/** Computes the bending force (Dupin2007 eqn. 20 and 21) and adds this
force to the particle forces (see \ref tclcommand_inter).
@param p1,p2,p3 Pointers to particles of triangle 1.
@param p2,p3,p4 Pointers to particles of triangle 2.
(triangles have particles p2 and p3 in common)
@param iaparams bending stiffness kb, initial rest angle phi0 (see \ref tclcommand_inter).
@param force1 returns force on particles of triangle 1
@param force2 returns force on particles of triangle 2
(p1 += force1; p2 += 0.5*force1+0.5*force2; p3 += 0.5*force1+0.5*force2; p4 += force2;
@return 0
*/
inline int calc_bending_force(Particle *p2, Particle *p1, Particle *p3, Particle *p4,
Bonded_ia_parameters *iaparams, double force1[3],
double force2[2])// first-fold-then-the-same approach
{
double n1[3],n2[3],dn1,dn2,phi,aa,fac,penal;
int k;
double fp1[3],fp2[3],fp3[3],fp4[3];
#ifdef LEES_EDWARDS
double vv[3];
#endif
int img[3];
memcpy(fp1, p1->r.p, 3*sizeof(double));
memcpy(img, p1->l.i, 3*sizeof(int));
fold_position(fp1, img);
memcpy(fp2, p2->r.p, 3*sizeof(double));
memcpy(img, p2->l.i, 3*sizeof(int));
fold_position(fp2, img);
memcpy(fp3, p3->r.p, 3*sizeof(double));
memcpy(img, p3->l.i, 3*sizeof(int));
fold_position(fp3, img);
memcpy(fp4, p4->r.p, 3*sizeof(double));
memcpy(img, p4->l.i, 3*sizeof(int));
fold_position(fp4, img);
get_n_triangle(fp2,fp1,fp3,n1);
dn1=normr(n1);
get_n_triangle(fp2,fp3,fp4,n2);
dn2=normr(n2);
phi = angle_btw_triangles(fp1,fp2,fp3,fp4);
if (iaparams->p.bending_force.phi0 < 0.001 || iaparams->p.bending_force.phi0 > 2*M_PI - 0.001)
printf("bending_force.h, calc_bending_force: Resting angle is close to zero!!!\n");
aa = (phi-iaparams->p.bending_force.phi0)/iaparams->p.bending_force.phi0;
fac = iaparams->p.bending_force.kb * aa;
penal = (1+1/pow(10*(2*M_PI-phi),2) + 1/pow(10*(phi),2));
if (penal > 5.) penal = 5.;
// fac = fac*penal; // This is to penalize the angles smaller than some threshold tr and also it penalizes angles greater than 2*Pi - tr. It prevents the objects to have negative angles.
if (phi < 0.001 || phi > 2*M_PI - 0.001) printf("bending_force.h, calc_bending_force: Angle approaches 0 or 2*Pi\n");
for(k=0;k<3;k++) {
force1[k]=fac * n1[k]/dn1;
force2[k]=fac * n2[k]/dn2;
}
return 0;
}
inline void calc_volume(double *volume, int molType){ //first-fold-then-the-same approach
double partVol=0.,A,norm[3],dn,hz;
/** loop over particles */
int c, np, i ,j;
Cell *cell;
Particle *p, *p1, *p2, *p3;
double p11[3],p22[3],p33[3];
int img[3];
Bonded_ia_parameters *iaparams;
int type_num, n_partners, id;
BondedInteraction type;
char *errtxt;
//int test=0;
//printf("rank%d, molType2: %d\n", rank,molType);
/* Loop local cells */
for (c = 0; c < local_cells.n; c++) {
cell = local_cells.cell[c];
p = cell->part;
np = cell->n;
/* Loop cell particles */
for(i=0; i < np; i++) {
j = 0;
p1 = &p[i];
//printf("rank%d, i=%d neigh=%d\n", rank, i, p1->bl.n);
while(j<p1->bl.n){
/* bond type */
type_num = p1->bl.e[j++]; //bond_number
iaparams = &bonded_ia_params[type_num];
type = iaparams->type; //type of interaction 14...volume_force
n_partners = iaparams->num; //bonded_neigbours
id=p1->p.mol_id; //mol_id of blood cell
if(type == BONDED_IA_VOLUME_FORCE && id == molType){ // BONDED_IA_VOLUME_FORCE with correct molType !!!!!!!!!!!!! needs area force local !!!!!!!!!!!!!!!!!!
