inline void calc_bonded_force(Particle *p1, Particle *p2, Bonded_ia_parameters *iaparams, int *i, double dx[3], double force[3]) {
#ifdef TABULATED
//char* errtxt;
#endif
/* Calculates the bonded force between two particles */
switch(iaparams->type) {
case BONDED_IA_FENE:
calc_fene_pair_force(p1,p2,iaparams,dx,force);
break;
#ifdef ROTATION
case BONDED_IA_HARMONIC_DUMBBELL:
calc_harmonic_dumbbell_pair_force(p1,p2,iaparams,dx,force);
break;
#endif
case BONDED_IA_HARMONIC:
calc_harmonic_pair_force(p1,p2,iaparams,dx,force);
break;
#ifdef LENNARD_JONES
case BONDED_IA_SUBT_LJ:
calc_subt_lj_pair_force(p1,p2,iaparams,dx,force);
break;
#endif
/* since it is not clear at the moment how to handle a many body interaction here, I skip it */
case BONDED_IA_ANGLE_HARMONIC:
(*i)++;
force[0] = force[1] = force[2] = 0;
break;
case BONDED_IA_ANGLE_COSINE:
(*i)++;
force[0] = force[1] = force[2] = 0;
break;
case BONDED_IA_ANGLE_COSSQUARE:
(*i)++;
force[0] = force[1] = force[2] = 0;
break;
case BONDED_IA_ANGLEDIST:
(*i)++;
force[0] = force[1] = force[2] = 0;
break;
case BONDED_IA_DIHEDRAL:
(*i)+=2;
force[0] = force[1] = force[2] = 0;
break;
#ifdef TABULATED
case BONDED_IA_TABULATED:
// printf("BONDED TAB, Particle: %d, P2: %d TYPE_TAB: %d\n",p1->p.identity,p2->p.identity,iparams->p.tab.type);
switch(iaparams->p.tab.type) {
case TAB_BOND_LENGTH:
calc_tab_bond_force(p1, p2, iaparams, dx, force);
break;
case TAB_BOND_ANGLE:
(*i)++;
force[0] = force[1] = force[2] = 0;
break;
case TAB_BOND_DIHEDRAL:
(*i)+=2;
force[0] = force[1] = force[2] = 0;
break;
default:
runtimeErrorMsg() <<"calc_bonded_force: tabulated bond type of atom " << p1->p.identity << " unknown\n";
return;
}
break;
#endif
#ifdef OVERLAPPED
case BONDED_IA_OVERLAPPED:
// printf("BONDED OVERLAP, Particle: %d, P2: %d TYPE_OVERLAP: %d\n",p1->p.identity,p2->p.identity,iparams->p.tab.type);
//char *errtxt;
switch(iaparams->p.overlap.type) {
case OVERLAP_BOND_LENGTH:
calc_overlap_bond_force(p1, p2, iaparams, dx, force);
break;
case OVERLAP_BOND_ANGLE:
(*i)++;
force[0] = force[1] = force[2] = 0;
break;
case OVERLAP_BOND_DIHEDRAL:
(*i)+=2;
force[0] = force[1] = force[2] = 0;
break;
default:
runtimeErrorMsg() <<"calc_bonded_force: overlapped bond type of atom " << p1->p.identity << " unknown\n";
return;
}
break;
#endif
#ifdef BOND_CONSTRAINT
case BONDED_IA_RIGID_BOND:
force[0] = force[1] = force[2] = 0;
break;
#endif
#ifdef BOND_VIRTUAL
case BONDED_IA_VIRTUAL_BOND:
force[0] = force[1] = force[2] = 0;
break;
#endif
default :
// fprintf(stderr,"add_bonded_virials: WARNING: Bond type %d of atom %d unhandled\n",bonded_ia_params[type_num].type,p1->p.identity);
fprintf(stderr,"add_bonded_virials: WARNING: Bond type %d , atom %d unhandled, Atom 2: %d\n",iaparams->type,p1->p.identity,p2->p.identity);
force[0] = force[1] = force[2] = 0;
break;
}
}
inline void add_bonded_force(Particle *p1)
{
double dx[3] = { 0., 0., 0. };
double force[3] = { 0., 0., 0. };
double force2[3] = { 0., 0., 0. };
double force3[3] = { 0., 0., 0. };
#if defined(HYDROGEN_BOND) || defined(TWIST_STACK) || defined(OIF_LOCAL_FORCES)
double force4[3] = { 0., 0., 0. };
#endif
#ifdef TWIST_STACK
double force5[3] = { 0., 0., 0. };
double force6[3] = { 0., 0., 0. };
double force7[3] = { 0., 0., 0. };
double force8[3] = { 0., 0., 0. };
Particle *p5 = NULL,*p6 = NULL,*p7 = NULL,*p8 = NULL;
#endif
#ifdef ROTATION
double torque1[3] = { 0., 0., 0. };
