/* monte carlo step of ghmc - evaluation stage */
void ghmc_mc()
{
INTEG_TRACE(fprintf(stderr,"%d: ghmc_mc:\n",this_node));
double boltzmann;
int ekin_update_flag = 0;
hamiltonian_calc(ekin_update_flag);
//make MC decision only on the master
if (this_node==0) {
ghmcdata.att++;
//metropolis algorithm
boltzmann = ghmcdata.hmlt_new - ghmcdata.hmlt_old;
if (boltzmann < 0)
boltzmann = 1.0;
else if (boltzmann > 30)
boltzmann = 0.0;
else
boltzmann = exp(-beta*boltzmann);
//fprintf(stderr,"old hamiltonian : %f, new hamiltonian: % f, boltzmann factor: %f\n",ghmcdata.hmlt_old,ghmcdata.hmlt_new,boltzmann);
if ( d_random() < boltzmann) {
ghmcdata.acc++;
ghmc_mc_res = GHMC_MOVE_ACCEPT;
} else {
ghmc_mc_res = GHMC_MOVE_REJECT;
}
}
//let all nodes know about the MC decision result
mpi_bcast_parameter(FIELD_GHMC_RES);
if (ghmc_mc_res == GHMC_MOVE_ACCEPT) {
save_last_state();
//fprintf(stderr,"%d: mc move accepted\n",this_node);
} else {
load_last_state();
//fprintf(stderr,"%d: mc move rejected\n",this_node);
//if the move is rejected we might need to resort particles according to the loaded configurations
cells_resort_particles(CELL_GLOBAL_EXCHANGE);
invalidate_obs();
if (ghmc_mflip == GHMC_MFLIP_ON) {
momentum_flip();
} else if (ghmc_mflip == GHMC_MFLIP_RAND) {
if (d_random() < 0.5) momentum_flip();
}
}
//fprintf(stderr,"%d: temp after mc: %f\n",this_node,calc_local_temp());
}
/** Computes the FENE pair force and adds this
force to the particle forces (see \ref interaction_data.cpp).
@param p1 Pointer to first particle.
@param p2 Pointer to second/middle particle.
@param iaparams bond type number of the angle interaction (see \ref interaction_data.cpp).
@param dx particle distance vector
@param force returns force of particle 1
@return true if the bond is broken
*/
inline int calc_fene_pair_force(Particle *p1, Particle *p2, Bonded_ia_parameters *iaparams, double dx[3], double force[3])
{
int i;
double fac, dr, len2, len;
len2 = sqrlen(dx);
len = sqrt(len2);
dr = len - iaparams->p.fene.r0;
if(dr >= iaparams->p.fene.drmax)
return 1;
fac = -iaparams->p.fene.k * dr / ((1.0 - dr*dr*iaparams->p.fene.drmax2i));
if (fabs(dr) > ROUND_ERROR_PREC) {
if(len > ROUND_ERROR_PREC) { /* Regular case */
fac /= len ;
} else { /* dx[] == 0: the force is undefined. Let's use a random direction */
for(i=0;i<3;i++) dx[i] = d_random()-0.5;
fac /= sqrt(sqrlen(dx));
}
} else {
fac = 0.0;
}
FENE_TRACE(if(fac > 50) fprintf(stderr,"WARNING: FENE force factor between Pair (%d,%d) large: %f at distance %f\n", p1->p.identity,p2->p.identity,fac,sqrt(len2)) );
for(i=0;i<3;i++)
force[i] = fac*dx[i];
ONEPART_TRACE(if(p1->p.identity==check_id) fprintf(stderr,"%d: OPT: FENE f = (%.3e,%.3e,%.3e) with part id=%d at dist %f fac %.3e\n",this_node,p1->f.f[0],p1->f.f[1],p1->f.f[2],p2->p.identity,sqrt(len2),fac));
ONEPART_TRACE(if(p2->p.identity==check_id) fprintf(stderr,"%d: OPT: FENE f = (%.3e,%.3e,%.3e) with part id=%d at dist %f fac %.3e\n",this_node,p2->f.f[0],p2->f.f[1],p2->f.f[2],p1->p.identity,sqrt(len2),fac));
return 0;
}
/** Computes the QUARTIC pair force and adds this
force to the particle forces (see \ref interaction_data.cpp).
@param p1 Pointer to first particle.
@param p2 Pointer to second/middle particle.
@param iaparams bond type number of the angle interaction (see \ref interaction_data.cpp).
@param dx particle distance vector
@param force returns force of particle 1
@return 0.
*/
inline int calc_quartic_pair_force(Particle *p1, Particle *p2, Bonded_ia_parameters *iaparams, double dx[3], double force[3])
{
int i;
double fac;
double dist2 = sqrlen(dx);
double dist = sqrt(dist2);
double dr;
if ((iaparams->p.quartic.r_cut > 0.0) &&
(dist > iaparams->p.quartic.r_cut))
return 1;
dr = dist - iaparams->p.quartic.r;
if (fabs(dr) > ROUND_ERROR_PREC) {
if(dist>ROUND_ERROR_PREC) { /* Regular case */
fac = dr / dist;
} else { /* dx[] == 0: the force is undefined. Let's use a random direction */
for(i=0;i<3;i++) dx[i] = d_random()-0.5;
fac = dr / sqrt(sqrlen(dx));
}
} else {
fac=0;
}
for(i=0;i<3;i++)
force[i] = -(iaparams->p.quartic.k0 + iaparams->p.quartic.k1 * dr * dr ) * fac*dx[i];
ONEPART_TRACE(if(p1->p.identity==check_id) fprintf(stderr,"%d: OPT: QUARTIC f = (%.3e,%.3e,%.3e) with part id=%d at dist %f fac %.3e\n",this_node,p1->f.f[0],p1->f.f[1],p1->f.f[2],p2->p.identity,dist2,fac));
ONEPART_TRACE(if(p2->p.identity==check_id) fprintf(stderr,"%d: OPT: QUARTIC f = (%.3e,%.3e,%.3e) with part id=%d at dist %f fac %.3e\n",this_node,p2->f.f[0],p2->f.f[1],p2->f.f[2],p1->p.identity,dist2,fac));
return 0;
}
double maxwell_velocitiesC(int part_id, int N_T) {
double v[3], v_av[3],uniran[2];
int i;
int flag=1;
uniran[0]=d_random();
uniran[1]=d_random();
v_av[0] = v_av[1] = v_av[2] = 0.0;
for (i=part_id; i < part_id+N_T; i++) {
if(flag == 1 ) {
v[0] = pow((-2. * log(uniran[0])),0.5) * cos (2. * PI * uniran[1]) * time_step;
v[1] = pow((-2. * log(uniran[1])),0.5) * sin (2. * PI * uniran[0]) * time_step;
uniran[0]=d_random();
uniran[1]=d_random();
v[2] = pow((-2. * log(uniran[0])),0.5) * cos (2. * PI * uniran[1]) * time_step;
flag = 0;
} else {
v[0] = pow((-2. * log(uniran[1])),0.5) * sin (2. * PI * uniran[0]) * time_step;
uniran[0]=d_random();
uniran[1]=d_random();
v[1] = pow((-2. * log(uniran[0])),0.5) * cos (2. * PI * uniran[1]) * time_step;
v[2] = pow((-2. * log(uniran[1])),0.5) * sin (2. * PI * uniran[0]) * time_step;
flag = 1;
}
//printf("%f \n %f \n %f \n",v[0],v[1],v[2]);
v_av[0]+=v[0]; v_av[1]+=v[1]; v_av[2]+=v[2];
if (set_particle_v(i, v)==ES_ERROR) {
fprintf(stderr, "INTERNAL ERROR: failed upon setting one of the velocities in Espresso (current average: %f)!\n",sqrt(SQR(v_av[0])+SQR(v_av[1])+SQR(v_av[2])));
fprintf(stderr, "Aborting...\n"); errexit();
}
}
// note that time_step == -1, as long as it is not yet set
return ( sqrt(SQR(v_av[0])+SQR(v_av[1])+SQR(v_av[2])) / fabs(time_step) );
}
/** Generator for Gaussian random numbers. Uses the Box-Muller
* transformation to generate two Gaussian random numbers from two
* uniform random numbers.
*
* @return Gaussian random number.
*
*/
inline double gaussian_random(void) {
double x1, x2, r2, fac;
static int calc_new = 1;
static double save;
/* On every second call two gaussian random numbers are calculated
via the Box-Muller transformation. One is returned as the result
and the second one is stored for use on the next call.
*/
if (calc_new) {
/* draw two uniform random numbers in the unit circle */
do {
x1 = 2.0*d_random()-1.0;
x2 = 2.0*d_random()-1.0;
r2 = x1*x1 + x2*x2;
} while (r2 >= 1.0 || r2 == 0.0);
/* perform Box-Muller transformation */
fac = sqrt(-2.0*log(r2)/r2);
/* save one number for later use */
save = x1*fac;
calc_new = 0;
/* return the second number */
return x2*fac;
} else {
calc_new = 1;
/* return the stored gaussian random number */
return save;
}
}
double velocitiesC(double v_max, int part_id, int N_T) {
double v[3], v_av[3];
int i;
v_av[0] = v_av[1] = v_av[2] = 0.0;
for (i=part_id; i < part_id+N_T; i++) {
do {
v[0] = v_max * 2.*(d_random()-.5) * time_step;
v[1] = v_max * 2.*(d_random()-.5) * time_step;
v[2] = v_max * 2.*(d_random()-.5) * time_step;
// note that time_step == -1, as long as it is not yet set
} while ( sqrt(SQR(v[0])+SQR(v[1])+SQR(v[2])) > v_max * fabs(time_step));
v_av[0]+=v[0]; v_av[1]+=v[1]; v_av[2]+=v[2];
if (set_particle_v(i, v)==ES_ERROR) {
fprintf(stderr, "INTERNAL ERROR: failed upon setting one of the velocities in Espresso (current average: %f)!\n",
sqrt(SQR(v_av[0])+SQR(v_av[1])+SQR(v_av[2])));
fprintf(stderr, "Aborting...\n"); errexit();
}
}
// note that time_step == -1, as long as it is not yet set
return ( sqrt(SQR(v_av[0])+SQR(v_av[1])+SQR(v_av[2])) / fabs(time_step) );
}
int counterionsC(int N_CI, int part_id, int mode, double shield, int max_try, double val_CI, int type_CI) {
int n, cnt1,max_cnt;
double pos[3];
cnt1 = max_cnt = 0;
for (n=0; n<N_CI; n++) {
for (cnt1=0; cnt1<max_try; cnt1++) {
pos[0]=box_l[0]*d_random();
pos[1]=box_l[1]*d_random();
pos[2]=box_l[2]*d_random();
if ((mode!=0) || (collision(pos, shield, 0, NULL)==0)) break;
POLY_TRACE(printf("c"); fflush(NULL));
}
if (cnt1 >= max_try) return (-1);
if (place_particle(part_id, pos)==ES_PART_ERROR) return (-3);
if (set_particle_q(part_id, val_CI)==ES_ERROR) return (-3);
if (set_particle_type(part_id, type_CI)==ES_ERROR) return (-3);
part_id++; max_cnt=imax(cnt1, max_cnt);
POLY_TRACE(printf("C"); fflush(NULL));
}
POLY_TRACE(printf(" %d->%d \n",cnt1,max_cnt));
if (cnt1 >= max_try) return(-1);
return(imax(max_cnt,cnt1));
}
/** Computes the HARMONIC pair force and adds this
force to the particle forces (see \ref interaction_data.cpp).
