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#include "primitives/SRI.hpp" |
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#include "primitives/Atom.hpp" |
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#include <math.h> |
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#include <iostream> |
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#include <stdlib.h> |
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#include "primitives/Torsion.hpp" |
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void Torsion::set_atoms( Atom &a, Atom &b, Atom &c, Atom &d){ |
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c_p_a = &a; |
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c_p_b = &b; |
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c_p_c = &c; |
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c_p_d = &d; |
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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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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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|
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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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|
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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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|
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K1 = -K1/cos_phi; |
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|
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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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|
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f3 = K1 *cross(dsindB,r23); |
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|
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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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|
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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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|
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void Torsion::calc_forces(){ |
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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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double aR[3], bR[3], cR[3], dR[3]; |
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double aF[3], bF[3], cF[3], dF[3]; |
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Vector3d aR, bR, cR, dR; |
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Vector3d aF, bF, cF, dF; |
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aR = c_p_a->getPos(); |
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bR = c_p_b->getPos(); |
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r_cr1_r_cr2 = r_cr1.length * r_cr2.length; |
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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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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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* This next section calculates derivatives needed for the force |
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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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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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- 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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+ 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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- 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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- 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 |
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- d_cos_dz_cr2 * (r_cb.x - r_cd.x)); |
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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 |
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- d_cos_dz_cr2 * (r_cb.x - r_cd.x)); |
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cF[2] = force * (- d_cos_dx_cr1 * r_ab.y |
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- d_cos_dx_cr2 * (r_cb.y - r_cd.y) |
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+ d_cos_dy_cr1 * r_ab.x |
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- d_cos_dy_cr2 * (r_cd.x - r_cb.x)); |
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- d_cos_dx_cr2 * (r_cb.y - r_cd.y) |
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+ d_cos_dy_cr1 * r_ab.x |
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- d_cos_dy_cr2 * (r_cd.x - r_cb.x)); |
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|
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dF[0] = force * (d_cos_dy_cr2 * r_cb.z - d_cos_dz_cr2 * r_cb.y); |
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dF[1] = force * (d_cos_dz_cr2 * r_cb.x - d_cos_dx_cr2 * r_cb.z); |
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c_p_b->addFrc(bF); |
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c_p_c->addFrc(cF); |
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c_p_d->addFrc(dF); |
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|
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//double firstDerivative; |
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//bondType_->calcForce(cos_phi, firstDerivative, potential_); |
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//f1 = force * cross (dcosdA, r32); |
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//f2 = |
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//f3 = |
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//f4 = force * cross(dcosdB, r32); |
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//atom1_->addFrc(f1); |
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//atom2_->addFrc(f2); |
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//atom3_->addFrc(f3); |
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//atom4_->addFrc(f4); |
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|
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|
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} |
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|
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} |