double torque2[3] = { 0., 0., 0. };
#endif
Particle *p2 = NULL, *p3 = NULL, *p4 = NULL;
Bonded_ia_parameters *iaparams;
int i, j, type_num, type, n_partners, bond_broken;
i = 0;
while (i<p1->bl.n) {
type_num = p1->bl.e[i++];
iaparams = &bonded_ia_params[type_num];
type = iaparams->type;
n_partners = iaparams->num;
/* fetch particle 2, which is always needed */
p2 = local_particles[p1->bl.e[i++]];
if (!p2) {
ostringstream msg;
msg << "bond broken between particles " << p1->p.identity << " and "
<< p1->bl.e[i-1] << " (particles are not stored on the same node)";
runtimeError(msg);
return;
}
/* fetch particle 3 eventually */
if (n_partners >= 2) {
p3 = local_particles[p1->bl.e[i++]];
if (!p3) {
ostringstream msg;
msg << "bond broken between particles "
<< p1->p.identity << ", "
<< p1->bl.e[i-2] << " and "
<< p1->bl.e[i-1] << " (particles are not stored on the same node)";
runtimeError(msg);
return;
}
}
/* fetch particle 4 eventually */
if (n_partners >= 3) {
p4 = local_particles[p1->bl.e[i++]];
if (!p4) {
ostringstream msg;
msg <<"bond broken between particles "<< p1->p.identity << ", " << p1->bl.e[i-3] << ", " << p1->bl.e[i-2]
<< " and " << p1->bl.e[i-1] << " (particles not stored on the same node)";
runtimeError(msg);
return;
}
}
#ifdef TWIST_STACK
if(n_partners >= 7) {
p5 = local_particles[p1->bl.e[i++]];
p6 = local_particles[p1->bl.e[i++]];
p7 = local_particles[p1->bl.e[i++]];
p8 = local_particles[p1->bl.e[i++]];
if(!p4 || !p5 || !p6 || !p7 || !p8) {
ostringstream msg;
msg << "bond broken between particles" <<
p1->p.identity << ", " << p1->bl.e[i-7] << ", " << p1->bl.e[i-6] << ", " << p1->bl.e[i-5] << ", " << p1->bl.e[i-4] << ", " << p1->bl.e[i-3] << ", " << p1->bl.e[i-2] << ", " << p1->bl.e[i-1] << " (particles not stored on the same node)";
return;
}
}
#endif
if (n_partners == 1) {
/* because of the NPT pressure calculation for pair forces, we need the
1->2 distance vector here. For many body interactions this vector is not needed,
and the pressure calculation not yet clear. */
get_mi_vector(dx, p1->r.p, p2->r.p);
}
switch (type) {
case BONDED_IA_FENE:
bond_broken = calc_fene_pair_force(p1, p2, iaparams, dx, force);
break;
#ifdef ROTATION
case BONDED_IA_HARMONIC_DUMBBELL:
bond_broken = calc_harmonic_dumbbell_pair_force(p1, p2, iaparams, dx, force);
break;
#endif
case BONDED_IA_HARMONIC:
bond_broken = calc_harmonic_pair_force(p1, p2, iaparams, dx, force);
break;
case BONDED_IA_QUARTIC:
bond_broken = calc_quartic_pair_force(p1, p2, iaparams, dx, force);
break;
#ifdef ELECTROSTATICS
case BONDED_IA_BONDED_COULOMB:
bond_broken = calc_bonded_coulomb_pair_force(p1, p2, iaparams, dx, force);
break;
#endif
#ifdef HYDROGEN_BOND
case BONDED_IA_CG_DNA_BASEPAIR:
bond_broken = calc_hydrogen_bond_force(p1, p2, p3, p4, iaparams, force, force2, force3, force4);
break;
#endif
#ifdef TWIST_STACK
case BONDED_IA_CG_DNA_STACKING:
bond_broken = calc_twist_stack_force(p1, p2, p3, p4, p5, p6, p7, p8, iaparams,
force, force2, force3, force4, force5, force6, force7, force8);
break;
#endif
#ifdef MEMBRANE_COLLISION
case BONDED_IA_OIF_OUT_DIRECTION:
bond_broken = calc_out_direction(p1, p2, p3, p4, iaparams);
break;
#endif
#ifdef OIF_GLOBAL_FORCES
case BONDED_IA_OIF_GLOBAL_FORCES:
bond_broken = 0;
break;
#endif
#ifdef OIF_LOCAL_FORCES
case BONDED_IA_OIF_LOCAL_FORCES:
bond_broken = calc_oif_local(p1, p2, p3, p4, iaparams, force, force2, force3, force4);
break;