@param p1 Pointer to first particle.
@param p2 Pointer to second/middle particle.
@param iaparams bond type number of the angle interaction (see \ref interaction_data.cpp).
@param dx particle distance vector
@param force returns force of particle 1
@return 0.
*/
inline int calc_harmonic_pair_force(Particle *p1, Particle *p2, Bonded_ia_parameters *iaparams, double dx[3], double force[3])
{
int i;
double fac;
double dist2 = sqrlen(dx);
double dist = sqrt(dist2);
double dr;
if ((iaparams->p.harmonic.r_cut > 0.0) &&
(dist > iaparams->p.harmonic.r_cut))
return 1;
dr = dist - iaparams->p.harmonic.r;
fac = -iaparams->p.harmonic.k * dr;
if (fabs(dr) > ROUND_ERROR_PREC) {
if(dist>ROUND_ERROR_PREC) { /* Regular case */
fac /= dist;
} else { /* dx[] == 0: the force is undefined. Let's use a random direction */
for(i=0;i<3;i++) dx[i] = d_random()-0.5;
fac /= sqrt(sqrlen(dx));
}
} else {
fac=0;
}
for(i=0;i<3;i++)
force[i] = fac*dx[i];
ONEPART_TRACE(if(p1->p.identity==check_id) fprintf(stderr,"%d: OPT: HARMONIC f = (%.3e,%.3e,%.3e) with part id=%d at dist %f fac %.3e\n",this_node,p1->f.f[0],p1->f.f[1],p1->f.f[2],p2->p.identity,dist2,fac));
ONEPART_TRACE(if(p2->p.identity==check_id) fprintf(stderr,"%d: OPT: HARMONIC f = (%.3e,%.3e,%.3e) with part id=%d at dist %f fac %.3e\n",this_node,p2->f.f[0],p2->f.f[1],p2->f.f[2],p1->p.identity,dist2,fac));
#ifdef CONFIGTEMP
extern double configtemp[2];
int numfac = 0;
if (p1->p.configtemp) numfac+=1;
if (p2->p.configtemp) numfac+=1;
configtemp[0] += numfac*SQR(iaparams->p.harmonic.k * dr);
configtemp[1] -= numfac*iaparams->p.harmonic.k*(3-2.*iaparams->p.harmonic.r/dist);
#endif
return 0;
}
/** Implementation of the tcl-command
t_random [{ int \<n\> | seed [\<seed(0)\> ... \<seed(n_nodes-1)\>] | stat [status-list] }]
<ul>
<li> Without further arguments, it returns a random double between 0 and 1.
<li> If 'int \<n\>' is given, it returns a random integer between 0 and n-1.
<li> If 'seed'/'stat' is given without further arguments, it returns a tcl-list with
the current seeds/status of the n_nodes active nodes; otherwise it issues the
given parameters as the new seeds/status to the respective nodes.
</ul>
*/
int tclcommand_t_random (ClientData data, Tcl_Interp *interp, int argc, char **argv) {
char buffer[100 + TCL_DOUBLE_SPACE + 3*TCL_INTEGER_SPACE];
if (argc == 1) { /* 't_random' */
sprintf(buffer, "%f", d_random());
Tcl_AppendResult(interp, buffer, (char *) NULL); return (TCL_OK);
}
/* argc > 1 */
argc--; argv++;
if ( ARG_IS_S(0,"int") ) /* 't_random int <n>' */
{
if(argc < 2)
{
Tcl_AppendResult(interp, "\nWrong # of args: Usage: 't_random int <n>'", (char *) NULL);
return (TCL_ERROR);
}
else
{
int i_max;
if( !ARG_IS_I(1,i_max) )
{
Tcl_AppendResult(interp, "\nWrong type: Usage: 't_random int <n>'", (char *) NULL);
return (TCL_ERROR);
}
sprintf(buffer, "%d", i_random(i_max));
Tcl_AppendResult(interp, buffer, (char *) NULL);
return (TCL_OK);
}
}
else if ( ARG_IS_S(0,"stat") ) {
if(argc == 1) {
Tcl_AppendResult(interp, Random::mpi_random_get_stat().c_str(), nullptr);
return TCL_OK;
} else {
auto error_msg = [interp]() {
Tcl_AppendResult(interp, "\nWrong # of args: Usage: 't_random stat \"<state(1)> ... <state(n_nodes*625)>\"'", (char *) NULL);
};
if(argc != 2) {
error_msg();
return TCL_ERROR;
}
std::vector<std::string> states(n_nodes);
std::istringstream iss(argv[1]);
std::string tmp;
/** Argument counter to check that the caller provided enough numbers. */
int n_args = 0;
for(int node = 0; (node < n_nodes) && std::getline(iss, tmp, ' '); node++) {
n_args++;
/** First one is handled different, because of the space */
states[node] = tmp;
for(int i = 0; (i < 624) && std::getline(iss, tmp, ' '); i++) {
n_args++;
states[node].append(" ");
states[node].append(tmp);
}
}
if(n_args == n_nodes*625) {
Random::mpi_random_set_stat(states);
return TCL_OK;
}
else {
error_msg();
return TCL_ERROR;
}
}
}
else if ( ARG_IS_S(0,"seed") ) /* 't_random seed [<seed(0)> ... <seed(n_nodes-1)>]' */
{
std::vector<int> seeds(n_nodes);
if ((argc > 1) && (argc < n_nodes+1)) /* Fewer seeds than nodes */
{
sprintf(buffer, "Wrong # of args (%d)! Usage: 't_random seed [<seed(0)> ... <seed(%d)>]'", argc,n_nodes-1);
Tcl_AppendResult(interp, buffer, (char *)NULL);
return (TCL_ERROR);
}
if (argc <= 1)
{
std::iota(seeds.begin(), seeds.end(), 1);
for(auto &seed: seeds)
{
sprintf(buffer, "%d ", seed);
Tcl_AppendResult(interp, buffer, (char *) NULL);
}
}
else /* Get seeds for different nodes */
{
for (int i = 0; i < n_nodes; i++) {
if( !ARG_IS_I(i+1,seeds[i]) ) {
sprintf(buffer, "\nWrong type for seed %d:\nUsage: 't_random seed [<seed(0)> ... <seed(%d)>]'", i+1 ,n_nodes-1);
Tcl_AppendResult(interp, buffer, (char *)NULL);
return (TCL_ERROR);
}
}
}
#ifdef RANDOM_TRACE
printf("Got ");
for(int i=0;i<n_nodes;i++)
printf("%d ",seeds[i]);
printf("as new seeds.\n");
#endif
Random::mpi_random_seed(n_nodes,seeds);
return(TCL_OK);
}
/* else */
sprintf(buffer, "Usage: 't_random [{ int <n> | seed [<seed(0)> ... <seed(%d)>] }]'",n_nodes-1);
Tcl_AppendResult(interp, "Unknown argument '",argv[0],"' requested!\n",buffer, (char *)NULL);
return (TCL_ERROR);
}
inline int calc_drude_forces(Particle *p1, Particle *p2, Bonded_ia_parameters *iaparams, double dx[3], double force1[3], double force2[3])
{
int dummy,i;
double dist2 = sqrlen(dx);
double dist = sqrt(dist2);
if ((iaparams->p.drude.r_cut > 0.0) && (dist > iaparams->p.drude.r_cut))
return 1;
double force_harmonic[3] = {0., 0., 0.};
double force_subt_elec[3] = {0., 0., 0.};
double force_lv_com[3] = {0., 0., 0.};
double force_lv_dist[3] = {0., 0., 0.};
double chgfac = p1->p.q*p2->p.q;
double fac_harmonic = -iaparams->p.drude.k;
double gamma_c = iaparams->p.drude.gamma_core;
double gamma_d = iaparams->p.drude.gamma_drude;
double temp_c = iaparams->p.drude.temp_core;
double temp_d = iaparams->p.drude.temp_drude;
double mass_c = p1->p.mass;
double mass_d = p2->p.mass;
double mass_tot = mass_d + mass_c;
double mass_tot_inv = 1.0 / mass_tot;
double mass_red = mass_d * mass_c / mass_tot;
double mass_red_inv = 1.0 / mass_red;
//double rnd_c[3] = { (d_random()-0.5), (d_random()-0.5), (d_random()-0.5) };
//double rnd_d[3] = { (d_random()-0.5), (d_random()-0.5), (d_random()-0.5) };
for (i=0;i<3;i++) {
double com_vel = mass_tot_inv * (mass_c * p1->m.v[i] + mass_d * p2->m.v[i]);
//force_lv_com[i] = -gamma_c / time_step * com_vel + sqrt(24.0 * gamma_c / time_step * temp_c) * (d_random()-0.5);
force_lv_com[i] = -gamma_c / time_step * com_vel + sqrt(2.0 * gamma_c / time_step * temp_c) * gaussian_random();
double dist_vel = p2->m.v[i] - p1->m.v[i];
//force_lv_dist[i] = -gamma_d / time_step * dist_vel + sqrt(24.0 * gamma_d / time_step * temp_d) * (d_random()-0.5);
force_lv_dist[i] = -gamma_d / time_step * dist_vel + sqrt(2.0 * gamma_d / time_step * temp_d) * gaussian_random();
}
/* Apply forces:
-Harmonic bond
-Langevin thermostat on distance core-drude and com in lab coords result in cross terms for velocities and rnd kicks */
if (dist<ROUND_ERROR_PREC) { /* dx[] == 0: the force is undefined. Let's use a random direction and no spring */
for(i=0;i<3;i++) {
dx[i] = d_random()-0.5;
}
dist2 = sqrlen(dx);
dist = sqrt(dist2);
fac_harmonic = 0;
fprintf(stderr,"dist<ROUND_ERROR_PREC");