p2 = local_particles[p1->bl.e[j++]];
if (!p2) {
printf("broken: particles sum %d, id %d, partn %d, bond %d\n", np,id,n_partners,type_num);
errtxt = runtime_error(128 + 2*ES_INTEGER_SPACE);
ERROR_SPRINTF(errtxt,"{volume calc 078 bond broken between particles %d and %d (particles not stored on the same node - volume_force1)} ",
p1->p.identity, p1->bl.e[j-1]);
return;
}
/* fetch particle 3 */
p3 = local_particles[p1->bl.e[j++]];
if (!p3) {
errtxt = runtime_error(128 + 3*ES_INTEGER_SPACE);
ERROR_SPRINTF(errtxt,"{volume calc 079 bond broken between particles %d, %d and %d (particles not stored on the same node); n %d max %d} ",
p1->p.identity, p1->bl.e[j-2], p1->bl.e[j-1],p1->bl.n,p1->bl.max);
return;
}
memcpy(p11, p1->r.p, 3*sizeof(double));
memcpy(img, p1->l.i, 3*sizeof(int));
fold_position(p11, img);
memcpy(p22, p2->r.p, 3*sizeof(double));
memcpy(img, p2->l.i, 3*sizeof(int));
fold_position(p22, img);
memcpy(p33, p3->r.p, 3*sizeof(double));
memcpy(img, p3->l.i, 3*sizeof(int));
fold_position(p33, img);
get_n_triangle(p11,p22,p33,norm);
dn=normr(norm);
A=area_triangle(p11,p22,p33);
hz=1.0/3.0 *(p11[2]+p22[2]+p33[2]);
partVol += A * -1*norm[2]/dn * hz;
}
else{
j+=n_partners;
}
}
}
}
MPI_Allreduce(&partVol, volume, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
}
inline void add_volume_force(double volume, int molType){ //first-fold-then-the-same approach
double A,norm[3],dn; //partVol=0.
double vv, force[3];
int k;
int img[3];
/** loop over particles */
int c, np, i ,j;
Cell *cell;
Particle *p, *p1, *p2, *p3;
double p11[3],p22[3],p33[3];
Bonded_ia_parameters *iaparams;
int type_num, n_partners, id;
BondedInteraction type;
char *errtxt;
int test=0;
/* Loop local cells */
for (c = 0; c < local_cells.n; c++) {
cell = local_cells.cell[c];
p = cell->part;
np = cell->n;
/* Loop cell particles */
for(i=0; i < np; i++) {
j = 0;
p1=&p[i];
//printf("i=%d neigh=%d\n", i, p1->bl.n);
while(j<p1->bl.n){
/* bond type */
type_num = p1->bl.e[j++];
iaparams = &bonded_ia_params[type_num];
type = iaparams->type;
n_partners = iaparams->num;
id=p1->p.mol_id;
if(type == BONDED_IA_VOLUME_FORCE && id == molType){ // BONDED_IA_VOLUME_FORCE with correct molType
test++;
/* fetch particle 2 */
p2 = local_particles[p1->bl.e[j++]];
if (!p2) {
errtxt = runtime_error(128 + 2*ES_INTEGER_SPACE);
ERROR_SPRINTF(errtxt,"{volume add 078 bond broken between particles %d and %d (particles not stored on the same node - volume_force2)} ",
p1->p.identity, p1->bl.e[j-1]);
return;
}
/* fetch particle 3 */
p3 = local_particles[p1->bl.e[j++]];
if (!p3) {
errtxt = runtime_error(128 + 3*ES_INTEGER_SPACE);
ERROR_SPRINTF(errtxt,"{volume add 079 bond broken between particles %d, %d and %d (particles not stored on the same node); n %d max %d} ",