#endif
// IMMERSED_BOUNDARY
#ifdef IMMERSED_BOUNDARY
/* case BONDED_IA_IBM_WALL_REPULSION:
IBM_WallRepulsion_CalcForce(p1, iaparams);
bond_broken = 0;
// These may be added later on, but we set them to zero because the force has already been added in IBM_WallRepulsion_CalcForce
force[0] = force2[0] = force3[0] = 0;
force[1] = force2[1] = force3[1] = 0;
force[2] = force2[2] = force3[2] = 0;
break;*/
case BONDED_IA_IBM_TRIEL:
bond_broken = IBM_Triel_CalcForce(p1, p2, p3, iaparams);
// These may be added later on, but we set them to zero because the force has already been added in IBM_Triel_CalcForce
force[0] = force2[0] = force3[0] = 0;
force[1] = force2[1] = force3[1] = 0;
force[2] = force2[2] = force3[2] = 0;
break;
case BONDED_IA_IBM_VOLUME_CONSERVATION:
bond_broken = 0;
// Don't do anything here. We calculate and add the global volume forces in IBM_VolumeConservation. They cannot be calculated on a per-bond basis
force[0] = force2[0] = force3[0] = 0;
force[1] = force2[1] = force3[1] = 0;
force[2] = force2[2] = force3[2] = 0;
break;
case BONDED_IA_IBM_TRIBEND:
{
// First build neighbor list. This includes all nodes around the central node.
const int numNeighbors = iaparams->num;
Particle **neighbors = new Particle *[numNeighbors];
// Three are already there
neighbors[0] = p2;
neighbors[1] = p3;
neighbors[2] = p4;
// Get rest
for (int j=3; j < numNeighbors; j++)
neighbors[j] = local_particles[p1->bl.e[i++]];
IBM_Tribend_CalcForce(p1, numNeighbors, neighbors, *iaparams);
bond_broken = 0;
// Clean up
delete []neighbors;
// These may be added later on, but we set them to zero because the force has
force[0] = force2[0] = force3[0] = 0;
force[1] = force2[1] = force3[1] = 0;
force[2] = force2[2] = force3[2] = 0;
break;
}
#endif
#ifdef LENNARD_JONES
case BONDED_IA_SUBT_LJ:
bond_broken = calc_subt_lj_pair_force(p1, p2, iaparams, dx, force);
break;
#endif
#ifdef BOND_ANGLE_OLD
/* the first case is not needed and should not be called */
case BONDED_IA_ANGLE_OLD:
bond_broken = calc_angle_force(p1, p2, p3, iaparams, force, force2);
break;
#endif
#ifdef BOND_ANGLE
case BONDED_IA_ANGLE_HARMONIC:
bond_broken = calc_angle_harmonic_force(p1, p2, p3, iaparams, force, force2);
break;
case BONDED_IA_ANGLE_COSINE:
bond_broken = calc_angle_cosine_force(p1, p2, p3, iaparams, force, force2);
break;
case BONDED_IA_ANGLE_COSSQUARE:
bond_broken = calc_angle_cossquare_force(p1, p2, p3, iaparams, force, force2);
break;
#endif
#ifdef BOND_ANGLEDIST
case BONDED_IA_ANGLEDIST:
bond_broken = calc_angledist_force(p1, p2, p3, iaparams, force, force2);
break;
#endif
#ifdef BOND_ENDANGLEDIST
case BONDED_IA_ENDANGLEDIST:
bond_broken = calc_endangledist_pair_force(p1, p2, iaparams, dx, force, force2);
break;
#endif
case BONDED_IA_DIHEDRAL:
bond_broken = calc_dihedral_force(p1, p2, p3, p4, iaparams, force, force2, force3);
break;
#ifdef BOND_CONSTRAINT
case BONDED_IA_RIGID_BOND:
//add_rigid_bond_pair_force(p1,p2, iaparams, force, force2);
bond_broken = 0;
force[0]=force[1]=force[2]=0.0;
break;
#endif
#ifdef TABULATED
case BONDED_IA_TABULATED:
switch(iaparams->p.tab.type) {
case TAB_BOND_LENGTH:
bond_broken = calc_tab_bond_force(p1, p2, iaparams, dx, force);
break;
case TAB_BOND_ANGLE:
bond_broken = calc_tab_angle_force(p1, p2, p3, iaparams, force, force2);
break;
case TAB_BOND_DIHEDRAL:
bond_broken = calc_tab_dihedral_force(p1, p2, p3, p4, iaparams, force, force2, force3);
