| 1 |
< |
#include "primitives/SRI.hpp" |
| 2 |
< |
#include "primitives/Atom.hpp" |
| 3 |
< |
|
| 4 |
< |
#include <math.h> |
| 5 |
< |
#include <iostream> |
| 6 |
< |
#include <stdlib.h> |
| 7 |
< |
|
| 8 |
< |
void Bend::set_atoms( Atom &a, Atom &b, Atom &c){ |
| 9 |
< |
|
| 10 |
< |
c_p_a = &a; |
| 11 |
< |
c_p_b = &b; |
| 12 |
< |
c_p_c = &c; |
| 13 |
< |
|
| 14 |
< |
c_potential_E = 0.0; |
| 15 |
< |
} |
| 16 |
< |
|
| 17 |
< |
|
| 18 |
< |
void Bend::calc_forces(){ |
| 19 |
< |
|
| 20 |
< |
double dx,dy,dz,gx,gy,gz,dx2,dy2,dz2,gx2,gy2,gz2; |
| 21 |
< |
double rij2, rkj2, riji2, rkji2, dot, denom, cosang, angl; |
| 22 |
< |
|
| 23 |
< |
double sina2, sinai; |
| 24 |
< |
|
| 25 |
< |
double comf2, comf3, comf4; |
| 26 |
< |
double dcsidx, dcsidy, dcsidz, dcskdx, dcskdy, dcskdz; |
| 27 |
< |
// double dcsjdx, dcsjdy, dcsjdz; |
| 28 |
< |
double dadxi, dadyi, dadzi; |
| 29 |
< |
double dadxk, dadyk, dadzk;//, dadxj, dadyj, dadzj; |
| 30 |
< |
double daxi, dayi, dazi, daxk, dayk, dazk, daxj, dayj, dazj; |
| 31 |
< |
|
| 32 |
< |
double aR[3], bR[3], cR[3]; |
| 33 |
< |
double aF[3], bF[3], cF[3]; |
| 34 |
< |
|
| 35 |
< |
c_p_a->getPos( aR ); |
| 36 |
< |
c_p_b->getPos( bR ); |
| 37 |
< |
c_p_c->getPos( cR ); |
| 38 |
< |
|
| 39 |
< |
|
| 40 |
< |
dx = aR[0] - bR[0]; |
| 41 |
< |
dy = aR[1] - bR[1]; |
| 42 |
< |
dz = aR[2] - bR[2]; |
| 1 |
> |
/* |
| 2 |
> |
* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
| 3 |
> |
* |
| 4 |
> |
* The University of Notre Dame grants you ("Licensee") a |
| 5 |
> |
* non-exclusive, royalty free, license to use, modify and |
| 6 |
> |
* redistribute this software in source and binary code form, provided |
| 7 |
> |
* that the following conditions are met: |
| 8 |
> |
* |
| 9 |
> |
* 1. Acknowledgement of the program authors must be made in any |
| 10 |
> |
* publication of scientific results based in part on use of the |
| 11 |
> |
* program. An acceptable form of acknowledgement is citation of |
| 12 |
> |
* the article in which the program was described (Matthew |
| 13 |
> |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
| 14 |
> |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 15 |
> |
* Parallel Simulation Engine for Molecular Dynamics," |
| 16 |
> |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 17 |
> |
* |
| 18 |
> |
* 2. Redistributions of source code must retain the above copyright |
| 19 |
> |
* notice, this list of conditions and the following disclaimer. |
| 20 |
> |
* |
| 21 |
> |
* 3. Redistributions in binary form must reproduce the above copyright |
| 22 |
> |
* notice, this list of conditions and the following disclaimer in the |
| 23 |
> |
* documentation and/or other materials provided with the |
| 24 |
> |
* distribution. |
| 25 |
> |
* |
| 26 |
> |
* This software is provided "AS IS," without a warranty of any |
| 27 |
> |