p1->p.identity, p1->bl.e[j-2], p1->bl.e[j-1],p1->bl.n,p1->bl.max);
return;
}
memcpy(p11, p1->r.p, 3*sizeof(double));
memcpy(img, p1->l.i, 3*sizeof(int));
fold_position(p11, img);
memcpy(p22, p2->r.p, 3*sizeof(double));
memcpy(img, p2->l.i, 3*sizeof(int));
fold_position(p22, img);
memcpy(p33, p3->r.p, 3*sizeof(double));
memcpy(img, p3->l.i, 3*sizeof(int));
fold_position(p33, img);
get_n_triangle(p11,p22,p33,norm);
dn=normr(norm);
A=area_triangle(p11,p22,p33);
{
}
vv=(volume - iaparams->p.volume_force.V0)/iaparams->p.volume_force.V0;
for(k=0;k<3;k++) {
force[k]=iaparams->p.volume_force.kv * vv * A * norm[k]/dn * 1.0 / 3.0;
//printf("%e ",force[k]);
p1->f.f[k] += force[k];
p2->f.f[k] += force[k];
p3->f.f[k] += force[k];
}
}
else{
j+=n_partners;
}
}
}
}
}
inline void calc_volume(double *volume, int molType){ //first-fold-then-the-same approach
double partVol=0.,A,norm[3],dn,hz;
/** loop over particles */
int c, np, i ,j;
Cell *cell;
Particle *p, *p1, *p2, *p3;
double p11[3],p22[3],p33[3];
int img[3];
double AA[3],BB[3];
Bonded_ia_parameters *iaparams;
int type_num, n_partners, id;
BondedInteraction type;
//int test=0;
//printf("rank%d, molType2: %d\n", rank,molType);
/* Loop local cells */
for (c = 0; c < local_cells.n; c++) {
cell = local_cells.cell[c];
p = cell->part;
np = cell->n;
/* Loop cell particles */
for(i=0; i < np; i++) {
j = 0;
p1 = &p[i];
//printf("rank%d, i=%d neigh=%d\n", rank, i, p1->bl.n);
while(j<p1->bl.n){
/* bond type */
type_num = p1->bl.e[j++]; //bond_number
iaparams = &bonded_ia_params[type_num];
type = iaparams->type; //type of interaction 14...volume_force
n_partners = iaparams->num; //bonded_neigbours
id=p1->p.mol_id; //mol_id of blood cell
if(type == BONDED_IA_VOLUME_FORCE && id == molType){ // BONDED_IA_VOLUME_FORCE with correct molType !!!!!!!!!!!!! needs area force local !!!!!!!!!!!!!!!!!!
p2 = local_particles[p1->bl.e[j++]];
if (!p2) {
printf("broken: particles sum %d, id %d, partn %d, bond %d\n", np,id,n_partners,type_num);
ostringstream msg;
msg <<"volume calc: bond broken between particles " << p1->p.identity << " and " << p1->bl.e[j-1] << " (particles not stored on the same node - volume_force1)";
runtimeError(msg);
return;
}
/* fetch particle 3 */
p3 = local_particles[p1->bl.e[j++]];
if (!p3) {
ostringstream msg;
msg <<"volume calc: bond broken between particles " << p1->p.identity << ", " << p1->bl.e[j-2] << " and " << p1->bl.e[j-1] << " (particles not stored on the same node); n " << p1->bl.n << " max " << p1->bl.max;
runtimeError(msg);
return;
}
// particles fetched
#ifdef GHOST_FLAG
// first find out which particle out of p1, p2 (possibly p3, p4) is not a ghost particle. In almost all cases it is p1, however, it might be other one. we call this particle reference particle.