break;
default:
ostringstream msg;
msg << "add_bonded_force: tabulated bond type of atom "<< p1->p.identity << " unknown\n";
runtimeError(msg);
return;
}
break;
#endif
#ifdef OVERLAPPED
case BONDED_IA_OVERLAPPED:
switch(iaparams->p.overlap.type) {
case OVERLAP_BOND_LENGTH:
bond_broken = calc_overlap_bond_force(p1, p2, iaparams, dx, force);
break;
case OVERLAP_BOND_ANGLE:
bond_broken = calc_overlap_angle_force(p1, p2, p3, iaparams, force, force2);
break;
case OVERLAP_BOND_DIHEDRAL:
bond_broken = calc_overlap_dihedral_force(p1, p2, p3, p4, iaparams, force, force2, force3);
break;
default:
ostringstream msg;
msg <<"add_bonded_force: overlapped bond type of atom "<< p1->p.identity << " unknown\n";
runtimeError(msg);
return;
}
break;
#endif
#ifdef BOND_VIRTUAL
case BONDED_IA_VIRTUAL_BOND:
bond_broken = 0;
force[0]=force[1]=force[2]=0.0;
break;
#endif
default :
ostringstream msg;
msg <<"add_bonded_force: bond type of atom "<< p1->p.identity << " unknown\n";
runtimeError(msg);
return;
}
switch (n_partners) {
case 1:
if (bond_broken) {
ostringstream msg;
msg <<"bond broken between particles " << p1->p.identity << " and " << p2->p.identity<<". Distance vector: "<<dx[0]<<" "<<dx[1]<<" "<<dx[2];
runtimeError(msg);
continue;
}
for (j = 0; j < 3; j++) {
switch (type) {
#ifdef BOND_ENDANGLEDIST
case BONDED_IA_ENDANGLEDIST:
p1->f.f[j] += force[j];
p2->f.f[j] += force2[j];
break;
#endif // BOND_ENDANGLEDIST
default:
p1->f.f[j] += force[j];
p2->f.f[j] -= force[j];
#ifdef ROTATION
p1->f.torque[j] += torque1[j];
p2->f.torque[j] += torque2[j];
#endif
}
#ifdef NPT
if(integ_switch == INTEG_METHOD_NPT_ISO)
nptiso.p_vir[j] += force[j] * dx[j];
#endif
}
break;
case 2:
if (bond_broken) {
ostringstream msg;
msg << "bond broken between particles "<< p1->p.identity << ", " << p2->p.identity << " and "
<< p3->p.identity;
runtimeError(msg);
continue;
}
for (j = 0; j < 3; j++) {
switch (type) {
#ifdef OIF_GLOBAL_FORCES
case BONDED_IA_OIF_GLOBAL_FORCES:
break;
#endif
default:
p1->f.f[j] += force[j];
p2->f.f[j] += force2[j];
p3->f.f[j] -= (force[j] + force2[j]);
}
}
break;
case 3:
if (bond_broken) {
ostringstream msg;
msg << "bond broken between particles "<< p1->p.identity << ", " << p2->p.identity
<< ", " << p3->p.identity << " and " << p4->p.identity;
runtimeError(msg);
continue;
}
switch (type) {
case BONDED_IA_DIHEDRAL:
for (j = 0; j < 3; j++) {
p1->f.f[j] += force[j];
p2->f.f[j] += force2[j];
p3->f.f[j] += force3[j];
p4->f.f[j] -= force[j] + force2[j] + force3[j];
}
break;
#ifdef OIF_LOCAL_FORCES
case BONDED_IA_OIF_LOCAL_FORCES:
for (j = 0; j < 3; j++) {
p1->f.f[j] += force2[j];
p2->f.f[j] += force[j];
p3->f.f[j] += force3[j];
p4->f.f[j] += force4[j];
}
break;
#endif
#ifdef CG_DNA
default:
for (j = 0; j < 3; j++) {
p1->f.f[j] += force[j];
p2->f.f[j] += force2[j];
p3->f.f[j] += force3[j];
p4->f.f[j] += force4[j];
}
break;
#endif
}
break;
case 7:
if (bond_broken) {
ostringstream msg;
msg << "bond broken between particles "<< p1->p.identity << ", " << p2->p.identity
<< ", " << p3->p.identity << " and " << p4->p.identity;
runtimeError(msg);
continue;
}
switch(type) {
case BONDED_IA_CG_DNA_STACKING:
#ifdef CG_DNA
for (j = 0; j < 3; j++) {
p1->f.f[j] += force[j];
p2->f.f[j] += force2[j];
p3->f.f[j] += force3[j];
p4->f.f[j] += force4[j];
p5->f.f[j] += force5[j];
p6->f.f[j] += force6[j];
p7->f.f[j] += force7[j];
p8->f.f[j] += force8[j];
}
#endif
break;
}
}
}
}
