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#include "primitives/Torsion.hpp" |
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namespace oopse { |
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|
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Torsion::Torsion(Atom* atom1, Atom* atom2, Atom* atom3, Atom* atom4, TorsionType* tt) |
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: atom1_(atom1), atom2_(atom2), atom3_(atom3), atom4_(atom4) { |
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|
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} |
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|
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void Torsion::calcForce() { |
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Vector3d pos1 = atom1_->getPos(); |
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Vector3d pos2 = atom2_->getPos(); |
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Vector3d pos3 = atom3_->getPos(); |
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Vector3d pos4 = atom4_->getPos(); |
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|
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Vector3d r12 = pos1 - pos2; |
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Vector3d r23 = pos2 - pos3; |
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Vector3d r34 = pos3 - pos4; |
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|
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// Calculate the cross products and distances |
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Vector3d A = cross(r12,r23); |
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double rA = A.length(); |
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Vector3d B = cross(r23,r34); |
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double rB = B.length(); |
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Vector3d C = cross(r23,A); |
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double rC = C.length(); |
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|
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// Calculate the sin and cos |
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double cos_phi = (A*B)/(rA*rB); |
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double sin_phi = (C*B)/(rC*rB); |
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|
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double phi= -atan2(sin_phi,cos_phi); |
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|
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double firstDerivative; |
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torsionType_->calcForce(phi, firstDerivative, potential_); |
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|
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|
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Vector3d f1,f2,f3; |
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|
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// Normalize B |
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rB = 1.0/rB; |
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B *= rB; |
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|
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// Next, we want to calculate the forces. In order |
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// to do that, we first need to figure out whether the |
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// sin or cos form will be more stable. For this, |
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// just look at the value of phi |
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if (fabs(sin_phi) > 0.1) { |
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// use the sin version to avoid 1/cos terms |
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|
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rA = 1.0/rA; |
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A *= rA; |
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Vector3d dcosdA = rA*(cos_phi*A-B); |
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Vector3d dcosdB = rB*(cos_phi*B-A); |
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|
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K1 = K1/sin_phi; |
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|
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//simple form |
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//f1 = K1 * cross(r23, dcosdA); |
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//f3 = K1 * cross(r23, dcosdB); |
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//f2 = K1 * ( cross(r34, dcosdB) - cross(r12, dcosdA)); |
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|
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f1.x = K1*(r23.y*dcosdA.z - r23.z*dcosdA.y); |
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f1.y = K1*(r23.z*dcosdA.x - r23.x*dcosdA.z); |
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f1.z = K1*(r23.x*dcosdA.y - r23.y*dcosdA.x); |
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f3.x = K1*(r23.z*dcosdB.y - r23.y*dcosdB.z); |