if (p1->l.ghost != 1) {
//unfold non-ghost particle using image, because for physical particles, the structure p->l.i is correctly set
memmove(p11, p1->r.p, 3*sizeof(double));
memmove(img, p1->l.i, 3*sizeof(int));
unfold_position(p11,img);
// other coordinates are obtained from its relative positions to the reference particle
get_mi_vector(AA, p2->r.p, p11);
get_mi_vector(BB, p3->r.p, p11);
for (int i=0; i < 3; i++) { p22[i] = p11[i] + AA[i]; p33[i] = p11[i] + BB[i]; }
} else {
// in case the first particle is a ghost particle
if (p2->l.ghost != 1) {
memmove(p22, p2->r.p, 3*sizeof(double));
memmove(img, p2->l.i, 3*sizeof(int));
unfold_position(p22,img);
get_mi_vector(AA, p1->r.p, p22);
get_mi_vector(BB, p3->r.p, p22);
for (int i=0; i < 3; i++) { p11[i] = p22[i] + AA[i]; p33[i] = p22[i] + BB[i]; }
} else {
// in case the first and the second particle are ghost particles
if (p3->l.ghost != 1) {
memmove(p33, p3->r.p, 3*sizeof(double));
memmove(img, p3->l.i, 3*sizeof(int));
unfold_position(p33,img);
get_mi_vector(AA, p1->r.p, p33);
get_mi_vector(BB, p2->r.p, p33);
for (int i=0; i < 3; i++) { p11[i] = p33[i] + AA[i]; p22[i] = p33[i] + BB[i]; }
} else {
printf("Something wrong in area_force_local.hpp: All particles in a bond are ghost particles, impossible to unfold the positions...");
return;
}
}
}
#endif
#ifndef GHOST_FLAG
// if ghost flag was not defined we have no other option than to assume the first particle is a physical one.
memmove(p11, p1->r.p, 3*sizeof(double));
memmove(img, p1->l.i, 3*sizeof(int));
unfold_position(p11,img);
// other coordinates are obtained from its relative positions to the reference particle
get_mi_vector(AA, p2->r.p, p11);
get_mi_vector(BB, p3->r.p, p11);
for (int i=0; i < 3; i++) { p22[i] = p11[i] + AA[i]; p33[i] = p11[i] + BB[i]; }
#endif
get_n_triangle(p11,p22,p33,norm);
dn=normr(norm);
A=area_triangle(p11,p22,p33);
hz=1.0/3.0 *(p11[2]+p22[2]+p33[2]);
partVol += A * -1*norm[2]/dn * hz;
}
else{
j+=n_partners;
}
}
}
}
MPI_Allreduce(&partVol, volume, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
}
inline void add_volume_force(double volume, int molType){ //first-fold-then-the-same approach
double A,norm[3],dn; //partVol=0.