}
for (i=0;i<3;i++) {
force_harmonic[i] = fac_harmonic*dx[i];
force1[i] = mass_c * mass_tot_inv * force_lv_com[i] - force_lv_dist[i] + force_harmonic[i]; //Core
force2[i] = mass_d * mass_tot_inv * force_lv_com[i] + force_lv_dist[i] - force_harmonic[i]; //Drude
//force_subt_elec[i] = -coulomb.prefactor * chgfac * dx[i] / dist / dist2;
//force1[i] = mass_c * mass_tot_inv * force_lv_com[i] - force_lv_dist[i] + force_harmonic[i] + force_subt_elec[i]; //Core
//force2[i] = mass_d * mass_tot_inv * force_lv_com[i] + force_lv_dist[i] - force_harmonic[i] - force_subt_elec[i]; //Drude
//force1[i] = force_com[i] + force_harmonic[i] + force_subt_elec[i]; //Core
//force2[i] = force_com[i] - force_harmonic[i] - force_subt_elec[i]; //Drude
}
//fprintf(stderr,"Core Tot: %g %g %g\n", force1[0],force1[1],force1[2]);
//fprintf(stderr,"Drude Tot: %g %g %g\n", force2[0],force2[1],force2[2]);
/*
fprintf(stderr,"\ndx: %g %g %g\n", dx[0],dx[1],dx[2]);
fprintf(stderr,"dv: %g %g %g\n", p2->m.v[0] - p1->m.v[0],p2->m.v[1] - p1->m.v[1],p2->m.v[2] - p1->m.v[2]);
fprintf(stderr,"Harmonic: %g %g %g\n", force_harmonic[0],force_harmonic[1],force_harmonic[2]);
fprintf(stderr,"Subt_elec: %g %g %g\n", force_subt_elec[0],force_subt_elec[1],force_subt_elec[2]);
fprintf(stderr,"Dist: %g %g %g\n", force_lv_dist[0],force_lv_dist[1],force_lv_dist[2]);
fprintf(stderr,"Com: %g %g %g\n", force_lv_com[0],force_lv_com[1],force_lv_com[2]);
fprintf(stderr,"Core Tot: %g %g %g\n", force1[0],force1[1],force1[2]);
fprintf(stderr,"Drude Tot: %g %g %g\n", force2[0],force2[1],force2[2]);
*/
ONEPART_TRACE(if(p1->p.identity==check_id) fprintf(stderr,"%d: OPT: DRUDE f = (%.3e,%.3e,%.3e)\n",this_node,p1->f.f[0]+force1[0],p1->f.f[1]+force1[1],p1->f.f[2]+force1[2]));
ONEPART_TRACE(if(p2->p.identity==check_id) fprintf(stderr,"%d: OPT: DRUDE f = (%.3e,%.3e,%.3e)\n",this_node,p2->f.f[0]+force2[0],p2->f.f[1]+force2[1],p2->f.f[2]+force2[2]));
return 0;
}
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;
}
}
}
void integrate_reaction() {
int c, np, n, i;
Particle * p1, *p2, **pairs;
Cell * cell;
double dist2, vec21[3], rand;
if(reaction.rate > 0) {
int reactants = 0, products = 0;
int tot_reactants = 0, tot_products = 0;
double ratexp, back_ratexp;
ratexp = exp(-time_step*reaction.rate);
on_observable_calc();
for (c = 0; c < local_cells.n; c++) {
/* Loop cell neighbors */
for (n = 0; n < dd.cell_inter[c].n_neighbors; n++) {
pairs = dd.cell_inter[c].nList[n].vList.pair;
np = dd.cell_inter[c].nList[n].vList.n;
/* verlet list loop */
for(i = 0; i < 2 * np; i += 2) {
p1 = pairs[i]; //pointer to particle 1
p2 = pairs[i+1]; //pointer to particle 2
if( (p1->p.type == reaction.reactant_type && p2->p.type == reaction.catalyzer_type) || (p2->p.type == reaction.reactant_type && p1->p.type == reaction.catalyzer_type) ) {
get_mi_vector(vec21, p1->r.p, p2->r.p);
dist2 = sqrlen(vec21);
if(dist2 < reaction.range * reaction.range) {
rand = d_random();
if(rand > ratexp) {
if(p1->p.type == reaction.reactant_type) {
p1->p.type = reaction.product_type;
}
else {
p2->p.type = reaction.product_type;
}
}
}
}
}
}
}
if (reaction.back_rate < 0) { // we have to determine it dynamically
/* we count now how many reactants and products are in the sim box */
for (c = 0; c < local_cells.n; c++) {
cell = local_cells.cell[c];
p1 = cell->part;
np = cell->n;
for(i = 0; i < np; i++) {
if(p1[i].p.type == reaction.reactant_type)
reactants++;
else if(p1[i].p.type == reaction.product_type)
products++;
}
}
MPI_Allreduce(&reactants, &tot_reactants, 1, MPI_INT, MPI_SUM, comm_cart);
MPI_Allreduce(&products, &tot_products, 1, MPI_INT, MPI_SUM, comm_cart);
back_ratexp = ratexp * tot_reactants / tot_products ; //with this the asymptotic ratio reactant/product becomes 1/1 and the catalyzer volume only determines the time that it takes to reach this
}
else { //use the back reaction rate supplied by the user
back_ratexp = exp(-time_step*reaction.back_rate);
}
if(back_ratexp < 1 ) {
for (c = 0; c < local_cells.n; c++) {
cell = local_cells.cell[c];
p1 = cell->part;
np = cell->n;
for(i = 0; i < np; i++) {
if(p1[i].p.type == reaction.product_type) {
rand = d_random();
if(rand > back_ratexp) {
printf("DEBUG: integrate_reaction; back_react\n"); //TODO delete
p1[i].p.type=reaction.reactant_type;
}
}
}
}
}
on_particle_change();
}
}
int saltC(int N_pS, int N_nS, int part_id, int mode, double shield, int max_try, double val_pS, double val_nS, int type_pS, int type_nS, double rad) {
int n, cnt1,max_cnt;
double pos[3], dis2;
cnt1 = max_cnt = 0;
/* Place positive salt ions */
for (n=0; n<N_pS; n++) {
for (cnt1=0; cnt1<max_try; cnt1++) {
if (rad > 0.) {
pos[0]=rad*(2.*d_random()-1.);
pos[1]=rad*(2.*d_random()-1.);
pos[2]=rad*(2.*d_random()-1.);
dis2 = pos[0]*pos[0]+pos[1]*pos[1]+pos[2]*pos[2];
pos[0] += box_l[0]*0.5;
pos[1] += box_l[1]*0.5;
pos[2] += box_l[2]*0.5;
if (((mode!=0) || (collision(pos, shield, 0, NULL)==0)) && (dis2 < (rad * rad))) break;
} else {
pos[0]=box_l[0]*d_random();
pos[1]=box_l[1]*d_random();
pos[2]=box_l[2]*d_random();
if ((mode!=0) || (collision(pos, shield, 0, NULL)==0)) break;
}
POLY_TRACE(printf("p"); fflush(NULL));
}
if (cnt1 >= max_try) return (-1);
if (place_particle(part_id, pos)==ES_PART_ERROR) return (-3);
if (set_particle_q(part_id, val_pS)==ES_ERROR) return (-3);
if (set_particle_type(part_id, type_pS)==ES_ERROR) return (-3);
part_id++; max_cnt=imax(cnt1, max_cnt);
POLY_TRACE(printf("P"); fflush(NULL));
}
POLY_TRACE(printf(" %d->%d \n",cnt1,max_cnt));
if (cnt1 >= max_try) return(-1);
/* Place negative salt ions */
for (n=0; n<N_nS; n++) {
for (cnt1=0; cnt1<max_try; cnt1++) {
if (rad > 0.) {
pos[0]=rad*(2.*d_random()-1.);
pos[1]=rad*(2.*d_random()-1.);
pos[2]=rad*(2.*d_random()-1.);
dis2 = pos[0]*pos[0]+pos[1]*pos[1]+pos[2]*pos[2];
pos[0] += box_l[0]*0.5;
pos[1] += box_l[1]*0.5;
pos[2] += box_l[2]*0.5;
if (((mode!=0) || (collision(pos, shield, 0, NULL)==0)) && (dis2 < (rad * rad))) break;
} else {
pos[0]=box_l[0]*d_random();
pos[1]=box_l[1]*d_random();
pos[2]=box_l[2]*d_random();
if ((mode!=0) || (collision(pos, shield, 0, NULL)==0)) break;
}
POLY_TRACE(printf("n"); fflush(NULL));
}
if (cnt1 >= max_try) return (-1);
if (place_particle(part_id, pos)==ES_PART_ERROR) return (-3);
if (set_particle_q(part_id, val_nS)==ES_ERROR) return (-3);
if (set_particle_type(part_id, type_nS)==ES_ERROR) return (-3);
part_id++; max_cnt=imax(cnt1, max_cnt);
POLY_TRACE(printf("N"); fflush(NULL));
}
POLY_TRACE(printf(" %d->%d \n",cnt1,max_cnt));
if (cnt1 >= max_try) return(-2);
return(imax(max_cnt,cnt1));
}
/** Generator for Gaussian random numbers. Uses the Box-Muller
* transformation to generate two Gaussian random numbers from two
* uniform random numbers. which generates numbers between -2 sigma and 2 sigma in the form of a Gaussian with standard deviation sigma=1.118591404 resulting in
* an actual standard deviation of 1.
*
* @return Gaussian random number.
*
*/
inline double gaussian_random_cut(void) {
double x1, x2, r2, fac;
static int calc_new = 1;
static double save, curr;
/* On every second call two gaussian random numbers are calculated
via the Box-Muller transformation. One is returned as the result
and the second one is stored for use on the next call.