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f3.y = K1*(r23.x*dcosdB.z - r23.z*dcosdB.x); |
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f3.z = K1*(r23.y*dcosdB.x - r23.x*dcosdB.y); |
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f2.x = K1*(r12.z*dcosdA.y - r12.y*dcosdA.z + r34.y*dcosdB.z - r34.z*dcosdB.y); |
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f2.y = K1*(r12.x*dcosdA.z - r12.z*dcosdA.x + r34.z*dcosdB.x - r34.x*dcosdB.z); |
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f2.z = K1*(r12.y*dcosdA.x - r12.x*dcosdA.y + r34.x*dcosdB.y - r34.y*dcosdB.x); |
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} else { |
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// This angle is closer to 0 or 180 than it is to |
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// 90, so use the cos version to avoid 1/sin terms |
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|
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// Normalize C |
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rC = 1.0/rC; |
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C *= rC; |
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Vector3d dsindC = rC*(sin_phi*C-B); |
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Vector3d dsindB = rB*(sin_phi*B-C); |
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K1 = -K1/cos_phi; |
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f1.x = K1*((r23.y*r23.y + r23.z*r23.z)*dsindC.x - r23.x*r23.y*dsindC.y - r23.x*r23.z*dsindC.z); |
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f1.y = K1*((r23.z*r23.z + r23.x*r23.x)*dsindC.y - r23.y*r23.z*dsindC.z - r23.y*r23.x*dsindC.x); |
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f1.z = K1*((r23.x*r23.x + r23.y*r23.y)*dsindC.z - r23.z*r23.x*dsindC.x - r23.z*r23.y*dsindC.y); |
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f3 = K1 *cross(dsindB,r23); |
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f2.x = K1*(-(r23.y*r12.y + r23.z*r12.z)*dsindC.x + (2.0*r23.x*r12.y - r12.x*r23.y)*dsindC.y |
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+ (2.0*r23.x*r12.z - r12.x*r23.z)*dsindC.z + dsindB.z*r34.y - dsindB.y*r34.z); |
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f2.y = K1*(-(r23.z*r12.z + r23.x*r12.x)*dsindC.y + (2.0*r23.y*r12.z - r12.y*r23.z)*dsindC.z |
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+ (2.0*r23.y*r12.x - r12.y*r23.x)*dsindC.x + dsindB.x*r34.z - dsindB.z*r34.x); |
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f2.z = K1*(-(r23.x*r12.x + r23.y*r12.y)*dsindC.z + (2.0*r23.z*r12.x - r12.z*r23.x)*dsindC.x |
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+(2.0*r23.z*r12.y - r12.z*r23.y)*dsindC.y + dsindB.y*r34.x - dsindB.x*r34.y); |
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} |
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|
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atom1_->addFrc(f1); |
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atom2_->addFrc(f2 - f1); |
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atom3_->addFrc(f3 - f2); |
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atom4_->addFrc(-f3); |
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|
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} |
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|
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double K=0; // energy |
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double K1=0; // force |
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|
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// get the dihedral information |
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int multiplicity = value->multiplicity; |
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|
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// Loop through the multiple parameter sets for this |
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// bond. We will only loop more than once if this |
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// has multiple parameter sets from Charmm22 |
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for (int mult_num=0; mult_num<multiplicity; mult_num++) |
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{ |
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/* get angle information */ |
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double k = value->values[mult_num].k * scale; |
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double delta = value->values[mult_num].delta; |
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int n = value->values[mult_num].n; |
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|
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// Calculate the energy |
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if (n) |
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{ |
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// Periodicity is greater than 0, so use cos form |
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K += k*(1+cos(n*phi + delta)); |
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K1 += -n*k*sin(n*phi + delta); |
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} |