double vv, force[3];
int k;
int img[3];
/** loop over particles */
int c, np, i ,j;
Cell *cell;
Particle *p, *p1, *p2, *p3;
double p11[3],p22[3],p33[3];
Bonded_ia_parameters *iaparams;
int type_num, n_partners, id;
BondedInteraction type;
double AA[3],BB[3];
int test=0;
/* Loop local cells */
for (c = 0; c < local_cells.n; c++) {
cell = local_cells.cell[c];
p = cell->part;
np = cell->n;
/* Loop cell particles */
for(i=0; i < np; i++) {
j = 0;
p1=&p[i];
//printf("i=%d neigh=%d\n", i, p1->bl.n);
while(j<p1->bl.n){
/* bond type */
type_num = p1->bl.e[j++];
iaparams = &bonded_ia_params[type_num];
type = iaparams->type;
n_partners = iaparams->num;
id=p1->p.mol_id;
if(type == BONDED_IA_VOLUME_FORCE && id == molType){ // BONDED_IA_VOLUME_FORCE with correct molType
test++;
/* fetch particle 2 */
p2 = local_particles[p1->bl.e[j++]];
if (!p2) {
ostringstream msg;
msg <<"volume add: bond broken between particles " << p1->p.identity << " and " << p1->bl.e[j-1] << " (particles not stored on the same node - volume_force2)";
runtimeError(msg);
return;
}
/* fetch particle 3 */
p3 = local_particles[p1->bl.e[j++]];
if (!p3) {
ostringstream msg;
msg <<"volume calc: bond broken between particles " << p1->p.identity << ", " << p1->bl.e[j-2] << " and " << p1->bl.e[j-1] << " (particles not stored on the same node); n " << p1->bl.n << " max " << p1->bl.max;
runtimeError(msg);
return;
}
// particles fetched
#ifdef GHOST_FLAG
// first find out which particle out of p1, p2 (possibly p3, p4) is not a ghost particle. In almost all cases it is p1, however, it might be other one. we call this particle reference particle.
if (p1->l.ghost != 1) {
//unfold non-ghost particle using image, because for physical particles, the structure p->l.i is correctly set
memmove(p11, p1->r.p, 3*sizeof(double));
memmove(img, p1->l.i, 3*sizeof(int));
unfold_position(p11,img);
// other coordinates are obtained from its relative positions to the reference particle
get_mi_vector(AA, p2->r.p, p11);
get_mi_vector(BB, p3->r.p, p11);
for (int i=0; i < 3; i++) { p22[i] = p11[i] + AA[i]; p33[i] = p11[i] + BB[i]; }
} else {
// in case the first particle is a ghost particle
if (p2->l.ghost != 1) {
memmove(p22, p2->r.p, 3*sizeof(double));
memmove(img, p2->l.i, 3*sizeof(int));
unfold_position(p22,img);
get_mi_vector(AA, p1->r.p, p22);
get_mi_vector(BB, p3->r.p, p22);
for (int i=0; i < 3; i++) { p11[i] = p22[i] + AA[i]; p33[i] = p22[i] + BB[i]; }
} else {
// in case the first and the second particle are ghost particles
if (p3->l.ghost != 1) {
memmove(p33, p3->r.p, 3*sizeof(double));
memmove(img, p3->l.i, 3*sizeof(int));
unfold_position(p33,img);
get_mi_vector(AA, p1->r.p, p33);
get_mi_vector(BB, p2->r.p, p33);
for (int i=0; i < 3; i++) { p11[i] = p33[i] + AA[i]; p22[i] = p33[i] + BB[i]; }
} else {
printf("Something wrong in area_force_local.hpp: All particles in a bond are ghost particles, impossible to unfold the positions...");
return;
}
}
}
#endif
#ifndef GHOST_FLAG
// if ghost flag was not defined we have no other option than to assume the first particle is a physical one.
memmove(p11, p1->r.p, 3*sizeof(double));
memmove(img, p1->l.i, 3*sizeof(int));
unfold_position(p11,img);
// other coordinates are obtained from its relative positions to the reference particle
get_mi_vector(AA, p2->r.p, p11);
get_mi_vector(BB, p3->r.p, p11);
for (int i=0; i < 3; i++) { p22[i] = p11[i] + AA[i]; p33[i] = p11[i] + BB[i]; }
#endif
get_n_triangle(p11,p22,p33,norm);
dn=normr(norm);
A=area_triangle(p11,p22,p33);
{
}
vv=(volume - iaparams->p.volume_force.V0)/iaparams->p.volume_force.V0;
for(k=0;k<3;k++) {
force[k]=iaparams->p.volume_force.kv * vv * A * norm[k]/dn * 1.0 / 3.0;
//printf("%e ",force[k]);
p1->f.f[k] += force[k];
p2->f.f[k] += force[k];
p3->f.f[k] += force[k];
}
}
else{
j+=n_partners;
}
}
}
}
}