/* Calculate the forces on the particles of the strand that are attributed
* to the structure of the strand itself. These are:
* Fbond, Fangle, Fdihedral, Fstack. */
static void strandForces(Strand *s) {
if (s->numMonomers < 0)
return;
assert(s->Ss != NULL && s->Ps != NULL && s->Bs != NULL);
/* Bottom monomer */
FbondSB(&s->Ss[0], &s->Bs[0]);
Fbond(&s->Ss[0], &s->Ps[0], BOND_S5_P);
FangleP5SB(&s->Ps[0], &s->Ss[0], &s->Bs[0]);
/* Rest of the monomers */
for (int i = 1; i < s->numMonomers; i++) {
FbondSB(&s->Ss[i], &s->Bs[i]);
Fbond(&s->Ss[i], &s->Ps[i], BOND_S5_P);
Fbond(&s->Ss[i], &s->Ps[i-1], BOND_S3_P);
Fstack(&s->Bs[i], &s->Bs[i-1], 0);
FangleP5SB(&s->Ps[ i ], &s->Ss[ i ], &s->Bs[ i ]);
Fangle (&s->Ps[ i ], &s->Ss[ i ], &s->Ps[i-1], ANGLE_P_5S3_P);
FangleP3SB(&s->Ps[i-1], &s->Ss[ i ], &s->Bs[ i ]);
Fangle (&s->Ss[i-1], &s->Ps[i-1], &s->Ss[ i ], ANGLE_S5_P_3S);
FdihedralBS3P5S(&s->Bs[i], &s->Ss[ i ], &s->Ps[i-1], &s->Ss[i-1]);
FdihedralS3P5SB(&s->Ss[i], &s->Ps[i-1], &s->Ss[i-1], &s->Bs[i-1]);
Fdihedral(&s->Ps[i], &s->Ss[ i ], &s->Ps[i-1], &s->Ss[i-1],
dihedralP5S3P5S);
if (i < 2) continue;
Fdihedral(&s->Ss[i], &s->Ps[i-1], &s->Ss[i-1], &s->Ps[i-2],
dihedralS3P5S3P);
Fstack(&s->Bs[i], &s->Bs[i-2], 1);
}
}
static void FangleP3SB(Particle *p, Particle *s, Particle *b)
{
AngleBaseInfo info = getAngleBaseInfo(b->type);
Fangle(p, s, b, info.P3SB);
}
array minlin(const array x,const array x0,const array dx,const array y0 )
{
array res = y0 + dx * Fangle((x-x0)/dx);
res.eval();
return res;
}
array limlin( const array x, const array x0, const array dx, const array y0 )
{
array res = y0 - dx * Fangle((x-x0)*(-1.)/dx);
res.eval();
return res;
}