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else |
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{ |
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// Periodicity is 0, so just use the harmonic form |
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double diff = phi-delta; |
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if (diff < -PI) diff += TWOPI; |
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else if (diff > PI) diff -= TWOPI; |
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|
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K += k*diff*diff; |
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K1 += 2.0*k*diff; |
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} |
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} /* for multiplicity */ |
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|
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void Torsion::calc_forces(){ |
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|
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/********************************************************************** |
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* |
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* initialize vectors |
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* |
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***********************************************************************/ |
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|
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vect r_ab; /* the vector whose origin is a and end is b */ |
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vect r_cb; /* the vector whose origin is c and end is b */ |
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vect r_cd; /* the vector whose origin is c and end is b */ |
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vect r_cr1; /* the cross product of r_ab and r_cb */ |
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vect r_cr2; /* the cross product of r_cb and r_cd */ |
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|
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double r_cr1_x2; /* the components of r_cr1 squared */ |
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double r_cr1_y2; |
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double r_cr1_z2; |
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|
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double r_cr2_x2; /* the components of r_cr2 squared */ |
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double r_cr2_y2; |
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double r_cr2_z2; |
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|
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double r_cr1_sqr; /* the length of r_cr1 squared */ |
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double r_cr2_sqr; /* the length of r_cr2 squared */ |
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|
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double r_cr1_r_cr2; /* the length of r_cr1 * length of r_cr2 */ |
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|
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Vector3d aR, bR, cR, dR; |
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Vector3d aF, bF, cF, dF; |
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|
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aR = c_p_a->getPos(); |
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bR = c_p_b->getPos(); |
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cR = c_p_c->getPos(); |
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dR = c_p_d->getPos(); |
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|
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r_ab.x = bR[0] - aR[0]; |
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r_ab.y = bR[1] - aR[1]; |
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r_ab.z = bR[2] - aR[2]; |
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r_ab.length = sqrt((r_ab.x * r_ab.x + r_ab.y * r_ab.y + r_ab.z * r_ab.z)); |
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|
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r_cb.x = bR[0] - cR[0]; |
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r_cb.y = bR[1] - cR[1]; |
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r_cb.z = bR[2] - cR[2]; |
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r_cb.length = sqrt((r_cb.x * r_cb.x + r_cb.y * r_cb.y + r_cb.z * r_cb.z)); |
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|
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r_cd.x = dR[0] - cR[0]; |
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r_cd.y = dR[1] - cR[1]; |
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r_cd.z = dR[2] - cR[2]; |
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r_cd.length = sqrt((r_cd.x * r_cd.x + r_cd.y * r_cd.y + r_cd.z * r_cd.z)); |
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|
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r_cr1.x = r_ab.y * r_cb.z - r_cb.y * r_ab.z; |
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r_cr1.y = r_ab.z * r_cb.x - r_cb.z * r_ab.x; |