* kind. All express or implied conditions, representations and |
| 28 |
> |
* warranties, including any implied warranty of merchantability, |
| 29 |
> |
* fitness for a particular purpose or non-infringement, are hereby |
| 30 |
> |
* excluded. The University of Notre Dame and its licensors shall not |
| 31 |
> |
* be liable for any damages suffered by licensee as a result of |
| 32 |
> |
* using, modifying or distributing the software or its |
| 33 |
> |
* derivatives. In no event will the University of Notre Dame or its |
| 34 |
> |
* licensors be liable for any lost revenue, profit or data, or for |
| 35 |
> |
* direct, indirect, special, consequential, incidental or punitive |
| 36 |
> |
* damages, however caused and regardless of the theory of liability, |
| 37 |
> |
* arising out of the use of or inability to use software, even if the |
| 38 |
> |
* University of Notre Dame has been advised of the possibility of |
| 39 |
> |
* such damages. |
| 40 |
> |
*/ |
| 41 |
|
|
| 42 |
< |
gx = cR[0] - bR[0]; |
| 45 |
< |
gy = cR[1] - bR[1]; |
| 46 |
< |
gz = cR[2] - bR[2]; |
| 47 |
< |
|
| 48 |
< |
dx2 = dx * dx; |
| 49 |
< |
dy2 = dy * dy; |
| 50 |
< |
dz2 = dz * dz; |
| 42 |
> |
#include "primitives/Bend.hpp" |
| 43 |
|
|
| 44 |
< |
gx2 = gx * gx; |
| 53 |
< |
gy2 = gy * gy; |
| 54 |
< |
gz2 = gz * gz; |
| 44 |
> |
namespace oopse { |
| 45 |
|
|
| 46 |
< |
rij2 = dx2 + dy2 + dz2; |
| 47 |
< |
rkj2 = gx2 + gy2 + gz2; |
| 48 |
< |
|
| 49 |
< |
riji2 = 1.0 / rij2; |
| 50 |
< |
rkji2 = 1.0 / rkj2; |
| 46 |
> |
/**@todo still a lot left to improve*/ |
| 47 |
> |
void Bend::calcForce(RealType& angle) { |
| 48 |
> |
Vector3d pos1 = atom1_->getPos(); |
| 49 |
> |
Vector3d pos2 = atom2_->getPos(); |
| 50 |
> |
Vector3d pos3 = atom3_->getPos(); |
| 51 |
> |
|
| 52 |
> |
Vector3d r21 = pos1 - pos2; |
| 53 |
> |
RealType d21 = r21.length(); |
| 54 |
> |
|
| 55 |
> |
RealType d21inv = 1.0 / d21; |
| 56 |
> |
|
| 57 |
> |
Vector3d r23 = pos3 - pos2; |
| 58 |
> |
RealType d23 = r23.length(); |
| 59 |
> |
|
| 60 |
> |
RealType d23inv = 1.0 / d23; |
| 61 |
> |
|
| 62 |
> |
RealType cosTheta = dot(r21, r23) / (d21 * d23); |
| 63 |
> |
|
| 64 |
> |
//check roundoff |
| 65 |
> |
if (cosTheta > 1.0) { |
| 66 |
> |
cosTheta = 1.0; |
| 67 |
> |
} else if (cosTheta < -1.0) { |
| 68 |
> |
cosTheta = -1.0; |
| 69 |
> |
} |
| 70 |
> |
|
| 71 |
> |
RealType theta = acos(cosTheta); |
| 72 |
> |
|
| 73 |
> |
RealType dVdTheta; |
| 74 |
|
|
| 75 |
< |
dot = dx * gx + dy * gy + dz * gz; |
| 76 |
< |
denom = sqrt((riji2 * rkji2)); |
| 77 |
< |
cosang = dot * denom; |
| 75 |
> |
bendType_->calcForce(theta, potential_, dVdTheta); |
| 76 |
> |
|
| 77 |
> |
RealType sinTheta = sqrt(1.0 - cosTheta * cosTheta); |
| 78 |
> |
|
| 79 |
> |
if (fabs(sinTheta) < 1.0E-6) { |
| 80 |
> |
sinTheta = 1.0E-6; |
| 81 |
> |
} |
| 82 |
> |
|
| 83 |
> |
RealType commonFactor1 = dVdTheta / sinTheta * d21inv; |