*/
if (calc_new) {
/* draw two uniform random numbers in the unit circle */
do {
x1 = 2.0*d_random()-1.0;
x2 = 2.0*d_random()-1.0;
r2 = x1*x1 + x2*x2;
} while (r2 >= 1.0 || r2 == 0.0);
/* perform Box-Muller transformation */
fac = sqrt(-2.0*log(r2)/r2);
// save one number for later use
save = x1*fac*1.042267973;
if ( fabs(save) > 2*1.042267973 ) {
if ( save > 0 ) save = 2*1.042267973;
else save = -2*1.042267973;
}
calc_new = 0;
// return the second number
curr = x2*fac*1.042267973;
if ( fabs(curr) > 2*1.042267973) {
if ( curr > 0 ) curr = 2*1.042267973;
else curr = -2*1.042267973;
}
return curr;
/* save one number for later use */
/*
save = x1*fac*1.118591404;
if ( fabs(save) > 2*1.118591404 ) {
save = (2.0*d_random()-1.0)*2*1.118591404;
}
calc_new = 0;
// return the second number
curr = x2*fac*1.118591404;
if ( fabs(curr) > 2*1.118591404) {
curr = (2.0*d_random()-1.0)*2*1.118591404;
}
return curr;
*/
} else {
calc_new = 1;
/* return the stored gaussian random number */
return save;
}
}
/** 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
}
/** Implementation of the tcl-command
t_random [{ int \<n\> | seed [\<seed(0)\> ... \<seed(n_nodes-1)\>] | stat [status-list] }]
<ul>
<li> Without further arguments, it returns a random double between 0 and 1.
<li> If 'int \<n\>' is given, it returns a random integer between 0 and n-1.
<li> If 'seed'/'stat' is given without further arguments, it returns a tcl-list with
the current seeds/status of the n_nodes active nodes; otherwise it issues the
given parameters as the new seeds/status to the respective nodes.
</ul>
*/
int tclcommand_t_random (ClientData data, Tcl_Interp *interp, int argc, char **argv) {
char buffer[100 + TCL_DOUBLE_SPACE + 3*TCL_INTEGER_SPACE];
int i,j,cnt, i_out, temp;
double d_out;
if (argc == 1) { /* 't_random' */
d_out = d_random();
sprintf(buffer, "%f", d_out); Tcl_AppendResult(interp, buffer, (char *) NULL); return (TCL_OK);
}
/* argc > 1 */
argc--; argv++;
if ( ARG_IS_S(0,"int") ) /* 't_random int <n>' */
{
if(argc < 2)
{
Tcl_AppendResult(interp, "\nWrong # of args: Usage: 't_random int <n>'", (char *) NULL);
return (TCL_ERROR);
}
else
{
if( !ARG_IS_I(1,i_out) )
{
Tcl_AppendResult(interp, "\nWrong type: Usage: 't_random int <n>'", (char *) NULL);
return (TCL_ERROR);
}
i_out = i_random(i_out);
sprintf(buffer, "%d", i_out);
Tcl_AppendResult(interp, buffer, (char *) NULL);
return (TCL_OK);
}
}
else if ( ARG_IS_S(0,"seed") ) /* 't_random seed [<seed(0)> ... <seed(n_nodes-1)>]' */
{
long *seed = (long *) malloc(n_nodes*sizeof(long));
if (argc <= 1) /* ESPResSo generates a seed */
{
mpi_random_seed(0,seed);
for (i=0; i < n_nodes; i++)
{
sprintf(buffer, "%ld ", seed[i]);
Tcl_AppendResult(interp, buffer, (char *) NULL);
}
}
else if (argc < n_nodes+1) /* Fewer seeds than nodes */
{
sprintf(buffer, "Wrong # of args (%d)! Usage: 't_random seed [<seed(0)> ... <seed(%d)>]'", argc,n_nodes-1);
Tcl_AppendResult(interp, buffer, (char *)NULL);
return (TCL_ERROR);
}
else /* Get seeds for different nodes */
{
for (i=0; i < n_nodes; i++)
{
if( !ARG_IS_I(i+1,temp) )
{
sprintf(buffer, "\nWrong type for seed %d:\nUsage: 't_random seed [<seed(0)> ... <seed(%d)>]'", i+1 ,n_nodes-1);
Tcl_AppendResult(interp, buffer, (char *)NULL);
return (TCL_ERROR);
}
else
{
seed[i] = (long)temp;
}
}
RANDOM_TRACE(
printf("Got ");
for(i=0;i<n_nodes;i++)
printf("%ld ",seed[i]);
printf("as new seeds.\n")
);
mpi_random_seed(n_nodes,seed);
}
free(seed);
return(TCL_OK);
}
void integrate_vv(int n_steps)
{
int i;
#ifdef REACTIONS
int c, np, n;
Particle * p1, *p2, **pairs;
Cell * cell;
double dist2, vec21[3], rand;
if(reaction.rate > 0) {
int reactants = 0, products = 0;
int tot_reactants = 0, tot_products = 0;
double ratexp, back_ratexp;
ratexp = exp(-time_step*reaction.rate);
on_observable_calc();
for (c = 0; c < local_cells.n; c++) {
/* Loop cell neighbors */
for (n = 0; n < dd.cell_inter[c].n_neighbors; n++) {
pairs = dd.cell_inter[c].nList[n].vList.pair;
np = dd.cell_inter[c].nList[n].vList.n;
/* verlet list loop */
for(i = 0; i < 2 * np; i += 2) {
p1 = pairs[i]; //pointer to particle 1
p2 = pairs[i+1]; //pointer to particle 2
if( (p1->p.type == reaction.reactant_type && p2->p.type == reaction.catalyzer_type) || (p2->p.type == reaction.reactant_type && p1->p.type == reaction.catalyzer_type) ) {
get_mi_vector(vec21, p1->r.p, p2->r.p);
dist2 = sqrlen(vec21);
if(dist2 < reaction.range * reaction.range) {
rand =d_random();
if(rand > ratexp) {
if(p1->p.type==reaction.reactant_type) {
p1->p.type = reaction.product_type;
}
else {
p2->p.type = reaction.product_type;
}
}
}
}
}
}
}
if (reaction.back_rate < 0) { // we have to determine it dynamically
/* we count now how many reactants and products are in the sim box */
for (c = 0; c < local_cells.n; c++) {
cell = local_cells.cell[c];
p1 = cell->part;
np = cell->n;
for(i = 0; i < np; i++) {
if(p1[i].p.type == reaction.reactant_type)
reactants++;
else if(p1[i].p.type == reaction.product_type)
products++;
}
}
MPI_Allreduce(&reactants, &tot_reactants, 1, MPI_INT, MPI_SUM, comm_cart);
MPI_Allreduce(&products, &tot_products, 1, MPI_INT, MPI_SUM, comm_cart);
back_ratexp = ratexp * tot_reactants / tot_products ; //with this the asymptotic ratio reactant/product becomes 1/1 and the catalyzer volume only determines the time that it takes to reach this
}
else { //use the back reaction rate supplied by the user
back_ratexp = exp(-time_step*reaction.back_rate);
}
if(back_ratexp < 1 ) {
for (c = 0; c < local_cells.n; c++) {
cell = local_cells.cell[c];
p1 = cell->part;
np = cell->n;
for(i = 0; i < np; i++) {
if(p1[i].p.type == reaction.product_type) {
rand = d_random();
if(rand > back_ratexp) {
p1[i].p.type=reaction.reactant_type;
}
}
}
}
}
on_particle_change();
}
#endif /* ifdef REACTIONS */
/* Prepare the Integrator */
on_integration_start();
/* if any method vetoes (P3M not initialized), immediately bail out */
if (check_runtime_errors())
return;
/* Verlet list criterion */
skin2 = SQR(0.5 * skin);
INTEG_TRACE(fprintf(stderr,"%d: integrate_vv: integrating %d steps (recalc_forces=%d)\n",
this_node, n_steps, recalc_forces));
/* Integration Step: Preparation for first integration step:
Calculate forces f(t) as function of positions p(t) ( and velocities v(t) ) */
if (recalc_forces) {
thermo_heat_up();
#ifdef LB
transfer_momentum = 0;
#endif
#ifdef LB_GPU
transfer_momentum_gpu = 0;
#endif
//VIRTUAL_SITES pos (and vel for DPD) update for security reason !!!
#ifdef VIRTUAL_SITES
update_mol_vel_pos();
ghost_communicator(&cell_structure.update_ghost_pos_comm);
if (check_runtime_errors()) return;
#ifdef ADRESS
// adress_update_weights();
if (check_runtime_errors()) return;
#endif
#endif
#ifdef COLLISION_DETECTION
prepare_collision_queue();
#endif
force_calc();
//VIRTUAL_SITES distribute forces
#ifdef VIRTUAL_SITES
ghost_communicator(&cell_structure.collect_ghost_force_comm);
init_forces_ghosts();
distribute_mol_force();
if (check_runtime_errors()) return;
#endif
ghost_communicator(&cell_structure.collect_ghost_force_comm);
#ifdef ROTATION
convert_initial_torques();
#endif
thermo_cool_down();
/* Communication Step: ghost forces */
/*apply trap forces to trapped molecules*/
#ifdef MOLFORCES
calc_and_apply_mol_constraints();
#endif
rescale_forces();
recalc_forces = 0;
#ifdef COLLISION_DETECTION
handle_collisions();
#endif
}
if (check_runtime_errors())
return;
n_verlet_updates = 0;
/* Integration loop */
for(i=0;i<n_steps;i++) {
INTEG_TRACE(fprintf(stderr,"%d: STEP %d\n",this_node,i));
#ifdef BOND_CONSTRAINT
save_old_pos();
#endif
/* Integration Steps: Step 1 and 2 of Velocity Verlet scheme:
v(t+0.5*dt) = v(t) + 0.5*dt * f(t)
p(t + dt) = p(t) + dt * v(t+0.5*dt)
NOTE 1: Prefactors do not occur in formulas since we use
rescaled forces and velocities.
NOTE 2: Depending on the integration method Step 1 and Step 2
cannot be combined for the translation.