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r_cr1.z = r_ab.x * r_cb.y - r_cb.x * r_ab.y; |
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r_cr1_x2 = r_cr1.x * r_cr1.x; |
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r_cr1_y2 = r_cr1.y * r_cr1.y; |
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r_cr1_z2 = r_cr1.z * r_cr1.z; |
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r_cr1_sqr = r_cr1_x2 + r_cr1_y2 + r_cr1_z2; |
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r_cr1.length = sqrt(r_cr1_sqr); |
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|
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r_cr2.x = r_cb.y * r_cd.z - r_cd.y * r_cb.z; |
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r_cr2.y = r_cb.z * r_cd.x - r_cd.z * r_cb.x; |
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r_cr2.z = r_cb.x * r_cd.y - r_cd.x * r_cb.y; |
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r_cr2_x2 = r_cr2.x * r_cr2.x; |
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r_cr2_y2 = r_cr2.y * r_cr2.y; |
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r_cr2_z2 = r_cr2.z * r_cr2.z; |
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r_cr2_sqr = r_cr2_x2 + r_cr2_y2 + r_cr2_z2; |
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r_cr2.length = sqrt(r_cr2_sqr); |
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|
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r_cr1_r_cr2 = r_cr1.length * r_cr2.length; |
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|
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//Vector3d pos1 = atom1_->getPos(); |
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//Vector3d pos2 = atom2_->getPos(); |
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//Vector3d pos3 = atom3_->getPos(); |
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//Vector3d pos4 = atom4_->getPos(); |
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|
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//Vector3d r12 = pos2 - pos1; |
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//Vector3d r32 = pos2 - pos3; |
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//Vector3d r34 = pos4 - pos3; |
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|
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//A = cross(r12, r32); |
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//B = cross(r32, r34); |
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|
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//rA = A.length(); |
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//rB = B.length(); |
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|
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/********************************************************************** |
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* |
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* dot product and angle calculations |
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* |
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***********************************************************************/ |
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|
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double cr1_dot_cr2; /* the dot product of the cr1 and cr2 vectors */ |
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double cos_phi; /* the cosine of the torsion angle */ |
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|
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cr1_dot_cr2 = r_cr1.x * r_cr2.x + r_cr1.y * r_cr2.y + r_cr1.z * r_cr2.z; |
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|
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cos_phi = cr1_dot_cr2 / r_cr1_r_cr2; |
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|
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/* adjust for the granularity of the numbers for angles near 0 or pi */ |
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|
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if(cos_phi > 1.0) cos_phi = 1.0; |
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if(cos_phi < -1.0) cos_phi = -1.0; |
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|
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//cos_phi = dot (A, B) / (rA * rB); |
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//if (cos_phi > 1.0) { |
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// cos_phi = 1.0; |
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//} |
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//if (cos_phi < -1.0) { |
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// cos_phi = -1.0; |
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//} |
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|
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|
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|
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/******************************************************************** |
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* |
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* This next section calculates derivatives needed for the force |
