
double friction, noise;
//Projection martix
#ifdef TRANS_DPD
int i;
double P_times_dist_sqr[3][3]={{dist2,0,0},{0,dist2,0},{0,0,dist2}},noise_vec[3];
double f_D[3],f_R[3];
#endif
double tmp;
#ifdef DPD_MASS
double massf;
#endif
#ifdef LEES_EDWARDS
if( le_chatterjee_test_pair(p1, p2) == 0 ) return;
#endif
#ifdef EXTERNAL_FORCES
// if any of the two particles is fixed in some direction then
// do not add any dissipative or stochastic dpd force part
// because dissipation-fluctuation theorem is violated
if (dpd_ignore_fixed_particles)
if ( (p1->l.ext_flag | p2->l.ext_flag) & COORDS_FIX_MASK) return;
#endif
#ifdef VIRTUAL_SITES
if (ifParticleIsVirtual(p1) || ifParticleIsVirtual(p2)) return;
#endif
#ifdef DPD_MASS_RED
massf=2*PMASS(*p1)*PMASS(*p2)/(PMASS(*p1)+PMASS(*p2));
#endif
#ifdef DPD_MASS_LIN
massf=0.5*(PMASS(*p1)+PMASS(*p2));
#endif
dist_inv = 1.0/dist;
if((dist < dpd_r_cut)&&(dpd_gamma > 0.0)) {
if ( dpd_wf == 1 ) //w_R=1
{
omega = dist_inv;
}
else //w_R=(1-r/r_c)
{
omega = dist_inv- dpd_r_cut_inv;
}
#ifdef DPD_MASS
omega*=sqrt(massf);
#endif
omega2 = SQR(omega);
//DPD part
// friction force prefactor
for(j=0; j<3; j++) vel12_dot_d12 += (p1->m.v[j] - p2->m.v[j]) * d[j];
friction = dpd_pref1 * omega2 * vel12_dot_d12;
// random force prefactor
noise = dpd_pref2 * omega * (d_random()-0.5);
for(j=0; j<3; j++) {
p1->f.f[j] += ( tmp = (noise - friction)*d[j] );
p2->f.f[j] -= tmp;
}
}
#ifdef TRANS_DPD
//DPD2 part
if ((dist < dpd_tr_cut)&&(dpd_tgamma > 0.0)){
if ( dpd_twf == 1 )
{
omega = dist_inv;
}
else
{
omega = dist_inv- dpd_tr_cut_inv;
}
#ifdef DPD_MASS
omega*=sqrt(massf);
#endif
omega2 = SQR(omega);
for (i=0;i<3;i++){
//noise vector
noise_vec[i]=d_random()-0.5;
// Projection Matrix
for (j=0;j<3;j++){
P_times_dist_sqr[i][j]-=d[i]*d[j];
}
}
for (i=0;i<3;i++){
//Damping force
f_D[i]=0;
//Random force
f_R[i]=0;
for (j=0;j<3;j++){
f_D[i]+=P_times_dist_sqr[i][j]*(p1->m.v[j] - p2->m.v[j]);
f_R[i]+=P_times_dist_sqr[i][j]*noise_vec[j];
}
//NOTE: velocity are scaled with time_step
f_D[i]*=dpd_pref3*omega2;
//NOTE: noise force scales with 1/sqrt(time_step
f_R[i]*=dpd_pref4*omega*dist_inv;
}
for(j=0; j<3; j++) {
tmp=f_R[j]-f_D[j];
p1->f.f[j] += tmp;
p2->f.f[j] -= tmp;
}
}
#endif
}
inline void add_inter_dpd_pair_force(Particle *p1, Particle *p2, IA_parameters *ia_params,
double d[3], double dist, double dist2)
{
int j;
// velocity difference between p1 and p2
double vel12_dot_d12=0.0;
// inverse distance
double dist_inv;
// weighting functions for friction and random force
double omega,omega2;// omega = w_R/dist
double friction, noise;
//Projection martix
int i;
double P_times_dist_sqr[3][3]={{0,0,0},{0,0,0},{0,0,0}},noise_vec[3];
double f_D[3],f_R[3];
double tmp;
#ifdef DPD_MASS
double massf;
#endif
#ifdef EXTERNAL_FORCES
// if any of the two particles is fixed in some direction then
// do not add any dissipative or stochastic dpd force part
// because dissipation-fluctuation theorem is violated
if (dpd_ignore_fixed_particles)
if ( (p1->l.ext_flag | p2->l.ext_flag) & COORDS_FIX_MASK) return;
#endif
#ifdef DPD_MASS_RED
massf=2*PMASS(*p1)*PMASS(*p2)/(PMASS(*p1)+PMASS(*p2));
#endif
#ifdef DPD_MASS_LIN
massf=0.5*(PMASS(*p1)+PMASS(*p2));
#endif
P_times_dist_sqr[0][0]=dist2;
P_times_dist_sqr[1][1]=dist2;
P_times_dist_sqr[2][2]=dist2;
dist_inv = 1.0/dist;
if((dist < ia_params->dpd_r_cut)&&(ia_params->dpd_gamma > 0.0)) {
if ( dpd_wf == 1 )
{
omega = dist_inv;
}
else
{
omega = dist_inv - 1.0/ia_params->dpd_r_cut;
}
#ifdef DPD_MASS
omega*=sqrt(massf);
#endif
omega2 = SQR(omega);
//DPD part
// friction force prefactor
for(j=0; j<3; j++) vel12_dot_d12 += (p1->m.v[j] - p2->m.v[j]) * d[j];
friction = ia_params->dpd_pref1 * omega2 * vel12_dot_d12;
// random force prefactor
noise = ia_params->dpd_pref2 * omega * (d_random()-0.5);
for(j=0; j<3; j++) {
p1->f.f[j] += ( tmp = (noise - friction)*d[j] );
p2->f.f[j] -= tmp;
}
}
//DPD2 part
if ((dist < ia_params->dpd_tr_cut)&&(ia_params->dpd_tgamma > 0.0)){
if ( ia_params->dpd_twf == 1 )
{
omega = dist_inv;
}
else
{
omega = dist_inv- 1.0/ia_params->dpd_tr_cut;
}
#ifdef DPD_MASS
omega*=sqrt(massf);
#endif
omega2 = SQR(omega);
for (i=0;i<3;i++){
//noise vector
noise_vec[i]=d_random()-0.5;
// Projection Matrix
for (j=0;j<3;j++){
P_times_dist_sqr[i][j]-=d[i]*d[j];
}
}
for (i=0;i<3;i++){
//Damping force
f_D[i]=0;
//Random force
f_R[i]=0;
for (j=0;j<3;j++){
f_D[i]+=P_times_dist_sqr[i][j]*(p1->m.v[j] - p2->m.v[j]);
f_R[i]+=P_times_dist_sqr[i][j]*noise_vec[j];
}
//NOTE: velocity are scaled with time_step
f_D[i]*=ia_params->dpd_pref3*omega2;
//NOTE: noise force scales with 1/sqrt(time_step
f_R[i]*=ia_params->dpd_pref4*omega*dist_inv;
}
for(j=0; j<3; j++) {
tmp=f_R[j]-f_D[j];
p1->f.f[j] += tmp;
p2->f.f[j] -= tmp;
}
}
}