*/
if(integ_switch == INTEG_METHOD_NPT_ISO || nemd_method != NEMD_METHOD_OFF) {
propagate_vel(); propagate_pos(); }
else
propagate_vel_pos();
#ifdef BOND_CONSTRAINT
/**Correct those particle positions that participate in a rigid/constrained bond */
cells_update_ghosts();
correct_pos_shake();
#endif
#ifdef ELECTROSTATICS
if(coulomb.method == COULOMB_MAGGS) {
maggs_propagate_B_field(0.5*time_step);
}
#endif
#ifdef NPT
if (check_runtime_errors())
break;
#endif
cells_update_ghosts();
//VIRTUAL_SITES update pos and vel (for DPD)
#ifdef VIRTUAL_SITES
update_mol_vel_pos();
ghost_communicator(&cell_structure.update_ghost_pos_comm);
if (check_runtime_errors()) break;
#if defined(VIRTUAL_SITES_RELATIVE) && defined(LB)
// This is on a workaround stage:
// When using virtual sites relative and LB at the same time, it is necessary
// to reassemble the cell lists after all position updates, also of virtual
// particles.
if (cell_structure.type == CELL_STRUCTURE_DOMDEC && (!dd.use_vList) )
cells_update_ghosts();
#endif
#ifdef ADRESS
//adress_update_weights();
if (check_runtime_errors()) break;
#endif
#endif
/* Integration Step: Step 3 of Velocity Verlet scheme:
Calculate f(t+dt) as function of positions p(t+dt) ( and velocities v(t+0.5*dt) ) */
#ifdef LB
transfer_momentum = 1;
#endif
#ifdef LB_GPU
transfer_momentum_gpu = 1;
#endif
#ifdef COLLISION_DETECTION
prepare_collision_queue();
#endif
force_calc();
//VIRTUAL_SITES distribute forces
#ifdef VIRTUAL_SITES
ghost_communicator(&cell_structure.collect_ghost_force_comm);
init_forces_ghosts();
distribute_mol_force();
if (check_runtime_errors()) break;
#endif
/* Communication step: ghost forces */
ghost_communicator(&cell_structure.collect_ghost_force_comm);
/*apply trap forces to trapped molecules*/
#ifdef MOLFORCES
calc_and_apply_mol_constraints();
#endif
if (check_runtime_errors())
break;
/* Integration Step: Step 4 of Velocity Verlet scheme:
v(t+dt) = v(t+0.5*dt) + 0.5*dt * f(t+dt) */
rescale_forces_propagate_vel();
recalc_forces = 0;
#ifdef LB
if (lattice_switch & LATTICE_LB) lattice_boltzmann_update();
if (check_runtime_errors()) break;
#endif
#ifdef LB_GPU
if(this_node == 0){
if (lattice_switch & LATTICE_LB_GPU) lattice_boltzmann_update_gpu();
}
#endif
#ifdef BOND_CONSTRAINT
ghost_communicator(&cell_structure.update_ghost_pos_comm);
correct_vel_shake();
#endif
#ifdef ROTATION
convert_torques_propagate_omega();
#endif
//VIRTUAL_SITES update vel
#ifdef VIRTUAL_SITES
ghost_communicator(&cell_structure.update_ghost_pos_comm);
update_mol_vel();
if (check_runtime_errors()) break;
#endif
#ifdef ELECTROSTATICS
if(coulomb.method == COULOMB_MAGGS) {
maggs_propagate_B_field(0.5*time_step);
}
#endif
#ifdef COLLISION_DETECTION
handle_collisions();
#endif
#ifdef NPT
if((this_node==0) && (integ_switch == INTEG_METHOD_NPT_ISO))
nptiso.p_inst_av += nptiso.p_inst;
#endif
/* Propagate time: t = t+dt */
sim_time += time_step;
}
/* verlet list statistics */
if(n_verlet_updates>0) verlet_reuse = n_steps/(double) n_verlet_updates;
else verlet_reuse = 0;
#ifdef NPT
if(integ_switch == INTEG_METHOD_NPT_ISO) {
nptiso.invalidate_p_vel = 0;
MPI_Bcast(&nptiso.p_inst, 1, MPI_DOUBLE, 0, comm_cart);
MPI_Bcast(&nptiso.p_diff, 1, MPI_DOUBLE, 0, comm_cart);
MPI_Bcast(&nptiso.volume, 1, MPI_DOUBLE, 0, comm_cart);
if(this_node==0) nptiso.p_inst_av /= 1.0*n_steps;
MPI_Bcast(&nptiso.p_inst_av, 1, MPI_DOUBLE, 0, comm_cart);
}
#endif
}
/** Calculate soft-sphere potential force between particle p1 and p2 */
inline void add_affinity_pair_force(Particle * p1, Particle * p2, IA_parameters *ia_params,
double d[3], double dist, double force[3])
{
// The affinity potential has the first argument affinity_type. This is to differentiate between different implementations. For example one implementation can take into account the detachment force, another not.
int aff_type_extracted = 0;
int period_for_output = -1;
if (ia_params->affinity_type > 10 ) {
aff_type_extracted = ia_params->affinity_type % 10;
period_for_output = ia_params->affinity_type - aff_type_extracted; }
else aff_type_extracted = ia_params->affinity_type;
if ( aff_type_extracted == 1 ) {
/************************
*
* Here I can implement the affinity force.
* I have the position of the particle - p1, and under p1->p.bond_site I have the coordinate of the bond_site.
* Also, under d[3] I have the vector towards the constraint meaning that force on p1 should be in the direction of d[3].
*
* Algorithm:
* 1. First check is, whether I am in the cut-off radius: ?dist < affinity_cut?.
* 2. Then I check whether there exists a bond from the current particle: ?bond_site != -1?
* 3. If yes, then I maintain the bond. I put the forces and afterwards I decide whether the bond will brake or not.
* 4. If no, I maintain the creation of a bond. First I check whether I am in the area of possible bond creation: ?dist < affinity_r0?
* 5. If yes, I run the decision algorithm for bond creation and I either create or does not create the bond.
* 6. If I am not in the area of possible bond creation I do nothing
*
* comments:
* strength of the force is proportiona to the difference of actual bond length and relaxed bond length
* bond is always created, no probability is involved
* if bondlength reaches maxBond, the bond imediately ruptures. No probability is involved
*********************/
int j;
double fac=0.0;
if(CUTOFF_CHECK(dist < ia_params->affinity_cut)) { // Checking whether I am inside the interaction cut-off radius.
if(dist > 0.0) {
//printf("bond_site: %f %f %f\n",p1->p.bond_site[0],p1->p.bond_site[1],p1->p.bond_site[2]);
if ((p1->p.bond_site[0] >= 0) && (p1->p.bond_site[1] >= 0) && (p1->p.bond_site[2] >= 0)) // Checking whether any bond exists
{ // Bond exists
double folded_pos[3], vec[3], len2, len;
int img[3];
/* fold the coordinates of the particle */
memmove(folded_pos, p1->r.p, 3*sizeof(double));
memmove(img, p1->l.i, 3*sizeof(int));
unfold_position(folded_pos, img);
//printf("folded positions: %f %f %f\n",folded_pos[0],folded_pos[1],folded_pos[2]);
for(j=0;j<3;j++)
vec[j] = p1->p.bond_site[j] - folded_pos[j]; // Shouldn't be the vec vector normalized? Yes, but with affinity_r0 and not by len!!!
len2 = sqrlen(vec);
len = sqrt(len2);
if (len > ia_params->affinity_r0) {
fac = ia_params->affinity_kappa*(len - ia_params->affinity_r0);
//printf("len %f r0 %f\n",len, ia_params->affinity_r0);
}
else fac = 0.0;
// double ftemp = 0;
for(j=0;j<3;j++)
{
force[j] += fac * vec[j] / len;
}
// printf("%f ",ftemp);
// Decision whether I should break the bond: if the bond length is greater than maxBond, it breaks.
if (len > ia_params->affinity_maxBond) {
for(j=0;j<3;j++) p1->p.bond_site[j] = -1;
}
}
else if (dist < ia_params->affinity_r0)
{ // Bond does not exist, we are inside of possible bond creation area, lets talk about creating a bond
// This implementation creates bond always
double folded_pos[3];
int img[3];
/* fold the coordinates of the particle */
memmove(folded_pos, p1->r.p, 3*sizeof(double));
memmove(img, p1->l.i, 3*sizeof(int));
unfold_position(folded_pos, img);
//printf("folded positions: %f %f %f\n",folded_pos[0],folded_pos[1],folded_pos[2]);
//printf("d: %f %f %f\n",d[0],d[1],d[2]);
for(j=0;j<3;j++)
p1->p.bond_site[j] = folded_pos[j] - d[j];
}
}
}
}
if ( aff_type_extracted == 2 ) { //second implementation of affinity
/************************
*
* Here I can implement the affinity force.
* I have the position of the particle - p1, and under p1->p.bond_site I have the coordinate of the bond_site.
* Also, under d[3] I have the vector towards the constraint meaning that force on p1 should be in the direction of d[3].
*
* Algorithm:
* 1. First check is whether I am in the cut-off radius: ?dist < affinity_cut?.
* 2. Then I check whether there exists a bond from the current particle: ?bond_site != -1?
* 3. If yes, then I maintaind the bond. I put the forces and afterwards I decide whether the bond will brake or not.
* 4. If no, I maintain the creation of a bond. First I check whether I am in the area of possible bond creation: ?dist < affinity_r0?
* 5. If yes, I run the decision algorithm for bond creation and I either create or does not create the bond.
* 6. If I am not in the area of possible bond creation I do nothing
*
*
* comments:
* strength of the force is proportiona to the difference of actual bond length and relaxed bond length
* bond is created with probability 1-exp(-Kon*timestep)
* maxBond is not used, we use probability 1-exp(-Koff*timestep) to brake the bond
* Koff depends on the bondlenth via Koff = K0*exp(F/Fd) = K0*exp(kappa(r-r0)/Fd)
* here, ia_params->Koff gives us K_0, off rate when bond is relaxed.