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* calculation |
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* |
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********************************************************************/ |
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|
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|
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/* the derivatives of cos phi with respect to the x, y, |
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and z components of vectors cr1 and cr2. */ |
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double d_cos_dx_cr1; |
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double d_cos_dy_cr1; |
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double d_cos_dz_cr1; |
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double d_cos_dx_cr2; |
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double d_cos_dy_cr2; |
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double d_cos_dz_cr2; |
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|
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d_cos_dx_cr1 = r_cr2.x / r_cr1_r_cr2 - (cos_phi * r_cr1.x) / r_cr1_sqr; |
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d_cos_dy_cr1 = r_cr2.y / r_cr1_r_cr2 - (cos_phi * r_cr1.y) / r_cr1_sqr; |
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d_cos_dz_cr1 = r_cr2.z / r_cr1_r_cr2 - (cos_phi * r_cr1.z) / r_cr1_sqr; |
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|
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d_cos_dx_cr2 = r_cr1.x / r_cr1_r_cr2 - (cos_phi * r_cr2.x) / r_cr2_sqr; |
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d_cos_dy_cr2 = r_cr1.y / r_cr1_r_cr2 - (cos_phi * r_cr2.y) / r_cr2_sqr; |
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d_cos_dz_cr2 = r_cr1.z / r_cr1_r_cr2 - (cos_phi * r_cr2.z) / r_cr2_sqr; |
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|
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//Vector3d dcosdA = B /(rA * rB) - cos_phi /(rA * rA) * A; |
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//Vector3d dcosdA = 1.0 /rA * (B.normalize() - cos_phi * A.normalize()); |
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//Vector3d dcosdB = 1.0 /rB * (A.normalize() - cos_phi * B.normalize()); |
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|
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/*********************************************************************** |
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* |
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* Calculate the actual forces and place them in the atoms. |
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* |
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***********************************************************************/ |
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|
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double force; /*the force scaling factor */ |
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|
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force = torsion_force(cos_phi); |
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|
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aF[0] = force * (d_cos_dy_cr1 * r_cb.z - d_cos_dz_cr1 * r_cb.y); |
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aF[1] = force * (d_cos_dz_cr1 * r_cb.x - d_cos_dx_cr1 * r_cb.z); |
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aF[2] = force * (d_cos_dx_cr1 * r_cb.y - d_cos_dy_cr1 * r_cb.x); |
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|
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bF[0] = force * ( d_cos_dy_cr1 * (r_ab.z - r_cb.z) |
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- d_cos_dy_cr2 * r_cd.z |
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+ d_cos_dz_cr1 * (r_cb.y - r_ab.y) |
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+ d_cos_dz_cr2 * r_cd.y); |
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bF[1] = force * ( d_cos_dx_cr1 * (r_cb.z - r_ab.z) |
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+ d_cos_dx_cr2 * r_cd.z |
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+ d_cos_dz_cr1 * (r_ab.x - r_cb.x) |
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- d_cos_dz_cr2 * r_cd.x); |
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bF[2] = force * ( d_cos_dx_cr1 * (r_ab.y - r_cb.y) |
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- d_cos_dx_cr2 * r_cd.y |
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+ d_cos_dy_cr1 * (r_cb.x - r_ab.x) |
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+ d_cos_dy_cr2 * r_cd.x); |
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|
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cF[0] = force * (- d_cos_dy_cr1 * r_ab.z |
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- d_cos_dy_cr2 * (r_cb.z - r_cd.z) |
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+ d_cos_dz_cr1 * r_ab.y |
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- d_cos_dz_cr2 * (r_cd.y - r_cb.y)); |
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cF[1] = force * ( d_cos_dx_cr1 * r_ab.z |