| 84 |
> |
RealType commonFactor2 = dVdTheta / sinTheta * d23inv; |
| 85 |
> |
|
| 86 |
> |
Vector3d force1 = commonFactor1 * (r23 * d23inv - r21*d21inv*cosTheta); |
| 87 |
> |
Vector3d force3 = commonFactor2 * (r21 * d21inv - r23*d23inv*cosTheta); |
| 88 |
|
|
| 89 |
< |
if(cosang > 1.0)cosang = 1.0; |
| 90 |
< |
if(cosang < -1.0) cosang = -1.0; |
| 89 |
> |
// Total force in current bend is zero |
| 90 |
> |
Vector3d force2 = force1 + force3; |
| 91 |
> |
force2 *= -1.0; |
| 92 |
> |
|
| 93 |
> |
atom1_->addFrc(force1); |
| 94 |
> |
atom2_->addFrc(force2); |
| 95 |
> |
atom3_->addFrc(force3); |
| 96 |
|
|
| 97 |
< |
angl = acos(cosang); |
| 98 |
< |
angl = angl * 180.0 / M_PI; |
| 97 |
> |
atom1_->addParticlePot(potential_); |
| 98 |
> |
atom2_->addParticlePot(potential_); |
| 99 |
> |
atom3_->addParticlePot(potential_); |
| 100 |
> |
|
| 101 |
> |
angle = theta /M_PI * 180.0; |
| 102 |
> |
} |
| 103 |
|
|
| 104 |
< |
sina2 = 1.0 - cosang*cosang; |
| 73 |
< |
if(fabs(sina2) < 1.0E-12 ) sina2 = 1.0E-12; |
| 74 |
< |
sinai = 1.0 / sqrt(sina2); |
| 75 |
< |
|
| 76 |
< |
comf2 = cosang * riji2; |
| 77 |
< |
comf3 = cosang * rkji2; |
| 78 |
< |
comf4 = bend_force(angl); |
| 79 |
< |
|
| 80 |
< |
|
| 81 |
< |
dcsidx = gx*denom - comf2*dx; |
| 82 |
< |
dcsidy = gy*denom - comf2*dy; |
| 83 |
< |
dcsidz = gz*denom - comf2*dz; |
| 84 |
< |
|
| 85 |
< |
dcskdx = dx*denom - comf3*gx; |
| 86 |
< |
dcskdy = dy*denom - comf3*gy; |
| 87 |
< |
dcskdz = dz*denom - comf3*gz; |
| 88 |
< |
|
| 89 |
< |
// dcsjdx = -dcsidx - dcskdx; |
| 90 |
< |
// dcsjdy = -dcsidy - dcskdy; |
| 91 |
< |
// dcsjdz = -dcsidz - dcskdz; |
| 92 |
< |
|
| 93 |
< |
dadxi = -sinai*dcsidx; |
| 94 |
< |
dadyi = -sinai*dcsidy; |
| 95 |
< |
dadzi = -sinai*dcsidz; |
| 96 |
< |
|
| 97 |
< |
dadxk = -sinai*dcskdx; |
| 98 |
< |
dadyk = -sinai*dcskdy; |
| 99 |
< |
dadzk = -sinai*dcskdz; |
| 100 |
< |
|
| 101 |
< |
// dadxj = -dadxi - dadxk; |
| 102 |
< |
// dadyj = -dadyi - dadyk; |
| 103 |
< |
// dadzj = -dadzi - dadzk; |
| 104 |
< |
|
| 105 |
< |
daxi = comf4*dadxi; |
| 106 |
< |
dayi = comf4*dadyi; |
| 107 |
< |
dazi = comf4*dadzi; |
| 108 |
< |
|
| 109 |
< |
daxk = comf4*dadxk; |
| 110 |
< |
dayk = comf4*dadyk; |
| 111 |
< |
dazk = comf4*dadzk; |
| 112 |
< |
|
| 113 |
< |
daxj = -daxi - daxk; |
| 114 |
< |
dayj = -dayi - dayk; |
| 115 |
< |
dazj = -dazi - dazk; |
| 116 |
< |
|
| 117 |
< |
aF[0] = daxi; |
| 118 |
< |
aF[1] = dayi; |
| 119 |
< |
aF[2] = dazi; |
| 120 |
< |
|
| 121 |
< |
bF[0] = daxj; |
| 122 |
< |
bF[1] = dayj; |
| 123 |
< |
bF[2] = dazj; |
| 124 |
< |
|
| 125 |
< |
cF[0] = daxk; |
| 126 |
< |
cF[1] = dayk; |
| 127 |
< |
cF[2] = dazk; |
| 128 |
< |
|
| 129 |
< |
c_p_a->addFrc(aF); |
| 130 |
< |
c_p_b->addFrc(bF); |
| 131 |
< |
c_p_c->addFrc(cF); |
| 132 |
< |
|
| 133 |
< |
return; |
| 134 |
< |
} |
| 104 |
> |
} //end namespace oopse |