* here, maxBond is used as detachment force F_d. The original check for ensuring, that partice flows out of the cut-off radius and the bond remains active is replaced with fixed check, that bond length must not be greater that 0.8 cut_off
*********************/
int j;
double fac=0.0;
if(CUTOFF_CHECK(dist < ia_params->affinity_cut)) { // Checking whether I am inside the interaction cut-off radius.
if(dist > 0.0) {
//printf("bond_site: %f %f %f\n",p1->p.bond_site[0],p1->p.bond_site[1],p1->p.bond_site[2]);
if ((p1->p.bond_site[0] >= 0) && (p1->p.bond_site[1] >= 0) && (p1->p.bond_site[2] >= 0)) // Checking whether any bond exists
{ // Bond exists
double folded_pos[3], vec[3], len2, len;
int img[3];
/* fold the coordinates of the particle */
memmove(folded_pos, p1->r.p, 3*sizeof(double));
memmove(img, p1->l.i, 3*sizeof(int));
unfold_position(folded_pos, img);
//printf("folded positions: %f %f %f\n",folded_pos[0],folded_pos[1],folded_pos[2]);
for(j=0;j<3;j++)
vec[j] = p1->p.bond_site[j] - folded_pos[j]; // Shouldn't be the vec vector normalized? Yes, but with affinity_r0 and not by len!!!
len2 = sqrlen(vec);
len = sqrt(len2);
if (len > ia_params->affinity_r0) {
fac = ia_params->affinity_kappa*(len - ia_params->affinity_r0);
//printf("len %f r0 %f\n",len, ia_params->affinity_r0);
}
else fac = 0.0;
//double ftemp = 0;
for(j=0;j<3;j++)
{
force[j] += fac * vec[j] / len;
// ftemp += abs(fac * vec[j] / len);
}
//if (ftemp > 0.000000000000001) printf("%f ",fac);
// Decision whether I should break the bond:
// First, force exerted on bond is stored in fac
double tmpF = fac;
// Then, zero force off rate K_0 is stored at ia_params_Koff
double tmpK0 = ia_params->affinity_Koff;
// Then, detachment force is stored in ia_params->affinity_maxBond
double tmpFd = ia_params->affinity_maxBond;
// Then, compute Koff
double tmpKoff = tmpK0*exp( tmpF / tmpFd);
// Finally, compute Poff
double Poff = 1.0 - exp( - tmpKoff*time_step);
//printf("%f ", Poff);
if (len < 0.8*ia_params->affinity_cut) { // in other implementation, maxBond is used here. However, in this implementation, we need maxBond for setting detachment force F_d
double decide = d_random();
if ( decide < Poff )
{
for(j=0;j<3;j++) p1->p.bond_site[j] = -1;
// printf("bond broken. Poff = %f, F = %f, Koff = %f, K0 = %f, len = %f \n",Poff,tmpF,tmpKoff,tmpK0,len);
}
} else {
for(j=0;j<3;j++) p1->p.bond_site[j] = -1;
//printf("breaking: out of cut");
}
// Checkpoint output:
if (period_for_output > 0 ) if (((int)floor(sim_time/time_step) % period_for_output == 0 ) && (len > ia_params->affinity_r0) ) {
FILE *fp;
double tmpPon = 1.0 - exp( - ia_params->affinity_Kon*time_step);
fp = fopen("affinity_check.dat","a");
fprintf(fp,"sim_time %f, period_for_output %d aff type: %d ",sim_time,period_for_output,aff_type_extracted);
fprintf(fp,"Pon %f, Kon %f, particle %d, Poff = %f, F = %f, Koff = %f, K0 = %f, len = %f \n",tmpPon, ia_params->affinity_Kon, p1->p.identity, Poff,tmpF,tmpKoff,tmpK0,len);
fclose(fp);
}
}
else if (dist < ia_params->affinity_r0)
{ // Bond does not exist, we are inside of possible bond creation area, lets talk about creating a bond
double Pon = 1.0 - exp( - ia_params->affinity_Kon*time_step);
// The probability is given by function Pon(x)= 1 - e^(-x) where x is Kon*dt. Here is a table of values of this function, just to have an idea about the values
// x | 0 | 0.25 | 0.5 | 0.75 | 1.0 | 1.5 | 2.0 | 3.0 | 5.0
// Pon(x) | 0 | 0.22 | 0.39 | 0.52 | 0.63 | 0.77 | 0.84 | 0.95 | 0.99
double decide = d_random();
if ( decide < Pon )
{ // the bond will be created only with probability Pon.
//printf("Creating: Pon = %f, decide = %f", Pon, decide);
double folded_pos[3];
int img[3];
/* fold the coordinates of the particle */
memmove(folded_pos, p1->r.p, 3*sizeof(double));
memmove(img, p1->l.i, 3*sizeof(int));
unfold_position(folded_pos, img);
//printf("folded positions: %f %f %f\n",folded_pos[0],folded_pos[1],folded_pos[2]);
//printf("d: %f %f %f\n",d[0],d[1],d[2]);
for(j=0;j<3;j++)
p1->p.bond_site[j] = folded_pos[j] - d[j];
} else {
//printf("In range, not creating: Pon = %f, decide = %f", Pon, decide);
}
}
}
}
}
if ( aff_type_extracted == 3 ) {
/************************
*
* Here I can implement the affinity force.
* I have the position of the particle - p1, and under p1->p.bond_site I have the coordinate of the bond_site.
* Also, under d[3] I have the vector towards the constraint meaning that force on p1 should be in the direction of d[3].
*
* Algorithm:
* 1. First check is whether I am in the cut-off radius: ?dist < affinity_cut?.
* 2. Then I check whether there exists a bond from the current particle: ?bond_site != -1?
* 3. If yes, then I maintaind the bond. I put the forces and afterwards I decide whether the bond will brake or not.
* 4. If no, I maintain the creation of a bond. First I check whether I am in the area of possible bond creation: ?dist < affinity_r0?
* 5. If yes, I run the decision algorithm for bond creation and I either create or does not create the bond.
* 6. If I am not in the area of possible bond creation I do nothing
*
*
* comments:
* strength of the force is proportiona to the difference of actual bond length and relaxed bond length
* bond is created with probability 1-exp(-Kon*timestep)
* bond is ruptured with probability 1-exp(-Koff*timestep) to brake the bond
* Koff is given as parameter, is not dependent on the force nor the bond length
* here, maxBond stands for ensuring, that partice flows out of the cut-off radius and the bond remains active. maxBond should be always less than cut_off radius
*********************/
int j;
double fac=0.0;
if(CUTOFF_CHECK(dist < ia_params->affinity_cut)) { // Checking whether I am inside the interaction cut-off radius.
if(dist > 0.0) {
//printf("bond_site: %f %f %f\n",p1->p.bond_site[0],p1->p.bond_site[1],p1->p.bond_site[2]);
if ((p1->p.bond_site[0] >= 0) && (p1->p.bond_site[1] >= 0) && (p1->p.bond_site[2] >= 0)) // Checking whether any bond exists
{ // Bond exists
double folded_pos[3], vec[3], len2, len;
int img[3];
/* fold the coordinates of the particle */
memmove(folded_pos, p1->r.p, 3*sizeof(double));
memmove(img, p1->l.i, 3*sizeof(int));
unfold_position(folded_pos, img);
//printf("folded positions: %f %f %f\n",folded_pos[0],folded_pos[1],folded_pos[2]);
for(j=0;j<3;j++)
vec[j] = p1->p.bond_site[j] - folded_pos[j]; // Shouldn't be the vec vector normalized? Yes, but with affinity_r0 and not by len!!!
len2 = sqrlen(vec);
len = sqrt(len2);
if (len > ia_params->affinity_r0) {
fac = ia_params->affinity_kappa*(len - ia_params->affinity_r0)/len;
//printf("len %f r0 %f\n",len, ia_params->affinity_r0);
}
else fac = 0.0;
// double ftemp = 0;
for(j=0;j<3;j++)
{
force[j] += fac * vec[j];
}
// printf("%f ",ftemp);
// Decision whether I should break the bond:
// The random decision algorithm is much more complicated with Fd detachment force etc. Here, I use much simpler rule, the same as with Kon, except that the probability of bond breakage increases with prolongation of the bond. If the bond reaches
double Poff = 1.0 - exp( - ia_params->affinity_Koff*time_step);
if (len < ia_params->affinity_maxBond) {
double decide = d_random();
if ( decide < Poff )
{
for(j=0;j<3;j++) p1->p.bond_site[j] = -1;
}
} else {
for(j=0;j<3;j++) p1->p.bond_site[j] = -1;
//printf("breaking: out of cut");
}
}
else if (dist < ia_params->affinity_r0)
{ // Bond does not exist, we are inside of possible bond creation area, lets talk about creating a bond
double Pon = 1.0 - exp( - ia_params->affinity_Kon*time_step);
// The probability is given by function Pon(x)= 1 - e^(-x) where x is Kon*dt. Here is a table of values of this function, just to have an idea about the values
// x | 0 | 0.25 | 0.5 | 0.75 | 1.0 | 1.5 | 2.0 | 3.0 | 5.0
// Pon(x) | 0 | 0.22 | 0.39 | 0.52 | 0.63 | 0.77 | 0.84 | 0.95 | 0.99
double decide = d_random();
if ( decide < Pon )
{ // the bond will be created only with probability Pon.
//printf("Creating: Pon = %f, decide = %f", Pon, decide);
double folded_pos[3];
int img[3];
/* fold the coordinates of the particle */
memmove(folded_pos, p1->r.p, 3*sizeof(double));
memmove(img, p1->l.i, 3*sizeof(int));
unfold_position(folded_pos, img);
//printf("folded positions: %f %f %f\n",folded_pos[0],folded_pos[1],folded_pos[2]);
//printf("d: %f %f %f\n",d[0],d[1],d[2]);
for(j=0;j<3;j++)
p1->p.bond_site[j] = folded_pos[j] - d[j];
} else {
//printf("In range, not creating: Pon = %f, decide = %f", Pon, decide);
}
}
}
}
}
if ( aff_type_extracted == 4 ) {
/************************
*
* Here I can implement the affinity force.
* I have the position of the particle - p1, and under p1->p.bond_site I have the coordinate of the bond_site.
* Also, under d[3] I have the vector towards the constraint meaning that force on p1 should be in the direction of d[3].
*
* Algorithm:
* 1. First check is whether I am in the cut-off radius: ?dist < affinity_cut?.
* 2. Then I check whether there exists a bond from the current particle: ?bond_site != -1?
* 3. If yes, then I maintaind the bond. I put the forces and afterwards I decide whether the bond will brake or not.
* 4. If no, I maintain the creation of a bond. First I check whether I am in the area of possible bond creation: ?dist < affinity_r0?
* 5. If yes, I run the decision algorithm for bond creation and I either create or does not create the bond.
* 6. If I am not in the area of possible bond creation I do nothing
*
*
* comments:
* strength of the force is proportional to the actual bond length
* bond is created with probability 1-exp(-Kon*timestep)
* maxBond is not used, we use probability 1-exp(-Koff*timestep) to brake the bond
* Koff depends on the bondlength via Koff = K0*exp(F/Fd) = K0*exp(kappa*r/Fd)
* here, ia_params->Koff gives us K_0, off rate when bond is relaxed.