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- d_cos_dx_cr2 * (r_cd.z - r_cb.z) |
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- d_cos_dz_cr1 * r_ab.x |
| 321 |
< |
- d_cos_dz_cr2 * (r_cb.x - r_cd.x)); |
| 322 |
< |
cF[2] = force * (- d_cos_dx_cr1 * r_ab.y |
| 323 |
< |
- d_cos_dx_cr2 * (r_cb.y - r_cd.y) |
| 324 |
< |
+ d_cos_dy_cr1 * r_ab.x |
| 325 |
< |
- d_cos_dy_cr2 * (r_cd.x - r_cb.x)); |
| 326 |
< |
|
| 327 |
< |
dF[0] = force * (d_cos_dy_cr2 * r_cb.z - d_cos_dz_cr2 * r_cb.y); |
| 328 |
< |
dF[1] = force * (d_cos_dz_cr2 * r_cb.x - d_cos_dx_cr2 * r_cb.z); |
| 329 |
< |
dF[2] = force * (d_cos_dx_cr2 * r_cb.y - d_cos_dy_cr2 * r_cb.x); |
| 330 |
< |
|
| 331 |
< |
|
| 332 |
< |
c_p_a->addFrc(aF); |
| 333 |
< |
c_p_b->addFrc(bF); |
| 334 |
< |
c_p_c->addFrc(cF); |
| 335 |
< |
c_p_d->addFrc(dF); |
| 336 |
< |
|
| 337 |
< |
//double firstDerivative; |
| 338 |
< |
//bondType_->calcForce(cos_phi, firstDerivative, potential_); |
| 339 |
< |
//f1 = force * cross (dcosdA, r32); |
| 340 |
< |
//f2 = |
| 341 |
< |
//f3 = |
| 342 |
< |
//f4 = force * cross(dcosdB, r32); |
| 343 |
< |
//atom1_->addFrc(f1); |
| 344 |
< |
//atom2_->addFrc(f2); |
| 345 |
< |
//atom3_->addFrc(f3); |
| 346 |
< |
//atom4_->addFrc(f4); |
| 347 |
< |
|
| 348 |
< |
|
| 349 |
< |
} |
| 350 |
< |
|
| 351 |
< |
} |
| 1 |
> |
#include "primitives/Torsion.hpp" |
| 2 |
> |
|
| 3 |
> |
namespace oopse { |
| 4 |
> |
|
| 5 |
> |
Torsion::Torsion(Atom *atom1, Atom *atom2, Atom *atom3, Atom *atom4, |
| 6 |
> |
TorsionType *tt) : |
| 7 |
> |
atom1_(atom1), |
| 8 |
> |
atom2_(atom2), |
| 9 |
> |
atom3_(atom3), |
| 10 |
> |
atom4_(atom4) { } |
| 11 |
> |
|
| 12 |
> |
void Torsion::calcForce() { |
| 13 |
> |
Vector3d pos1 = atom1_->getPos(); |
| 14 |
> |
Vector3d pos2 = atom2_->getPos(); |
| 15 |
> |
Vector3d pos3 = atom3_->getPos(); |
| 16 |
> |
Vector3d pos4 = atom4_->getPos(); |
| 17 |
> |
|
| 18 |
> |
Vector3d r12 = pos1 - pos2; |
| 19 |
> |
Vector3d r23 = pos2 - pos3; |
| 20 |
> |
Vector3d r34 = pos3 - pos4; |
| 21 |
> |
|
| 22 |
> |
// Calculate the cross products and distances |
| 23 |
> |
Vector3d A = cross(r12, r23); |
| 24 |
> |
double rA = A.length(); |
| 25 |
> |
Vector3d B = cross(r23, r34); |
| 26 |
> |
double rB = B.length(); |
| 27 |
> |
Vector3d C = cross(r23, A); |
| 28 |
> |
double rC = C.length(); |
| 29 |
> |
|
| 30 |
> |
A.normalize(); |
| 31 |
> |
B.normalize(); |
| 32 |
> |
C.normalize(); |
| 33 |
> |
|
| 34 |
> |
// Calculate the sin and cos |
| 35 |
> |
double cos_phi = dot(A, B) ; |
| 36 |
> |
double sin_phi = dot(C, B); |
| 37 |
> |
|
| 38 |
> |
double phi = -atan2(sin_phi, cos_phi); |
| 39 |
> |
|
| 40 |
> |
double dVdPhi; |
| 41 |
> |
torsionType_->calcForce(phi, potential_, dVdPhi); |
| 42 |
> |
|
| 43 |
> |
Vector3d f1; |
| 44 |
> |
Vector3d f2; |
| 45 |
> |
Vector3d f3; |
| 46 |
> |
|
| 47 |
> |
// Next, we want to calculate the forces. In order |
| 48 |
> |
// to do that, we first need to figure out whether the |
| 49 |
> |
// sin or cos form will be more stable. For this, |
| 50 |
> |
// just look at the value of phi |
| 51 |
> |
if (fabs(sin_phi) > 0.1) { |
| 52 |
> |
// use the sin version to avoid 1/cos terms |
| 53 |
> |
|
| 54 |
> |
Vector3d dcosdA = (cos_phi * A - B) /rA; |
| 55 |
> |
Vector3d dcosdB = (cos_phi * B - A) /rB; |
| 56 |
> |
|
| 57 |
> |
double dVdcosPhi = dVdPhi / sin_phi; |
| 58 |
> |
|
| 59 |
> |
f1 = dVdcosPhi * cross(r23, dcosdA); |
| 60 |
> |
f2 = dVdcosPhi * ( cross(r34, dcosdB) - cross(r12, dcosdA)); |
| 61 |
> |
f3 = dVdcosPhi * cross(r23, dcosdB); |
| 62 |
> |
|
| 63 |
> |
} else { |
| 64 |
> |
// This angle is closer to 0 or 180 than it is to |
| 65 |
> |
// 90, so use the cos version to avoid 1/sin terms |
| 66 |
> |
|
| 67 |
> |
double dVdsinPhi = -dVdPhi /cos_phi; |
| 68 |
> |
Vector3d dsindB = (sin_phi * B - C) /rB; |
| 69 |
> |
Vector3d dsindC = (sin_phi * C - B) /rC; |
| 70 |
> |
|
| 71 |
> |
f1.x = dVdsinPhi*((r23.y*r23.y + r23.z*r23.z)*dsindC.x - r23.x*r23.y*dsindC.y - r23.x*r23.z*dsindC.z); |
| 72 |
> |
|
| 73 |
> |
f1.y = dVdsinPhi*((r23.z*r23.z + r23.x*r23.x)*dsindC.y - r23.y*r23.z*dsindC.z - r23.y*r23.x*dsindC.x); |
| 74 |
> |
|
| 75 |
> |
f1.z = dVdsinPhi*((r23.x*r23.x + r23.y*r23.y)*dsindC.z - r23.z*r23.x*dsindC.x - r23.z*r23.y*dsindC.y); |
| 76 |
> |
|
| 77 |
> |
f2.x = dVdsinPhi*(-(r23.y*r12.y + r23.z*r12.z)*dsindC.x + (2.0*r23.x*r12.y - r12.x*r23.y)*dsindC.y |
| 78 |
> |
+ (2.0*r23.x*r12.z - r12.x*r23.z)*dsindC.z + dsindB.z*r34.y - dsindB.y*r34.z); |
| 79 |
> |
|
| 80 |
> |
f2.y = dVdsinPhi*(-(r23.z*r12.z + r23.x*r12.x)*dsindC.y + (2.0*r23.y*r12.z - r12.y*r23.z)*dsindC.z |
| 81 |
> |
+ (2.0*r23.y*r12.x - r12.y*r23.x)*dsindC.x + dsindB.x*r34.z - dsindB.z*r34.x); |
| 82 |
> |
|
| 83 |
> |
f2.z = dVdsinPhi*(-(r23.x*r12.x + r23.y*r12.y)*dsindC.z + (2.0*r23.z*r12.x - r12.z*r23.x)*dsindC.x |
| 84 |
> |
+(2.0*r23.z*r12.y - r12.z*r23.y)*dsindC.y + dsindB.y*r34.x - dsindB.x*r34.y); |
| 85 |
> |
|
| 86 |
> |
f3 = dVdsinPhi * cross(dsindB, r23); |
| 87 |
> |
|
| 88 |
> |
} |
| 89 |
> |
|
| 90 |
> |
atom1_->addFrc(f1); |
| 91 |
> |
atom2_->addFrc(f2 - f1); |
| 92 |
> |
atom3_->addFrc(f3 - f2); |
| 93 |
> |
atom4_->addFrc(-f3); |
| 94 |
> |
} |
| 95 |
> |
|
| 96 |
> |
} |