* here, maxBond is used as detachment force F_d. The original check for ensuring, that partice flows out of the cut-off radius and the bond remains active is replaced with fixed check, that bond length must not be greater that 0.8 cut_off
*********************/
int j;
double fac=0.0;
if(CUTOFF_CHECK(dist < ia_params->affinity_cut)) { // Checking whether I am inside the interaction cut-off radius.
if(dist > 0.0) {
//printf("bond_site: %f %f %f\n",p1->p.bond_site[0],p1->p.bond_site[1],p1->p.bond_site[2]);
if ((p1->p.bond_site[0] >= 0) && (p1->p.bond_site[1] >= 0) && (p1->p.bond_site[2] >= 0)) // Checking whether any bond exists
{ // Bond exists
double folded_pos[3], vec[3], len2, len;
int img[3];
/* fold the coordinates of the particle */
memmove(folded_pos, p1->r.p, 3*sizeof(double));
memmove(img, p1->l.i, 3*sizeof(int));
unfold_position(folded_pos, img);
//printf("folded positions: %f %f %f\n",folded_pos[0],folded_pos[1],folded_pos[2]);
for(j=0;j<3;j++)
vec[j] = p1->p.bond_site[j] - folded_pos[j]; // Shouldn't be the vec vector normalized? Yes, but with affinity_r0 and not by len!!!
len2 = sqrlen(vec);
len = sqrt(len2);
fac = ia_params->affinity_kappa*len;
//double ftemp = 0;
for(j=0;j<3;j++)
{
force[j] += fac * vec[j] / len;
}
// Decision whether I should break the bond:
// First, force exerted on bond is stored in fac
double tmpF = fac;
// Then, zero force off rate K_0 is stored at ia_params_Koff
double tmpK0 = ia_params->affinity_Koff;
// Then, detachment force is stored in ia_params->affinity_maxBond
double tmpFd = ia_params->affinity_maxBond;
// Then, compute Koff
double tmpKoff = tmpK0*exp( tmpF / tmpFd);
// Finally, compute Poff
double Poff = 1.0 - exp( - tmpKoff*time_step);
//printf("%f ", Poff);
if (len < 0.8*ia_params->affinity_cut) { // in other implementation, maxBond is used here. However, in this implementation, we need maxBond for setting detachment force F_d
double decide = d_random();
if ( decide < Poff )
{
for(j=0;j<3;j++) p1->p.bond_site[j] = -1;
// printf("bond broken. Poff = %f, F = %f, Koff = %f, K0 = %f, len = %f \n",Poff,tmpF,tmpKoff,tmpK0,len);
}
} else {
for(j=0;j<3;j++) p1->p.bond_site[j] = -1;
//printf("breaking: out of cut");
}
// Checkpoint output:
if (period_for_output > 0 ) if ((int)floor(sim_time/time_step) % period_for_output == 0 ) {
FILE *fp;
double tmpPon = 1.0 - exp( - ia_params->affinity_Kon*time_step);
fp = fopen("affinity_check.dat","a");
fprintf(fp,"sim_time %f, period_for_output %d aff type: %d ",sim_time,period_for_output,aff_type_extracted);
fprintf(fp,"Pon %f, Kon %f, particle %d, Poff = %f, F = %f, Koff = %f, K0 = %f, len = %f \n",tmpPon, ia_params->affinity_Kon, p1->p.identity, Poff,tmpF,tmpKoff,tmpK0,len);
fclose(fp);
}
}
else if (dist < ia_params->affinity_r0)
{ // Bond does not exist, we are inside of possible bond creation area, lets talk about creating a bond
double Pon = 1.0 - exp( - ia_params->affinity_Kon*time_step);
// The probability is given by function Pon(x)= 1 - e^(-x) where x is Kon*dt. Here is a table of values of this function, just to have an idea about the values
// x | 0 | 0.25 | 0.5 | 0.75 | 1.0 | 1.5 | 2.0 | 3.0 | 5.0
// Pon(x) | 0 | 0.22 | 0.39 | 0.52 | 0.63 | 0.77 | 0.84 | 0.95 | 0.99
double decide = d_random();
if ( decide < Pon )
{ // the bond will be created only with probability Pon.
//printf("Creating: Pon = %f, decide = %f", Pon, decide);
double folded_pos[3];
int img[3];
/* fold the coordinates of the particle */
memmove(folded_pos, p1->r.p, 3*sizeof(double));
memmove(img, p1->l.i, 3*sizeof(int));
unfold_position(folded_pos, img);
//printf("folded positions: %f %f %f\n",folded_pos[0],folded_pos[1],folded_pos[2]);
//printf("d: %f %f %f\n",d[0],d[1],d[2]);
for(j=0;j<3;j++)
p1->p.bond_site[j] = folded_pos[j] - d[j];
} else {
//printf("In range, not creating: Pon = %f, decide = %f", Pon, decide);
}
}
}
}
}
if ( aff_type_extracted == 5 ) { //second implementation of affinity
/************************
*
* Here I can implement the affinity force.
* I have the position of the particle - p1, and under p1->p.bond_site I have the coordinate of the bond_site.
* Also, under d[3] I have the vector towards the constraint meaning that force on p1 should be in the direction of d[3].
*
* Algorithm:
* 1. First check is whether I am in the cut-off radius: ?dist < affinity_cut?.
* 2. Then I check whether there exists a bond from the current particle: ?bond_site != -1?
* 3. If yes, then I maintaind the bond. I put the forces and afterwards I decide whether the bond will brake or not.
* 4. If no, I maintain the creation of a bond. First I check whether I am in the area of possible bond creation: ?dist < affinity_r0?
* 5. If yes, I run the decision algorithm for bond creation and I either create or does not create the bond.
* 6. If I am not in the area of possible bond creation I do nothing
*
*
* comments:
* strength of the force is proportiona to the difference of actual bond length and 75% of the relaxed bond length
* bond is created with probability 1-exp(-Kon*timestep)
* maxBond is not used, we use probability 1-exp(-Koff*timestep) to brake the bond
* Koff depends on the bondlenth via Koff = K0*exp(F/Fd) = K0*exp(kappa(r-0.75*r0)/Fd)
* here, ia_params->Koff gives us K_0, off rate when bond is relaxed.
* here, maxBond is used as detachment force F_d. The original check for ensuring, that partice flows out of the cut-off radius and the bond remains active is replaced with fixed check, that bond length must not be greater that 0.8 cut_off
*********************/
int j;
double fac=0.0;
if(CUTOFF_CHECK(dist < ia_params->affinity_cut)) { // Checking whether I am inside the interaction cut-off radius.
if(dist > 0.0) {
//printf("bond_site: %f %f %f\n",p1->p.bond_site[0],p1->p.bond_site[1],p1->p.bond_site[2]);
if ((p1->p.bond_site[0] >= 0) && (p1->p.bond_site[1] >= 0) && (p1->p.bond_site[2] >= 0)) // Checking whether any bond exists
{ // Bond exists
double folded_pos[3], vec[3], len2, len;
int img[3];
/* fold the coordinates of the particle */
memmove(folded_pos, p1->r.p, 3*sizeof(double));
memmove(img, p1->l.i, 3*sizeof(int));
unfold_position(folded_pos, img);
//printf("folded positions: %f %f %f\n",folded_pos[0],folded_pos[1],folded_pos[2]);
for(j=0;j<3;j++)
vec[j] = p1->p.bond_site[j] - folded_pos[j]; // Shouldn't be the vec vector normalized? Yes, but with affinity_r0 and not by len!!!
len2 = sqrlen(vec);
len = sqrt(len2);
if (len > 0.75*(ia_params->affinity_r0)) {
fac = ia_params->affinity_kappa*(len - 0.75*(ia_params->affinity_r0));
//printf("len %f r0 %f\n",len, ia_params->affinity_r0);
}
else fac = 0.0;
//double ftemp = 0;
for(j=0;j<3;j++)
{
force[j] += fac * vec[j] / len;
// ftemp += abs(fac * vec[j] / len);
}
//if (ftemp > 0.000000000000001) printf("%f ",fac);
// Decision whether I should break the bond:
// First, force exerted on bond is stored in fac
double tmpF = fac;
// Then, zero force off rate K_0 is stored at ia_params_Koff
double tmpK0 = ia_params->affinity_Koff;
// Then, detachment force is stored in ia_params->affinity_maxBond
double tmpFd = ia_params->affinity_maxBond;
// Then, compute Koff
double tmpKoff = tmpK0*exp( tmpF / tmpFd);
// Finally, compute Poff
double Poff = 1.0 - exp( - tmpKoff*time_step);
//printf("%f ", Poff);
if (len < 0.8*ia_params->affinity_cut) { // in other implementation, maxBond is used here. However, in this implementation, we need maxBond for setting detachment force F_d
double decide = d_random();
if ( decide < Poff )
{
for(j=0;j<3;j++) p1->p.bond_site[j] = -1;
// printf("bond broken. Poff = %f, F = %f, Koff = %f, K0 = %f, len = %f \n",Poff,tmpF,tmpKoff,tmpK0,len);
}
} else {
for(j=0;j<3;j++) p1->p.bond_site[j] = -1;
//printf("breaking: out of cut");
}
// Checkpoint output:
if (period_for_output > 0 ) if (((int)floor(sim_time/time_step) % period_for_output == 0 ) && (len > ia_params->affinity_r0) ) {
FILE *fp;
double tmpPon = 1.0 - exp( - ia_params->affinity_Kon*time_step);
fp = fopen("affinity_check.dat","a");
fprintf(fp,"sim_time %f, period_for_output %d aff type: %d ",sim_time,period_for_output,aff_type_extracted);
fprintf(fp,"Pon %f, Kon %f, particle %d, Poff = %f, F = %f, Koff = %f, K0 = %f, len = %f \n",tmpPon, ia_params->affinity_Kon, p1->p.identity, Poff,tmpF,tmpKoff,tmpK0,len);
fclose(fp);
}
}
else if (dist < ia_params->affinity_r0)
{ // Bond does not exist, we are inside of possible bond creation area, lets talk about creating a bond
double Pon = 1.0 - exp( - ia_params->affinity_Kon*time_step);
// The probability is given by function Pon(x)= 1 - e^(-x) where x is Kon*dt. Here is a table of values of this function, just to have an idea about the values
// x | 0 | 0.25 | 0.5 | 0.75 | 1.0 | 1.5 | 2.0 | 3.0 | 5.0
// Pon(x) | 0 | 0.22 | 0.39 | 0.52 | 0.63 | 0.77 | 0.84 | 0.95 | 0.99
double decide = d_random();
if ( decide < Pon )
{ // the bond will be created only with probability Pon.
//printf("Creating: Pon = %f, decide = %f", Pon, decide);
double folded_pos[3];
int img[3];
/* fold the coordinates of the particle */
memmove(folded_pos, p1->r.p, 3*sizeof(double));
memmove(img, p1->l.i, 3*sizeof(int));
unfold_position(folded_pos, img);
//printf("folded positions: %f %f %f\n",folded_pos[0],folded_pos[1],folded_pos[2]);
//printf("d: %f %f %f\n",d[0],d[1],d[2]);
for(j=0;j<3;j++)
p1->p.bond_site[j] = folded_pos[j] - d[j];
} else {
//printf("In range, not creating: Pon = %f, decide = %f", Pon, decide);
}
}
}
}
}
}
int polymerC(int N_P, int MPC, double bond_length, int part_id, double *posed,
int mode, double shield, int max_try, double val_cM, int cM_dist,
int type_nM, int type_cM, int type_bond,
double angle, double angle2, double *posed2, int constr) {
int p,n, cnt1,cnt2,max_cnt, bond_size, *bond, i;
double phi,zz,rr;
double *poly;
double pos[3];
double poz[3];
double poy[3] = {0, 0, 0};
double pox[3] = {0, 0, 0};
double a[3] = {0, 0, 0};
double b[3],c[3]={0., 0., 0.},d[3];
double absc;
poly = (double*)malloc(3*MPC*sizeof(double));
bond_size = bonded_ia_params[type_bond].num;
bond = (int*)malloc(sizeof(int) * (bond_size + 1));
bond[0] = type_bond;
cnt1 = cnt2 = max_cnt = 0;
for (p=0; p < N_P; p++) {
for (cnt2=0; cnt2 < max_try; cnt2++) {
/* place start monomer */
if (posed!=NULL) {
/* if position of 1st monomer is given */
if (p > 0) {
free(posed);
posed=NULL;
} else {
pos[0]=posed[0];
pos[1]=posed[1];
pos[2]=posed[2];
}
} else {
/* randomly set position */
for (cnt1=0; cnt1<max_try; cnt1++) {
pos[0]=box_l[0]*d_random();
pos[1]=box_l[1]*d_random();
pos[2]=box_l[2]*d_random();
if ((mode==1) || (collision(pos, shield, 0, NULL)==0)) break;
POLY_TRACE(printf("s"); fflush(NULL));
}
if (cnt1 >= max_try) { free(poly); return (-1); }
}
poly[0] = pos[0]; poly[1] = pos[1]; poly[2] = pos[2];
max_cnt=imax(cnt1, max_cnt);
POLY_TRACE(printf("S"); fflush(NULL));
//POLY_TRACE(/* printf("placed Monomer 0 at (%f,%f,%f)\n",pos[0],pos[1],pos[2]) */);
poz[0]=pos[0]; poz[1]=pos[1]; poz[2]=pos[2];
/* place 2nd monomer */
n=1;
if (posed2 != NULL && posed != NULL && angle2 > -1.0) {
/* if position of 2nd monomer is given */
pos[0]=posed2[0];
pos[1]=posed2[1];
pos[2]=posed2[2];
/* calculate preceding monomer so that bond_length is correct */
absc=sqrt(SQR(pos[0]-poz[0])+SQR(pos[1]-poz[1])+SQR(pos[2]-poz[2]));
poz[0]=pos[0]+(poz[0]-pos[0])*bond_length/absc;
poz[1]=pos[1]+(poz[1]-pos[1])*bond_length/absc;
poz[2]=pos[2]+(poz[2]-pos[2])*bond_length/absc;
//POLY_TRACE(/* printf("virtually shifted position of first monomer to (%f,%f,%f)\n",poz[0],poz[1],poz[2]) */);
} else {
/* randomly place 2nd monomer */
for (cnt1=0; cnt1<max_try; cnt1++) {
zz = (2.0*d_random()-1.0)*bond_length;
rr = sqrt(SQR(bond_length)-SQR(zz));
phi = 2.0*PI*d_random();
pos[0] = poz[0]+rr*cos(phi);
pos[1] = poz[1]+rr*sin(phi);
pos[2] = poz[2]+zz;
#ifdef CONSTRAINTS
if(constr==0 || constraint_collision(pos,poly+3*(n-1))==0){
#endif
if (mode==1 || collision(pos, shield, n, poly)==0) break;
if (mode==0) { cnt1 = -1; break; }
#ifdef CONSTRAINTS
}
#endif
POLY_TRACE(printf("m"); fflush(NULL));
}
if (cnt1 >= max_try) {
fprintf(stderr,"\nWarning! Attempt #%d to build polymer %d failed while placing monomer 2!\n",cnt2+1,p);
fprintf(stderr," Retrying by re-setting the start-monomer of current chain...\n");
}
if (cnt1 == -1 || cnt1 >= max_try) {
continue; /* continue the main loop */
}
}
if(posed2!=NULL && p>0) {
free(posed2);
posed2=NULL;
}
poly[3*n] = pos[0]; poly[3*n+1] = pos[1]; poly[3*n+2] = pos[2];
max_cnt=imax(cnt1, max_cnt);
POLY_TRACE(printf("M"); fflush(NULL));
//POLY_TRACE(/* printf("placed Monomer 1 at (%f,%f,%f)\n",pos[0],pos[1],pos[2]) */);
/* place remaining monomers */
for (n=2; n<MPC; n++) {
if (angle2 > -1.0) {
if(n==2) { /* if the 2nd angle is set, construct preceding monomer
with resulting plane perpendicular on the xy-plane */
poy[0]=2*poz[0]-pos[0];
poy[1]=2*poz[1]-pos[1];
if(pos[2]==poz[2])
poy[2]=poz[2]+1;
else
poy[2]=poz[2];
} else {
/* save 3rd last monomer */
pox[0]=poy[0]; pox[1]=poy[1]; pox[2]=poy[2];
}
}
if (angle > -1.0) {
/* save one but last monomer */
poy[0]=poz[0]; poy[1]=poz[1]; poy[2]=poz[2];
}
/* save last monomer */
poz[0]=pos[0]; poz[1]=pos[1]; poz[2]=pos[2];
if(angle > -1.0){
a[0]=poy[0]-poz[0];
a[1]=poy[1]-poz[1];
a[2]=poy[2]-poz[2];
b[0]=pox[0]-poy[0];
b[1]=pox[1]-poy[1];
b[2]=pox[2]-poy[2];
vector_product(a,b,c);
}
for (cnt1=0; cnt1<max_try; cnt1++) {
if(angle > -1.0) {
if (sqrlen(c) < ROUND_ERROR_PREC) {
fprintf(stderr, "WARNING: rotation axis is 0,0,0, check the angles given to the polymer command\n");
c[0] = 1; c[1] = 0; c[2] = 0;
}
if(angle2 > -1.0 && n>2) {
vec_rotate(a,angle2,c,d);
} else {
phi = 2.0*PI*d_random();
vec_rotate(a,phi,c,d);
}
vec_rotate(d,angle,a,b);
pos[0] = poz[0] + b[0];
pos[1] = poz[1] + b[1];
pos[2] = poz[2] + b[2];
} else {
zz = (2.0*d_random()-1.0)*bond_length;
rr = sqrt(SQR(bond_length)-SQR(zz));
phi = 2.0*PI*d_random();
pos[0] = poz[0]+rr*cos(phi);
pos[1] = poz[1]+rr*sin(phi);
pos[2] = poz[2]+zz;
}
//POLY_TRACE(/* printf("a=(%f,%f,%f) absa=%f M=(%f,%f,%f) c=(%f,%f,%f) absMc=%f a*c=%f)\n",a[0],a[1],a[2],sqrt(SQR(a[0])+SQR(a[1])+SQR(a[2])),M[0],M[1],M[2],c[0],c[1],c[2],sqrt(SQR(M[0]+c[0])+SQR(M[1]+c[1])+SQR(M[2]+c[2])),a[0]*c[0]+a[1]*c[1]+a[2]*c[2]) */);
//POLY_TRACE(/* printf("placed Monomer %d at (%f,%f,%f)\n",n,pos[0],pos[1],pos[2]) */);
#ifdef CONSTRAINTS
if(constr==0 || constraint_collision(pos,poly+3*(n-1))==0){
#endif
if (mode==1 || collision(pos, shield, n, poly)==0) break;
if (mode==0) { cnt1 = -2; break; }
#ifdef CONSTRAINTS
}
#endif
POLY_TRACE(printf("m"); fflush(NULL));
}
if (cnt1 >= max_try) {
fprintf(stderr,"\nWarning! Attempt #%d to build polymer %d failed after %d unsuccessful trials to place monomer %d!\n",cnt2+1,p,cnt1,n);
fprintf(stderr," Retrying by re-setting the start-monomer of current chain...\n");
}
if (cnt1 == -2 || cnt1 >= max_try) {
n=0; break;
}
poly[3*n] = pos[0]; poly[3*n+1] = pos[1]; poly[3*n+2] = pos[2];
max_cnt=imax(cnt1, max_cnt);
POLY_TRACE(printf("M"); fflush(NULL));
}
if (n>0) break;
} /* cnt2 */
POLY_TRACE(printf(" %d/%d->%d \n",cnt1,cnt2,max_cnt));
if (cnt2 >= max_try) { free(poly); return(-2); } else max_cnt = imax(max_cnt,imax(cnt1,cnt2));
/* actually creating current polymer in ESPResSo */
for (n=0; n<MPC; n++) {
pos[0] = poly[3*n]; pos[1] = poly[3*n+1]; pos[2] = poly[3*n+2];
if (place_particle(part_id, pos)==ES_PART_ERROR ||
(set_particle_q(part_id, ((n % cM_dist==0) ? val_cM : 0.0) )==ES_ERROR) ||
(set_particle_type(part_id, ((n % cM_dist==0) ? type_cM : type_nM) )==ES_ERROR))
{ free(poly); return (-3); }
if(n>=bond_size){
bond[1] = part_id - bond_size;
for(i=2;i<=bond_size;i++){
bond[i] = part_id - bond_size + i;
}
if(change_particle_bond(part_id-bond_size+1, bond, 0)==ES_ERROR)
{ free(poly); return (-3); }
}
part_id++;
//POLY_TRACE(/* printf("placed Monomer %d at (%f,%f,%f)\n",n,pos[0],pos[1],pos[2]) */);
}
}
free(poly);
return(imax(max_cnt,cnt2));
}